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Article

Effects of Grafting on the Structure and Function of Coffee Rhizosphere Microbiome

by
Yan Sun
1,2,3,
Lin Yan
1,2,3,
Ang Zhang
1,2,3,*,
Jianfeng Yang
1,2,3,*,
Qingyun Zhao
1,2,3,
Xingjun Lin
1,2,3,
Zixiao Zhang
1,2,3,
Lifang Huang
1,2,3,
Xiao Wang
1,2,3 and
Xiaoyang Wang
1,2,3
1
Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China
2
Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China
3
Key Laboratory of Genetic Resource Utilization of Spice and Beverage Crops of Ministry of Agriculture and Rural Affairs, Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China
*
Authors to whom correspondence should be addressed.
Agriculture 2024, 14(10), 1854; https://doi.org/10.3390/agriculture14101854
Submission received: 6 August 2024 / Revised: 16 October 2024 / Accepted: 17 October 2024 / Published: 21 October 2024
(This article belongs to the Section Crop Production)
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Abstract

:
Heterologous double-root grafting represents an effective strategy to mitigate challenges associated with continuous coffee cropping and reduce soil-borne diseases. However, its specific regulatory mechanism remains unclear. Therefore, a field experiment was conducted including six different grafting combinations for C. canephora cv. Robusta (Robusta) and Coffea Liberica (Liberica): Robusta scion with a homologous double root (R/RR), Liberica scion with a homologous double root (L/LL), Robusta scion with a heterologous double root (R/RL and L/RL), and Liberica scion with a heterologous double root (L/LR and R/LR); these combinations were conducted to clarify the effects of heterologous double-root grafting combinations on the root exudates and soil microbial diversity, structure, and function of Robusta and Liberica. The results demonstrated notable differences in root exudates, rhizosphere microbial structure, and function between Robusta and Liberica. Despite Liberica having lower diversity in its rhizosphere microbial communities and relatively higher levels of potential pathogenic bacteria, it showed stronger resistance to diseases. Roots of Robusta in heterologous double-root coffee seedlings significantly enhanced the secretion of resistance compounds, increased the relative abundance of potentially beneficial bacteria, and reduced the relative abundance of potential pathogenic fungi. This enhances the rhizosphere immunity of Robusta against soil-borne diseases. The results indicated that grafting onto Liberica roots can strengthen resistance mechanisms and enhance the rhizosphere immunity of Robusta, thereby mitigating challenges associated with continuous cropping.

1. Introduction

Coffee is one of the world’s important cash crops, and it has become a main component of agriculture in many tropical and subtropical countries and regions [1]. It serves as a crucial income source for stakeholders and farmers alike, playing a pivotal role in local economic development [2,3]. Currently, the global coffee trade is predominantly led by C. Arabica and C. canephora cv. Robusta species, with C. canephora cv. Robusta witnessing significant growth in demand [4,5]. However, C. canephora cv. Robusta is a perennial economic crop. In some long-term C. canephora cv. Robusta plantations, there will be challenges of plant aging and continuous cropping obstacles, which may become the main reasons affecting C. canephora cv. Robusta yield [6]. Previous studies indicated that the deterioration of soil properties [7], damage of root-knot nematodes [8,9], and accumulation of soil fungi [10] may be the key factors for the occurrence of continuous cropping obstacles in C. canephora cv. Robusta. However, other research has found that although some C. canephora cv. Robusta plantations in Hainan Province, China, are also facing the challenge of continuous cropping obstacles, sufficient soil nutrients (nitrogen, phosphorus, potassium) and high nematode diversity indicate that nutritional stress or nematode destruction are not the main causes of continuous cropping obstacles in this C. canephora cv. Robusta-producing area [11]. Conversely, the gradual decline in rhizosphere microorganism diversity and imbalanced community structure, which enriches harmful bacteria, directly contributes to coffee diseases in long-standing continuous plantations [11,12].
Grafting is an effective agronomic technique for mitigating continuous cropping obstacles in production, and it has been widely utilized in tropical cultivations such as cocoa and tea [13,14]. Similarly, coffee species that can tolerate continuous cropping obstacles were selected by using soil from C. canephora cv. Robusta plantations planted for a long time, and Coffea liberica Bull ex Hiern was identified as highly resistance in such conditions (i.e., Coffea liberica coffee can grow normally in soil environments with C. canephora cv. Robusta continuous cropping obstacles) in the preliminary study of the author’s research team. Therefore, grafting C. canephora cv. Robusta onto Coffea Liberica rootstock can maintain plant health, enhance coffee yield, and mitigate continuous cropping obstacles. However, single-rootstock grafted seedlings (with Coffea Liberica as a rootstock and C. canephora cv. Robusta as a scion) have a non-productive period of up to 4 years, and replanting this coffee seedling in the continuous cropping obstacle garden has high economic losses. Therefore, a new method involves heterologous double-root grafting, where the Coffea Liberica root is grafted onto C. canephora cv. Robusta, preserving existing C. canephora cv. Robusta plants while introducing a new Coffea Liberica root. This approach significantly accelerates plant recovery in the first year, with production beginning by the second year. Heterologous double-root grafting represents a novel agronomic approach to mitigate continuous cropping challenges in C. canephora cv. Robusta, thereby reducing economic losses associated with replanting and facilitating rapid production recovery. However, further exploration is needed to elucidate the specific mechanisms underlying the alleviation of continuous cropping challenges in C. canephora cv. Robusta.
The coffee rhizosphere soil microecosystem represents the area of most intense interaction between plants, soil microorganisms, and environmental conditions [15,16]. Rhizosphere microorganisms are pivotal components of the soil ecosystem, regulating allelochemicals, activating soil nutrients, and secreting plant hormones like cytokinins and auxins, thereby enhancing plant stress resistance [17,18]. Specifically, crop root exudates serve as crucial carriers for material exchange and information transmission between crops and microorganisms [19], and they provide an important regulatory role in plant growth, development, and rhizosphere ecological processes, especially in maintaining the structure and function of rhizosphere ecological systems [20]. Accumulation of allelochemicals in root exudates is widely believed to disrupt crop rhizosphere flora and promote the enrichment of harmful bacteria, thus contributing significantly to continuous cropping obstacles [21]. However, some studies suggest that root exudates drive the microbial community succession by providing carbon and nitrogen sources to the rhizosphere environment, directly affecting the diversity of rhizosphere soil microbial community structure and functionality, thereby promoting plant growth [22]. Hence, further research is needed to elucidate the regulatory mechanisms of coffee root exudates on crop rhizosphere microorganisms.
Previous studies have demonstrated that the continuous cropping obstacle of coffee under the intercropping mode can be mitigated [23], which is related to the interaction effect of root exudates secreted from different crops and its regulation mechanism on the soil microbial community [11]. The pathways and mechanisms of regulating the function and structure of C. canephora cv. Robusta rhizosphere microbial community by Coffea Liberica root exudates are still unknown. Therefore, this study analyzed the differences between root exudates and the function and structure of the rhizosphere microbial community among C. canephora cv. Robusta, Coffea Liberica, and heterologous double-root-grafted coffee through field experiments. It identified the components of rhizosphere exudates in heterologous double-root coffee and the key factors driving the reconstruction of the rhizosphere microbial community. Furthermore, it elucidated the microbial ecological mechanisms of double-root exudate interactions in alleviating continuous cropping challenges in coffee, particularly after the introduction of Coffea Liberica.

2. Materials and Methods

2.1. Experimental Site

The experiment was located in the Coffee Germplasm Resource Plantations of Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wannin, China (110°11′ E, 18°44′ N). The annual precipitation of the experimental site is 2100 mm. The annual sunshine duration is 1750 h. The soil was mainly classified as tidal sand-mud (US Soil Taxonomy classification). The soil pH of the experimental site was 6.15. Soil organic matter content (SOM), total nitrogen content (STN), total phosphorus content (STP), and total potassium content (STK) were 22.06 gkg−1, 1.49 gkg−1, 1.28 gkg−1, and 6.29 gkg−1, respectively. The coffee species used in this experiment was Coffea Canephora Pierre ex A. Froehner cv. Reyan No.1 (C. canephora cv. Robusta) and Coffea liberica Bull ex Hiern (Coffea Liberica).

2.2. Experimental Material

C. canephora cv. Robusta and Coffea Liberica seedlings were selected as experimental materials. Seeds of both species of coffee were germinated by a sand bed and grafted when in the period of the leaf cotyledonary stage (approximately 45 days). Sterilized sharp blades were used to perform a flat cut exposing the stem tissues (usually 0.5–1 cm long and 1–2 mm wide) at the same height of two coffee seedlings during grafting. The exposed stem tissues of the two seedlings were tightly fitted together as the union of a new seedling. The union was initially held in place by pressure exerted by grafting tape (polyethylene film). These grafted coffee seedlings had two scions and two rootstocks during the initial growth stage. A transparent bag was folded over the cotyledons to cover the two scions, reducing water loss and protecting the incision from infection until the union of callus formation cells fused into a mass that was continuous in compatible grafts. One of the scions was removed with scissors when the grafted seedlings reached 2–3 pairs of true leaves, and fungicide was applied to prevent pathogen infection. When the seedlings in the experiment grew four pairs of leaves, they were transplanted into larger flower pots (25 cm in diameter) filled with 5 kg of soil from a coffee plantation with continuous cropping obstacles.
C. canephora cv. Robusta was grafted with C. canephora cv. Robusta to produce Robusta homologous double-root coffee (intolerant to continuous cropping soil). Coffea Liberica was grafted with Coffea Liberica to produce Liberica homologous double-root coffee (tolerate continuous cropping soil). Robusta–Liberica heterologous double-root coffee (tolerate continuous cropping soil) was created by grafting C. canephora cv. Robusta with Coffea Liberica (Figure 1).

2.3. Experimental Design

This experiment was commenced in September 2022. Six treatments were designed using a randomized block design: a C. canephora cv. Robusta scion grafted onto its own rootstock (R/R, grafting one C. canephora cv. Robusta scion with one identical root) and Coffea Liberica scion grafted onto its own rootstock (L/L, grafting one Coffea Liberica scion with one identical root), Robusta homologous double-root coffee seedling (R/RR, grafting one C. canephora cv. Robusta scion with two identical roots), Liberica homologous double-root coffee seedling (L/LL, grafting one Coffea Liberica scion with two identical roots), Robusta heterologous double-root coffee seedling (R/RL and L/RL, simultaneously grafting one C. canephora cv. Robusta scion with one identical root and one Coffea Liberica root), and Liberica heterologous double-root coffee seedling (L/LR and R/LR, simultaneously grafting one Coffea Liberica scion with one identical root and one C. canephora cv. Robusta root) in the current experiment. Each treatment was replicated three times. A 50% shade canopy was erected above the coffee seedlings, and we watered them once every two days to maintain soil moisture. Other management practices followed standard procedures.

2.4. Sampling Method

After 180 days of growth, the entire root system of each plant was excavated, and the rhizosphere soil from all coffee seedlings in each plot was collected by using the root shaking method, and they were quickly mixed, freeze-dried, and stored in a −80 °C refrigerator. Soil samples were analyzed to identify coffee root exudates and rhizosphere microorganisms.

2.5. Root Exudation Analysis

An amount of 50 g of coffee rhizosphere soil was weighed, placed in a wide-mouth bottle, extracted with methanol at a ratio of 1 g/2 mL for 24 h, filtered, evaporated to dryness under reduced pressure at 40 °C and 100 rpm, re-dissolved in 2 mL of methanol, dehydrated with anhydrous sodium sulfate, filtered through a 0.45 µm organic microporous filter membrane, transferred to gas sample bottles, and stored in a refrigerator at 4 °C for GC-MS separation and identification.
Coffee root exudates were analyzed by gas chromatography–mass spectrometry (Agilent 7890a gas chromatography and 5975c mass spectrometer). The GC conditions included a db-wax chromatographic column (30 m × 0.25 mm × 0.25 µm), no split injection, an injection volume of 1 µL, an injection port temperature of 250 °C, and a temperature program of initial temperature 50 °C, 6 °C/min to 220 °C, maintained for 15 min. Nitrogen was the carrier gas and was used at a flow rate of 1.0 mL/min. The MS condition involved an electron ionization (EI) mode with an electron energy of 70 eV, an ion source temperature of 230 °C and a full-scan acquisition mode. The solvent delay time was 5 min. The components (benzenoids; lignans, neolignans, and related compounds; organic acids and derivatives; organic nitrogen compounds; organic oxygen compounds; organoheterocyclic compounds; and organonitrogen compounds) were identified, and peak areas were normalized to calculate the relative percentage content of each component, providing specific components and the relative content in the sample.

2.6. Extraction, Sequencing, and Bioinformatics Analysis of Soil Total DNA

The extraction and determination methods of soil total DNA were the same as those used in previous study [11]. Microbiome bioinformatics analysis was performed with QIIME 22019.4 [24,25,26], and the specific analysis method was also consistent with previous studies [27,28,29].

2.7. Statistical Analysis

The effects of grafting combinations and coffee species on the relative content of coffee root exudates and rhizosphere soil microbial characteristics (including richness, diversity, Pielou index, and relative abundance of bacteria and fungi) were evaluated using a two-way analysis of variance (Two-way ANOVA). Normality tests were conducted on all data prior to analysis. Differences between mean values were determined using the least significant difference (LSD) test. Shannon indices for bacterial and fungal communities were calculated separately using MOTHER v.1.33.3 to assess their taxonomic alpha diversity. A principal coordinate analysis (PCoA) based on the Bray–Curtis distance was employed to analyze differences in bacterial and fungal community structure (beta diversity) due to grafting combinations and coffee species, respectively. Spearman correlation matrices in SPSS 23.0 were used to examine correlations between coffee root exudates and rhizosphere soil microbial characteristics. Network interactions between coffee root exudates and microbial composition (bacteria and fungi) were analyzed using Cytoscape V3.8.2 software. Graphs were generated using Origin 2021b and R 4.0.5.

3. Results

3.1. The Difference Between C. canephora cv. Robusta and Coffea Liberica Root Exudates Under Grafting Treatments

A total of 534 compounds were identified in rhizosphere soil of coffee grafted seedlings and categorized into 17 groups. Lipids and lipid-like molecules constituted the largest proportion, comprising over 53% of the total content of root exudates (Figure 2). Other main root exudates with contents higher than 1% of the total content were benzenoids; lignans, neolignans, and related compounds; organic acids and derivatives; organic nitrogen compounds; organic oxygen compounds; organoheterocyclic compounds; and organonitrogen compounds. Specifically, the content of benzenoids; lignans, neolignans, and related compounds; organic acids and derivatives; organic oxygen compounds; organoheterocyclic compounds; and organonitrogen compounds in C. canephora cv. Robusta root exudates were significantly higher compared with Coffea Liberica by 16.94%, 22.19%, 17.41%, 19.52%, 18.65%, and 30.45%, respectively (p < 0.05). Conversely, phenylpropanoids and polyketides in root exudates of C. canephora cv. Robusta was significantly lower than that of Coffea Liberica by 11.47% (p < 0.05).
There were significant differences in the types of coffee root exudates among different grafting combinations (Table 1). An interaction effect between grafting combinations and coffee species was observed on certain coffee root exudates (Table 1). The contents of lignans, neolignans, and related compounds and organic oxygen compounds in C. canephora cv. Robusta root exudates were significantly reduced by 12.01% and 9.06% when adjacent to the Coffea Liberica root. Conversely, the contents of benzenoids, lignans; neolignans, and related compounds; organic acids and derivatives; organic oxygen compounds; organoheterocyclic compounds; and phenylpropanoids and polyketides in Coffea Liberica root exudates decreased significantly by 20.42%, 21.06%, 22.94%, 24.37%, 23.06%, and 32.56%, respectively, compared with the control seedlings after being grafted with C. canephora cv. Robusta root system.
Regarding the effect of scion on root exudates in different coffee species, compared with C. canephora cv. Robusta roots, Coffea Liberica scion significantly increased the contents of lignans, neolignans, and related compounds and phenylpropanoids and polyketides in C. canephora cv. Robusta roots by 11.57% and 20.05%, respectively. In contrast, compared with the Coffea Liberica roots, C. canephora cv. Robusta scions significantly increased the contents of benzenoids; lignans, neolignans, and related compounds; organic acids and derivatives; organic oxygen compounds; and organoheterocyclic compounds in Coffea Liberica roots by 18.56%, 17.66%, 25.15%, 19.84%, and 20.62%, respectively, while decreasing the contents of lipids and lipid-like molecules by 10.12% (Figure 2).

3.2. The Difference Between C. canephora cv. Robusta and Coffea Liberica Rhizosphere Soil Microbial Diversity Under Grafting Treatments

Various indicators of microbial community diversity in the coffee plant rhizosphere were assessed. Coffee species, grafting combinations, or their interactions did not affect bacterial and fungal evenness (Table 2, Figure 3c,f) in this study. Coffee species, rather than grafting combinations, significantly influenced bacterial and fungal richness and diversity. Interactions between these factors did not affect bacterial and fungal richness (Table 2, Figure 3a,b,d,e). C. canephora cv. Robusta exhibited significantly higher richness and diversity of rhizosphere bacteria compared with Coffea Liberica by 13.98% and 1.95%, respectively. Conversely, the richness and diversity of rhizosphere fungi in C. canephora cv. Robusta were significantly lower than those in Coffea Liberica by 20.23% and 4.75%, respectively. Root interactions among different coffee species did not affect the richness and diversity indices of bacteria and fungi in the coffee rhizosphere. Similarly, scions also had no effect on the richness and diversity index of bacteria and fungi in the rhizosphere of different coffee species (Figure 3a,b,d,e).
A principal coordinate analysis (PCoA) was conducted to reflect soil microbial beta diversity (Figure 3a). For the soil bacterial community, there was a significant difference between the rhizosphere soil bacterial beta diversity in Robusta and Liberica homologous double-root coffee seedlings, indicating that the rhizosphere bacterial community of coffee was sensitive to increased root biomass. However, there was no significant difference in the bacterial community structure between different grafting treatment and coffee species. For soil fungal communities, soil fungal characteristics under grafting treatments and different species showed no significant differences, indicating that soil fungal characteristics were not affected by grafting treatments (Figure 4b).

3.3. The Difference Between C. canephora cv. Robusta and Coffea Liberica Rhizosphere Soil Microbial Composition of Dominant Genera Under Grafting Treatments

There were 1005 bacterial genera that were observed in all coffee seedling rhizosphere soils. A total of 27 major bacterial genera (relative abundance > 1%) were screened out in this study. Coffee species, grafting combinations, and their interactions significantly affected the bacterial composition of dominant genera (Table 3). Specifically, most of the dominant genera of coffee rhizosphere bacteria have great differences among different coffee species, and the relative abundance of Vicinamibacteraceae, Vicinamibacterales, Gaiella, Gaiellales, Xanthobacteraceae, Actinobacteriota, KD4-96, MB-A2-108, SC-I-84, IMCC26256, Roseiflexaceae, and Solirubrobacter in C. canephora cv. Robusta rhizosphere soil were significantly lower than that of Coffea Liberica by 17.69%, 19.59%, 32.19%, 28.73%, 19.53%, 20.99%, 17.02%, 24.03%, 15.83%, 12.81%, 13.47%, and 17.74%, respectively; however, the relative abundance of Rokubacteriales, Subgroup, Gemmatimonadaceae, Proteobacteria, MND1, Haliangium, Gemmatimonadota, and Nitrospirad were significantly increased by 12.20%, 25.08%, 39.85%, 27.08%, 60.66%, 73.29%, 18.99%, and 35.09%, respectively (Figure 5a).
As for the influence of the root system interaction of different species of coffee on the dominant genera of bacteria in the rhizosphere of coffee, the dominant genera of bacteria in the rhizosphere of C. canephora cv. Robusta, such as Vicinamibacteraceae, Rokubacteriales, Gemmatimonadaceae, MND1, Acidobacteriota, SC-I-84, and IMCC26256, were significantly decreased by 17.24%, 34.01%, 17.05%, 35.77%, 35.42%, 32.19%, and 15.43%, respectively, after being connected to the Coffea Liberica root system; but the relative abundance of Gaiella, TK10, and Solirubrobacter were significantly increased by 24.24%, 39.09%, and 115.98%, respectively. The dominant bacteria in the rhizosphere soil of Coffea Liberica, such as Vicinamibacterales, Rokubacteriales, Gaiellales, Subgroup, KD4-96, MB-A2-108, Nitrospira, and SC-I-84 were significantly decreased by 32.07%, 20.75%, 17.69%, 20.77%, 42.45%, 13.25%, 27.23%, and 36.44%, respectively, after connecting the C. canephora cv. Robusta root system; but the relative abundance of Gemmatimonadaceae, Xanthobacteraceae, Proteobacteria, Pedomicrobium, RB41, Gemmatimonadota, Gemmatimonas, IMCC26256, Roseiflexaceae, TK10, and Candidatus were increased by 35.15%, 69.69%, 58.33%, 137.51%, 28.62%, 99.08%, 181.76%, 26.74%, 47.02%, 69.15%, and 20.75%, respectively. As for the effect of scions on the dominant genera of bacteria in the rhizosphere soil of different species of coffee, compared with the dominant genera of bacteria in the rhizosphere soil of Robusta homologous coffee, the relative abundance of Gemmatimonadaceae and Nitrospira in the rhizosphere soil of C. canephora cv. Robusta was significantly reduced by 29.78% and 15.69%, but the relative abundance of Vicinamiceraceae, Vicinamicerales, Vaiellales, Subgroups, Xanthobacteraceae, RB41, Haliangium, Acidobacterita, and TK10 were significantly increased by 41.38%, 36.46%, 23.13%, 19.42%, 30.91%, 53%, 49.95%, 45.00%, and 28.73%, respectively. Compared with the dominant genus of bacteria in the rhizosphere soil of Coffea Liberica, C. canephora cv. Robusta scion significantly reduced the relative abundance of Gaiella, Gaiellales, and MB-A2-108 in the rhizosphere soil of Coffea Liberica by 12.83%, 18.27%, and 20.59%, respectively, but significantly increased the relative abundance of Vicinamibacteria and MND1 by 14.52% and 39.32%, respectively (Figure 5a).
There were 275 fungal genera were observed in all coffee seedling rhizosphere soils. A total of 14 major fungal genera (relative abundance > 1%) were screened out in this study. Coffee species, grafting combinations, and their interactions significantly affected the fungal composition of dominant genera (Table 3). Specifically, most of the dominant genera of coffee rhizosphere fungi had great differences among different coffee species; especially, the relative abundance of Haematonectria, Agaricomycetes_unclassified, and Cochliobolus in the C. canephora cv. Robusta rhizosphere soil were significantly decreased by 34.55%, 78.83%, and 57.50%, respectively. However, the relative abundance of Ascomycota_unclassified, Chaetomiaceae_unclassified, Hypocrea, and Preussia were significantly increased by 59.72%, 23.39%, 24.90%, and 51.01%, respectively. For the influence of different species of coffee root interaction on the dominant genera of coffee rhizosphere fungi, the dominant fungal genus Preussia in C. canephora cv. Robusta rhizosphere soil significantly increased by 122.93% after being adjacent to Coffea Liberica roots. And the dominant fungi in the rhizosphere soil of Coffea Liberica, such as Ascomycota_unclassified Chaetomiaceae_unclassified, Chaetomium, and Agaricomycotes_unclassified, were significantly reduced by 45.40%, 69.50%, 152.06%, and 907.94%, respectively, while Cochliobolus was significantly increased by 79.48% when compared with the Coffea Liberica seedlings. As for the effect of scions on the dominant genera of fungi in the rhizosphere soil of different species of coffee, compared with the dominant genera of fungi in the rhizosphere soil of Robusta homologous coffee, the relative abundance of Ascomycota_unclassified and Preussia in the rhizosphere soil of C. canephora cv. Robusta was significantly reduced by 33.79% and 40.87%, respectively, but the relative abundance of Sordariomycetes_unclassified was significantly increased by 382.12%. Compared with the dominant genera in the rhizosphere soil of Coffea Liberica, C. canephora cv. Robusta scions did not affect the relative abundance of dominant genera in the rhizosphere soil of Coffea Liberica (Figure 5b).

3.4. The Difference Between C. canephora cv. Robusta and Coffea Liberica Rhizosphere Soil Microbial Function Under Grafting Treatments

Coffee species, grafting combinations, and their interactions significantly affected some coffee rhizosphere soil bacterial functions (Table 4). Specifically, certain functions of coffee rhizosphere bacteria vary significantly among different coffee species. Among them, the relative abundance of parasite functions was significantly increased by 74.50%. As for the effect of different species of coffee root interaction on the bacterial function of coffee rhizosphere, the bacterial function of C. canephora cv. Robusta rhizosphere soil, such as chemoheterotrophy, degradation, nitrate reduction, fermentation, nitrogen fixation, were significantly increased by 54.60%, 68.20%, 66.86%, 380.62%, 145.37%, respectively, when compared with the intraspecific grafting of C. canephora cv. Robusta. The bacterial function of rhizosphere soil of Coffea Liberica, such as photoautotrophy, denitrification, fermentation, and denitrification after connecting C. canephora cv. Robusta root, were significantly increased by 78.98%, 79.11%, 125.83%, and 79.09%, respectively, when compared with the intraspecific grafting of Coffea Liberica, while the function of nitrate reduction was significantly decreased by 16.79%. As for the effect of scions on the bacterial function of the rhizosphere soil of different species of coffee, the relative abundance of photoautotrophy, and denitrification of C. canephora cv. Robusta rhizosphere soils were significantly increased by 37.18%, 38.00%, and 37.80%, respectively, when compared with the rhizosphere soil of intraspecifically grafting C. canephora cv. Robusta. C. canephora cv. Robusta scion only significantly reduced the relative abundance of the bacterial function of Coffea Liberica rhizosphere soil by 50.37% (Figure 6a).
The coffee rhizosphere soil fungal predicted function was not affected by coffee species, grafting combinations, and their interactions (Table 4). Among different coffee species, only the relative abundance of arbuscular mycorrhizal function of fungi in C. canephora cv. Robusta rhizosphere soil was significantly lower than that in Coffea Liberica by 89.93%. The interaction of different species of coffee roots had little effect on the predicted function of bacteria in the rhizosphere of coffee. Except for after being adjacent to C. canephora cv. Robusta roots, the function of Coffea Liberica rhizosphere fungus saprotroph was significantly reduced by 61.83% compared with Coffea Liberica seedlings. The effect of different species of scions on the fungal function of coffee rhizosphere soil was also small. Compared with the bacterial function of Robusta homologous coffee rhizosphere soil, the relative abundance of endomycorrhizal function of C. canephora cv. Robusta rhizosphere soil was only significantly increased by 1796.60%. The C. canephora cv. Robusta scion significantly increased the relative abundance of arbuscular mycorrhizal function in the rhizosphere soil of Coffea Liberica by 179.75% compared with that of the rhizosphere soil of Coffea Liberica (Figure 6b).
For different species of coffee, the interaction of the root system had no effect on the predicted function of bacteria in the rhizosphere of coffee, except for the function of Coffea Liberica rhizosphere fungal saprotroph after being adjacent to C. canephora cv. Robusta root, which was significantly reduced by 61.83% when compared with Coffea Liberica seedlings. The effects of different species of scions on the fungal function of the coffee rhizosphere soil were almost the same. The relative abundance of the endomycorrhizal function of C. canephora cv. Robusta rhizosphere soil was significantly increased by 1796.60% when compared with the bacterial function of Robusta homologous coffee rhizosphere soil. The C. canephora cv. Robusta scion significantly increased the relative abundance of arbuscular mycorrhizal function in the rhizosphere soil of Coffea Liberica by 179.75% compared with that of the rhizosphere soil of Coffea Liberica (Figure 6b).

3.5. The Correlation Between Coffee Rhizosphere Soil Microbial Diversity and Root Exudates

There was a significant negative correlation between the nucleosides, nucleotides, and analogs and bacterial richness (R = 0.45, p < 0.01). There was a significant negative correlation between the alkaloids and derivatives and bacterial diversity (R = 0.39, p < 0.05), although nucleosides, nucleotides, and analogs had negative correlations with bacterial evenness (R = 0.36, p < 0.05), but the response of bacterial evenness to different species and grafting combinations was not significant, showing that nucleosides, nucleotides, and analogs may not be the main reason for affecting bacterial evenness. In contrast, there was a significant positive correlation between the alkaloids and derivatives (R = 0.45, p < 0.01), phenylpropanoids and polyketides (R = 0.56, p < 0.01), and fungal richness; The alkaloids and derivatives (R = 0.42, p < 0.05) and phenylpropanoids and polyketides (R = 0.56, p < 0.01) were positively correlated with fungal diversity (Figure 7).

3.6. The Correlation Between Coffee Rhizosphere Soil Microbial Composition of Dominant Genera and Root Exudates

A network analysis was used to determine the co-occurrence patterns of the coffee rhizosphere soil microbial composition (bacteria and fungi) of dominant genera and root exudates based on strong and significant correlations (Figure 8). The values of average path length (APL), average connectivity (avgK), average clustering coefficient (avgCC), and graph density in these empirical networks of coffee rhizosphere soil microbial composition and root exudates were 4.74, 12.03, 0.211, and 0.51, respectively (Table 5). More positive co-occurrence relationships were shown between coffee rhizosphere soil microbial composition and root exudates, while more negative co-occurrence relationships were shown from coffee root exudates to coffee rhizosphere soil bacterial or fungal composition, which indicated that the improvements in soil properties were conducive to increasing component numbers and relative contents of volatile substances in different categories; this indicates that the coffee root exudates from different sources can promote the succession of microbial communities in coffee roots, but the inhibition effect of coffee root exudates on dominant bacterial and fungal flora is greater than the promotion effect. Strikingly, subneutral co-occurrence relationships were shown between soil bacterial and fungal composition of dominant genera, while more negative co-occurrence relationships were shown among dominant bacterial or fungal genera composition themselves, indicating that the intensity of interspecific competition is greater than the synergistic effect under different microbial populations. Altogether, coffee root exudates had a negative impact on the dominant microbial community in the coffee rhizosphere, and the intraspecific competition of coffee rhizosphere microorganisms mediated by coffee root exudates was higher than that of interspecific competition, indicating that there is a potential balance between the individual and collective survival of different microbes, and they dominate the most rare soil microbes.

4. Discussion

4.1. Effects of Different Grafting Treatments on C. canephora cv. Robusta and Coffea Liberica Root Exudates

Root exudates are complex compounds released from plant roots into the soil. They significantly influence the interaction between plants and soil microorganisms, soil nutrient cycling, and the plant growth environment [20]. C. canephora cv. Robusta and Coffea Liberica have different genetic bases, resulting in differences in their growth habits, adaptability, and metabolic pathways [30]. These differences may directly affect the type and quantity of root exudates [31]. Previous studies have indicated that C. canephora cv. Robusta typically exhibits strong drought resistance, disease, and insect resistance, whereas Coffea Liberica may be more suited to a specific growth environment [30,32]. These differences in growth characteristics may lead to the release of different compounds in root exudates to adapt to their respective growth conditions. The two kinds of coffee root exudates include a species of organic and inorganic compounds, such as amino acids, organic acids, phenolic compounds, sugars, and secondary metabolites in this study (Figure 2). Some compounds may only appear in the C. canephora cv. Robusta root exudates, while others may only be detected in the Coffea Liberica root exudates. Additionally, even if both coffees secrete the same compounds, there may be significant differences in their concentrations.
Grafting treatment can alter the growth environment and physiological state of plants [33]. The interaction between different species of coffee scions and rootstocks can influence the overall growth and development of plants, thereby affecting the production of root exudates [34]. On the one hand, grafting different species of coffee scions onto the same rootstock may lead to changes in the composition and quantity of root exudates of the rootstock due to the physiological integration between the scions and the rootstock [35]; on the other hand, various grafting combinations can alter the nutrient absorption and utilization efficiency of plants, thereby affecting the composition and content of root exudates [36]. Changes in root exudates may be influenced by various factors such as scion species, grafting combinations, and environmental conditions. The effects of different species of coffee scions on root exudates of rootstocks in this study contribute to a deeper understanding of the interaction mechanism between coffee trees and the soil environment.

4.2. Effects of Different Grafting Treatments on C. canephora cv. Robusta and Coffea Liberica Rhizosphere Soil Microbial Diversity and Structure

C. canephora cv. Robusta and Coffea Liberica differ in root morphology and in physiological characteristics, resulting in significant differences in the composition and quantity of their root exudates [34]. Root exudates are vital nutrients for soil microorganisms, and the organic acids, amino acids, or sugars in them can attract specific microbial groups, thereby changing the diversity of soil microorganisms [37]. Thus, alterations in the composition and concentration of root exudates of coffee trees under various grafting treatments can directly affect the community structure and diversity of soil microorganisms. The significantly negative correlation between bacterial richness, diversity and nucleosides, nucleotides and analogs, and alkaloids and their derivatives in this study (Figure 6) is consistent with the findings from previous studies. Variations in root exudates under different grafting treatments may modify soil physicochemical properties such as pH, organic matter content, nutrient content, and soil structure, as well as soil micro-environmental indicators such as bulk density and water status [38,39]. Changes in soil physicochemical properties and micro-environment directly affect the metabolic pathways, enzyme activity, and conditions for growth and reproduction, thereby regulating microbial diversity and community structure [40].
General research indicates that rootstocks, rather than scions, influence the diversity and structure of microbial communities [41]. However, the different combinations of rootstocks and scions may indirectly affect the living environment of soil microorganisms, including oxygen content, water status, and nutrient availability around the roots, thereby regulating the diversity and function of soil microorganisms [37]. Interaction among coffee roots from different sources leads to the recombination and dynamic evolution of rhizosphere microbial communities. Root system interactions may also trigger the migration and diffusion of microorganisms. Coffee roots from different sources grow intermittently in the soil, creating pathways for microbial migration and diffusion. The composition and structure of the rhizosphere microbial community will change by causing the exchange and redistribution of rhizosphere microorganisms between different coffee roots. Coffee root exudates from different sources promote the succession of microbial communities in coffee roots in this study, but the inhibitory effect of coffee root exudates on dominant bacterial and fungal communities is greater than the promoting effect (Figure 8). Moreover, the coffee root exudates negatively affected the dominant microbial community in the coffee rhizosphere. Intraspecific competition among coffee rhizosphere microorganisms mediated by these exceeded interspecific competition, suggesting a potential balance between the individual and collective survival of different microbes, with dominance being exerted by the majority of rare soil microbes.
Furthermore, different scions may significantly differ in their impact on the microbial community structure and diversity of coffee rhizosphere soil. On the one hand, the existing microbial community may be impacted by new microorganisms introduced by scions, leading to changes in population size or population substitution, as already seen in apple [41]; on the other hand, new microorganisms may exploit the new environmental conditions introduced by scions and gradually establish dominance in the rhizosphere environment, as already seen in grapevines [42]. Additionally, grafting treatment may alter the interactions among soil microorganisms. Previous studies have demonstrated that grafting can enhance competition, symbiosis, and antagonism among soil microorganisms, as already seen in vegetables [43]. Some beneficial microorganisms, such as mycorrhizal fungi that promote plant growth or bacteria with disease inhibition functions, may increase due to the introduction of scions; conversely, some potential pathogens or microorganisms detrimental to plant growth may be suppressed or their numbers may decrease, as already seen in watermelon [44]. Therefore, during root interaction, microbial attraction or repulsion may intensify competition or alter symbiotic relationships among microorganisms, thereby influencing the structural composition, diversity, and stability of rhizosphere microbial communities.

4.3. Effects of Different Grafting Treatments on C. canephora cv. Robusta and Coffea Liberica Rhizosphere Soil Microbial Function

The structure and function of soil microorganisms are indivisible; thus, differences in rhizosphere microbial structure between C. canephora cv. Robusta and Coffea Liberica may alter the functional profiles of these microbial communities, as already seen in Camellia sinensis [45]. Rhizosphere soil microorganisms play a crucial role in plant growth, nutrient cycling, and pest and disease prevention [46]. The nutrient cycling function of rhizosphere microorganisms in Coffea Liberica was stronger compared with C. canephora cv. Robusta in this study, with significantly fewer potentially pathogenic microorganisms in the rhizosphere of Coffea Liberica (Figure 6), suggesting a stronger rhizosphere immunity in Coffea Liberica. Furthermore, the functions of chemoheterotrophy, degradation, nitrate reduction, fertilization, and nitrogen fixation in the rhizosphere microorganisms of C. canephora cv. Robusta were significantly improved after grafting with various coffee species in Coffea Liberica (Figure 6). Hence, the efficacy of heterologous double-root grafting in mitigating continuous cropping obstacles in C. canephora cv. Robusta may be related to the stronger rhizosphere immune ability of Coffea Liberica and significant enhancement of nutrient mineralization function in the C. canephora cv. Robusta rhizosphere.
Various grafting combinations (e.g., interspecific grafting and intraspecific grafting) and coffee species may affect coffee function by modifying the community structure of rhizosphere soil microorganisms, as already seen in coffee [6] and cucumber [47]. Multiple regulatory pathways may be involved in the effects of heterologous double-root grafting combinations on the rhizosphere microbial function in this study. Firstly, the composition and quantity of root exudates may change following the combination of scions and rootstocks. These secretions are primary nutrients for rhizosphere microorganisms, so their changes directly affect the types and quantities of rhizosphere microorganisms; thus, alterations directly impact the types and quantities of these microorganisms, thereby altering coffee microbial community functions [37]. Conversely, grafting scions may regulate rootstock rhizosphere microbial function through indirect effects on soil properties and the microenvironment [38]. Secondly, genetic differences between scions and rootstocks may lead to varying affinities for specific microorganisms, as already seen in apples [48]. Grafting treatment may enhance some beneficial microorganisms in the coffee rhizosphere microbial community and suppress potential harmful ones, as already seen in apple, optimizing rhizosphere microorganism function and enhancing plant nutrient absorption, disease resistance, and adaptability [41]. Thirdly, complex signaling and interaction mechanisms may exist between grafting scions and rootstocks. Grafting scions regulate the activity, metabolic pathways, and function of rhizosphere microorganisms through signals, including chemical signal (e.g., hormones, secondary metabolites, etc.) and physical signal (e.g., root structure) transmission and response, as already seen in coffee [31] and vegetables [49]. Fourthly, grafting treatment may alter the interaction between coffee plants and rhizosphere microorganisms, affecting the attachment and colonization ability of rhizosphere microorganisms and thus coffee rhizosphere microbial functions, as already seen in cucumber [50]. Furthermore, the interaction among coffee roots influences both the types and quantities of rhizosphere microorganisms and the competition and symbiotic relationships among different functional microorganisms. Further research is needed on the interactions between coffee scions and rootstocks from different sources and their impacts on rhizosphere microbial functions and regulatory mechanisms.

5. Conclusions

There were significant differences in the root exudates, rhizosphere microbial structure, and function between C. canephora cv. Robusta and Coffea Liberica in this study. Despite the lower diversity and higher abundance of potential pathogenicity in the Coffea Liberica rhizosphere, it still exhibited stronger resistance to diseases. Grafting onto Coffea Liberica roots significantly enhances the secretion of resistance substances in C. canephora cv. Robusta roots, increases the relative abundance of potential beneficial bacteria, and reduces the relative abundance of potential pathogenic fungi, which enhance the resistance of C. canephora cv. Robusta roots to soil-borne diseases. Grafting onto Coffea Liberica roots allows C. canephora cv. Robusta to enhance its rhizosphere immunity, thus mitigating continuous cropping challenges. These findings provide a crucial foundation for further exploring the regulatory mechanisms of grafting on coffee rhizosphere microorganisms and for optimizing coffee cultivation techniques. However, this study only explored the effects of heterologous double-root grafting methods on different coffee rhizosphere microbiota, and its impact on coffee plant growth still needs further investigation.

Author Contributions

Conceptualization, A.Z. and J.Y.; methodology, Y.S. and L.Y.; software, A.Z.; validation, Y.S., J.Y. and L.Y.; investigation, Q.Z. and X.W. (Xiaoyang Wang); resources, L.H.; data curation, Z.Z.; writing—original draft preparation, Y.S.; writing—review and editing, L.Y., A.Z. and J.Y.; visualization, X.W. (Xiao Wang); supervision, J.Y. and X.L.; project administration, Y.S.; funding acquisition, Y.S. All authors have read and agreed to the published version of the manuscript.

Funding

This research was supported by the National Natural Science Foundation of China (N0.32101847) and the Natural Science Foundation of Hainan (321MS0804).

Institutional Review Board Statement

Not applicable.

Data Availability Statement

The data presented in the study are deposited in the Mendeley Data repository, https://data.mendeley.com/datasets/3t4jx27j9x/1 (accessed on 25 April 2024).

Acknowledgments

We are grateful for Xinglong Tropical Botanical Garden for providing experimental materials for the research.

Conflicts of Interest

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as potential conflicts of interest, and the authors declare no conflict of interest.

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Figure 1. Illustrative photo of various coffee grafting treatments.
Figure 1. Illustrative photo of various coffee grafting treatments.
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Figure 2. Effects of different grafting treatments on C. canephora cv. Robusta and Coffea Liberica root exudates. R/RR represents the rhizosphere soil of Robusta homologous double-root coffee seedlings. R/RL represents the Robusta rhizosphere soil of Robusta heterologous double-root seedlings, R/LR represents the Robusta rhizosphere soil of Liberica heterologous double roots, L/LL represents the rhizosphere soil of Liberica homologous double-root coffee seedlings, L/RL represents the Liberica rhizosphere soil of Robusta heterologous double-root seedlings, and L/LR represents the Liberica rhizosphere soil of Liberica heterologous double-root seedlings.
Figure 2. Effects of different grafting treatments on C. canephora cv. Robusta and Coffea Liberica root exudates. R/RR represents the rhizosphere soil of Robusta homologous double-root coffee seedlings. R/RL represents the Robusta rhizosphere soil of Robusta heterologous double-root seedlings, R/LR represents the Robusta rhizosphere soil of Liberica heterologous double roots, L/LL represents the rhizosphere soil of Liberica homologous double-root coffee seedlings, L/RL represents the Liberica rhizosphere soil of Robusta heterologous double-root seedlings, and L/LR represents the Liberica rhizosphere soil of Liberica heterologous double-root seedlings.
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Figure 3. Effects of different grafting treatments on Robusta and Liberica rhizosphere soil microbial (bacterial (a–c) and fungal (d–f)) richness (a,d), alpha diversity (Shannon index, (b,e)), and evenness (c,f). See Figure 2 for treatment abbreviations. Different letters represents p < 0.05.
Figure 3. Effects of different grafting treatments on Robusta and Liberica rhizosphere soil microbial (bacterial (a–c) and fungal (d–f)) richness (a,d), alpha diversity (Shannon index, (b,e)), and evenness (c,f). See Figure 2 for treatment abbreviations. Different letters represents p < 0.05.
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Figure 4. Effects of different grafting treatments on Robusta and Liberica rhizosphere soil bacterial (a) and fungal (b) beta diversity (PCoA) across the experimental period. See Figure 2 for treatment abbreviations.
Figure 4. Effects of different grafting treatments on Robusta and Liberica rhizosphere soil bacterial (a) and fungal (b) beta diversity (PCoA) across the experimental period. See Figure 2 for treatment abbreviations.
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Figure 5. Clustering heat map of rhizosphere bacterial (a) and fungal (b) diversity in C. canephora cv. Robusta and Coffea Liberica at the genus level. See Figure 2 for treatment abbreviations.
Figure 5. Clustering heat map of rhizosphere bacterial (a) and fungal (b) diversity in C. canephora cv. Robusta and Coffea Liberica at the genus level. See Figure 2 for treatment abbreviations.
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Figure 6. Predicted functional profiles of C. canephora cv. Robusta and Coffea Liberica rhizosphere soil bacteria (a) and fungi (b) under different grafting treatments. See Figure 1 for treatment abbreviations.
Figure 6. Predicted functional profiles of C. canephora cv. Robusta and Coffea Liberica rhizosphere soil bacteria (a) and fungi (b) under different grafting treatments. See Figure 1 for treatment abbreviations.
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Figure 7. Relationships between the coffee rhizosphere soil microbial (bacterial and fungal) richness, diversity, evenness, and coffee root exudates. Significant level: “*” represents p < 0.05; “**” represents p < 0.01.
Figure 7. Relationships between the coffee rhizosphere soil microbial (bacterial and fungal) richness, diversity, evenness, and coffee root exudates. Significant level: “*” represents p < 0.05; “**” represents p < 0.01.
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Figure 8. Network interaction diagram of coffee root exudates and soil microbial (bacterial and fungal) taxa at the gene level. The size of the points represents the magnitude of coffee root exudates and soil microbial taxa. Red lines represent the positive correlation, while blue lines represents the negative correlation, and the thickness of the line represents the correlation size.
Figure 8. Network interaction diagram of coffee root exudates and soil microbial (bacterial and fungal) taxa at the gene level. The size of the points represents the magnitude of coffee root exudates and soil microbial taxa. Red lines represent the positive correlation, while blue lines represents the negative correlation, and the thickness of the line represents the correlation size.
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Table 1. Results (F-values) of repeated measures of ANOVAs on the effects of coffee species (S), grafting combinations (C), and their potential interactions (S × C) on C. canephora cv. Robusta and Coffea Liberica root exudates.
Table 1. Results (F-values) of repeated measures of ANOVAs on the effects of coffee species (S), grafting combinations (C), and their potential interactions (S × C) on C. canephora cv. Robusta and Coffea Liberica root exudates.
TreatmentsAlkaloids and DerivativesBenzenoidsHomogeneous Non-Metal CompoundsHydrocarbonsLignans, Neolignans, and Related CompoundsLipids and Lipid-like MoleculesNucleosides, Nucleotides, and AnalogsOrganic Acids and Derivatives
S0.7440.91 **3.575.70 *66.21 **1.560.9632.18 **
C0.155.12 *5.57 **0.0517.97 **5.89 **2.0211.42 **
S × C0.298.88 **0.141.450.734.21 *0.962.96
Organic CompoundsOrganic Nitrogen CompoundsOrganic Oxygen CompoundsOrganohalogen CompoundsOrganoheterocyclic CompoundsOrganonitrogen CompoundsOrganooxygen CompoundsOrganosulfur CompoundsPhenylpropanoids and Polyketides
9.88 **0.1135.6 6 **19.93 **26.47 **8.76 **81.69 **1.298.93 **
6.95 **0.6212.07 ***4.11 *8.89 **2.9812.17 **6.37 **14.45 **
1.10.043.130.081.860.116.71 **0.566.96 **
Notes: Significant level: “*” represents p < 0.05; “**” represents p < 0.01; “***” represents p < 0.001.
Table 2. Results (F-values) of repeated measures of ANOVAs on the effects of coffee species (S), grafting combinations (C), and their potential interactions (S × C) on soil microbial (bacterial and fungal) richness, alpha diversity (Shannon index), and evenness (Pielou index).
Table 2. Results (F-values) of repeated measures of ANOVAs on the effects of coffee species (S), grafting combinations (C), and their potential interactions (S × C) on soil microbial (bacterial and fungal) richness, alpha diversity (Shannon index), and evenness (Pielou index).
Treatments Bacteria Fungi
RichnessShannonPielouRichnessShannonPielou
S5.38 *4.97 *1.224.36 *5.56 *0.36
C1.432.172.846.04 **5.33 **1.52
S × C0.960.740.410.50.891.6
Notes: Significant level: “*” represents p < 0.05; “**” represents p < 0.01.
Table 3. Results (F-values) of repeated measures of ANOVAs on the effects of coffee species (S), grafting combinations (C), and their potential interactions (S × C) on soil microbial (bacterial and fungal) composition.
Table 3. Results (F-values) of repeated measures of ANOVAs on the effects of coffee species (S), grafting combinations (C), and their potential interactions (S × C) on soil microbial (bacterial and fungal) composition.
TaxonGenus NameSCS × C
BacteriaVicinamibacteraceae40.05 ***14.02 ***5.12 **
Vicinamibacterales38.41 ***19.39 ***19.41 ***
Rokubacteriales8.97 **34.73 ***5.63 **
Gaiella86.19 ***1.347.19 **
Gaiellales55.47 ***5.27 **14.86 ***
Subgroup34.46 ***7.63 **1.76
Gemmatimonadaceae107.91 ***7.71 **71.31 ***
Xanthobacteraceae11.93 **11.40 ***4.15 *
Proteobacteria30.04 ***2.6322.02 ***
Actinobacteriota13.62 ***0.070.73
Pedomicrobium0.0116.36 ***18.63 ***
RB410.089.814.67
MND1117.68 ***22.78 ***26.88 ***
KD4-9621.24 ***54.19 ***19.50 ***
MB-A2-10851.31 ***15.26 ***5.77 **
Haliangium15.41 ***3.64 *1.08
Acidobacteriota2.7710.41 ***1.48
Gemmatimonadota5.72 *2.8815.64 ***
Nitrospira54.67 ***10.25 ***4.54 *
Gemmatimonas0.0120.17 ***17.05 ***
SC-I-846.07 *19.71 ***2.66
IMCC2625615.02 ***3.0814.49 ***
Roseiflexaceae10.96 **8.81 ***8.97 ***
Gemmataceae0.040.670.19
TK100.0536.61 ***1.10
Candidatus1.7718.02 ***15.95 ***
Solirubrobacter7.77 **7.49 **14.86 ***
FungiAscomycota_unclassified43.97 ***1.6119.01 ***
Haematonectria11.04 **0.460.76
Thermomyces1.631.410.89
Actinomucor1.301.850.21
Chaetomiaceae_unclassified5.80 *3.45 *1.40
Myrothecium1.071.403.24 *
Hypocrea6.25 *0.370.40
Chaetomium2.533.142.29
Agaricomycetes_unclassified4.77 *1.651.46
Cochliobolus17.06 ***14.16 ***22.03 ***
Nectriaceae_unclassified0.830.941.30
Sordariomycetes_unclassified3.249.84 ***4.04 *
Hypocreales0.335.21 **0.84
Preussia6.21 *6.05 **5.54 **
Notes: Significant level: “*” represents p < 0.05; “**” represents p < 0.01; “***” represents p < 0.001.
Table 4. Results (F-values) of repeated measures of ANOVAs on the effects of coffee species (S), grafting combinations (C), and their potential interactions (S × C) on soil microbial (bacterial and fungal) predicted function.
Table 4. Results (F-values) of repeated measures of ANOVAs on the effects of coffee species (S), grafting combinations (C), and their potential interactions (S × C) on soil microbial (bacterial and fungal) predicted function.
TaxonPredicted FunctionSCS × C
Bacteria Chemoheterotrophy1.176.10 **2.49
Nitrate reduction4.37 *0.1514.75 ***
Denitrification1.1316.76 ***2.64
Photoautotrophy1.0416.58 ***2.67
Parasites17.93 ***3.55 *0.22
Degradation1.215.97 **1.46
Fermentation0.0124.73 ***2.75
Nitrogen fixation0.025.33 **2.76
Human pathogen1.520.904.16 *
FungiSaprotroph0.034.17 *0.58
Pathogen0.010.860.54
Endophyte0.051.890.77
Epiphyte0.371.223.33 *
Parasite0.71.740.3
Arbuscular mycorrhizal15.10 ***5.08 *3.41 *
Ectomycorrhizal0.322.800.89
Endomycorrhizal 1.342.151.61
Notes: Significant level: “*” represents p < 0.05; “**” represents p < 0.01; “***” represents p < 0.001.
Table 5. Topological properties of co-occurring coffee root exudates and microbial (bacterial and fungal) component networks obtained in several coffee species and grafting combination treatments.
Table 5. Topological properties of co-occurring coffee root exudates and microbial (bacterial and fungal) component networks obtained in several coffee species and grafting combination treatments.
Network MetricsSource
Number of nodes58
Number of edges710
Number of positive correlations373
Number of negative correlations337
Percentage of the positive link (p%)52.54%
p% from coffee rhizosphere to dominant bacterial genera41.50%
p% from coffee rhizosphere to dominant fungal genera35.71%
p% from dominant bacterial genera to fungal genera50.83%
p% among dominant bacterial genera48.56%
p% among dominant fungal genera35.71%
Average connectivity (avgK)12.03
Average clustering coefficient (avgCC)0.211
Average path length (APL)4.738
Graph density0.508
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MDPI and ACS Style

Sun, Y.; Yan, L.; Zhang, A.; Yang, J.; Zhao, Q.; Lin, X.; Zhang, Z.; Huang, L.; Wang, X.; Wang, X. Effects of Grafting on the Structure and Function of Coffee Rhizosphere Microbiome. Agriculture 2024, 14, 1854. https://doi.org/10.3390/agriculture14101854

AMA Style

Sun Y, Yan L, Zhang A, Yang J, Zhao Q, Lin X, Zhang Z, Huang L, Wang X, Wang X. Effects of Grafting on the Structure and Function of Coffee Rhizosphere Microbiome. Agriculture. 2024; 14(10):1854. https://doi.org/10.3390/agriculture14101854

Chicago/Turabian Style

Sun, Yan, Lin Yan, Ang Zhang, Jianfeng Yang, Qingyun Zhao, Xingjun Lin, Zixiao Zhang, Lifang Huang, Xiao Wang, and Xiaoyang Wang. 2024. "Effects of Grafting on the Structure and Function of Coffee Rhizosphere Microbiome" Agriculture 14, no. 10: 1854. https://doi.org/10.3390/agriculture14101854

APA Style

Sun, Y., Yan, L., Zhang, A., Yang, J., Zhao, Q., Lin, X., Zhang, Z., Huang, L., Wang, X., & Wang, X. (2024). Effects of Grafting on the Structure and Function of Coffee Rhizosphere Microbiome. Agriculture, 14(10), 1854. https://doi.org/10.3390/agriculture14101854

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