Community structure and niche differentiation of endosphere bacterial microbiome in Camellia oleifera

ABSTRACT Understanding the changes in bacterial community structure in different microenvironments of Camellia oleifera is essential to better explore the benign interaction between beneficial microorganisms and plants. Using Camellia oleifera trees, a Chinese wooden oil plant as a model ecosystem, we characterized the archaeal and bacterial microbiome across five different tissue-level niches using 16S rRNA gene analyses. Our research indicates that the diversity of Camellia oleifera endophytic bacterial communities is highly dependent on the plant compartment. The species replacement process (69.90%) is the dominant factor in the differences in bacterial community structure. The dominant bacteria phyla (Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Chloroflexi, and Verrucomicrobia) of Camellia oleifera show a significant plant compartment (roots, stems, leaves, fruits) enrichment effects. A variety of bacteria (Hymenobacter, Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Mesorhizobium, Bradyrhizobium, Bacillus, Ochrobactrum, Pantoea, Pseudomonas, etc.) with nitrogen-fixed potentials are enriched in Camellia oleifera tissue. In addition, the hub bacterial groups of Camellia oleifera are Nitrospira, Haemophilus, Staphylococcus, Ruminiclostridium, and Ochrobactrum. They are widespread colonization in various tissues with a low relative abundance and may play an important role in the nitrogen cycle, host life promotion, and plant defense. This study provides a holistic understanding of the endosphere bacterial community structure, which is one of the most complete ecological niche-level analyses of Camellia oleifera. These results provide a scientific theoretical basis for an in-depth discussion of plant-endosphere microbial interaction and better exploration of benign interaction of beneficial microorganisms and plants. IMPORTANCE Microorganisms inhabited various tissues of plants and play a key role in promoting plant growth, nutritional absorption, and resistance. Our research indicates that the diversity of Camellia oleifera endophytic bacterial communities is highly dependent on the plant compartment. Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Chloroflexi, and Verrucomicrobia are dominant bacteria phyla. The tissues of Camellia oleifera contain various bacteria with nitrogen fixation potential, host life promotion, and plant defense. This study provides a scientific theoretical basis for an in-depth discussion of plant-endosphere microbial interaction and better exploration of benign interaction of beneficial microorganisms and plants.

thereby avoiding competing for land resources with grain.However, the long-term predatory and extensive management have led to a significant decrease in soil nutrients and in a low-yield state.
Plants are colonized by complicated multi-kingdom microbial communities (bacteria, fungi, native creatures, etc.) (2,3).Each part of the plant is a unique ecosystem of microorganisms.Compared with other plant tissues (including roots, stems, leaves, flowers, and seeds), it has a unique microbial assembly (4)(5)(6)(7).The results of Xiong et al. (8) pointed out that some members of Burkholderiaceae, Microbacteriaceae, Streptomy cetaceae, and Rhizobiaceae were enriched on the surface of phylloplane and rhizoplane at the maize seedling stage.Lei et al. (9) show that the bacterial community structure between different parts of Macleaya cordata has a significant change, among which Sphingomonas and Methylobacterium dominate the fruits and leaves, respectively.In addition, a significant plant compartment effect was observed in the microbiome of tomato, willow, poplar, agave, and cactus (10)(11)(12)(13).In addition, only adaptive or non-picky bacterial populations can survive or flourish within plant tissues due to filtration and selection, which leads to a low degree of microbial diversity (14).
These microorganisms inhabiting various parts of plants can play a key role in promoting plant growth, nutrient absorption, and resistance to biotic or abiotic stresses (diseases, insect pests, high temperature, saline-alkali soil or drought, etc.) (15)(16)(17).One of the strategies developed by non-legume plants to increase the supply of nitrogen is to form a nutritional alliance with endophyte nitrogen fixation bacteria.So far, a large number of nitrogenfixed nutrient bacteria (Azospirrillum brasiliense, Gluconaceto bacter diazotrophicus, Herbaspirillum seropedicae, Azoarcus, etc.) have been identified as epibiotic or endophyte bacteria, combined with cereal and grass (18).Recently, Deynze et al. (19) reported that they identified landrace maize that could benefit from the atmospheric nitrogen fixed by the related endophytic nitrogenfixing bacteria (Azospir illum brasilense, Herbaspirillum seropodicae, and Burkholderia unamae).The aerial root mucus produced by this special maize is proved to be the environmental niche of the nif gene pool, which can provide up to 85% of assimilated nitrogen.Under drought stress, Bacillus sp.(12D6) and Enterobacter sp.(16i) will rapidly colonize in the rhizosphere of maize seedlings, stimulate the secretion of auxins and gibberellins, significantly increase the root length, root surface area, and number of root tips of maize seedlings, to obtain more water and alleviate drought stress (20).Therefore, analyzing the charac teristics of bacterial communities in different ecological niches of healthy hosts may help to improve soil quality, crop growth, and stress resistance, thus reducing the dependence on fertilizers in production activities.It is of great importance for promoting the sustainable development of Camellia oleifera production and understanding the contribution of Camellia oleifera to ecosystem services.
Most of the previous research is concentrated in the ecological position of the bacterial community of the soil-root interface (21)(22)(23).Contrary to the knowledge of bacterial microbial community differentiation related to the rhizosphere (24)(25)(26), there are few reports on the structural composition of bacterial communities in different tissues of Camellia oleifera, especially the relationship between underground and aboveground communities.Here, we employed 16S rRNA sequencing to evaluate the niche differentiation of bacterial communities related to bulk soil and roots, stems, leaves, and fruits of Camellia oleifera.The analysis of niche differentiation (bulk soil, root, stem, leaf, and fruit) of endophytic bacteria community in Camellia oleifera can provide a scientific basis for further exploring the mechanism of plant endophytic microbial interaction and tapping the biological potential of benign interaction between plant growth and development and beneficial microorganisms.

Study location and sampling methods
The Camellia oleifera tree (planted for about 10 years) planted in Hualong New Village, Yongxiu County, Jiujiang City was selected to obtain samples for this study.The forest land was established in April 2012.The planting density of Camellia oleifera is 1,100-1,300 trees per hectare, and the row spacing is 3.0 m.The samples were collected on 12 April 2021.At the time of sampling, the average height of Camellia oleifera was about 2.0 m.Six healthy individuals with basically the same growth vigor were selected, and the samples collected included bulk soil, roots, stems, leaves, and fruits.Samples of bulk soil and roots were collected at a depth of 5-20 cm below ground level.Sterile tools were used to take out the root, and the soil that is not tightly attached was removed by shaking.The roots were cut into 2-3 cm fragments, put it in a tube equipped with PBS buffer and glass beads, and the vortex was washed to obtain the root sample.Bulk soil samples were collected at a distance of 30-50 cm from the main stem using a sterile soil drill.For leaf, stem, and fruit samples, a fruiting branch was collected from six Camellia oleifera individuals.The average circumference of the sampled branches is about 1 cm and the height is about 120 cm. 10 subsmall stems with bark were collected from each plant as stem samples.All leaves and fruits collected from the sampled branches are called leaf and fruit samples.Weeds were controlled manually in each autumn.No obvious diseases or pest damage heve been observed in recent years.Irrigation was not applied throughout the plant period.

Sample preparation
The samples were processed as described by Beckers et al. (11).The soil particles that are tightly attached to the root surface are removed by shaking on the oscillator (20 min, 120 rpm).Subsequently, the root, stem, leaf, and fruit samples were sterilized by 75% (vol/vol) ethanol (2 min), NaClO (2.5% active Cl − and 0.1% Tween 80) (5 min), 70% (vol/ vol) ethanol (30 s), and sterile ultrapure water (washing the samples for five times).A sterile scalpel was used to divide the plant sample into small segments, and a Polytron PR1200 mixer (Kinematica A6) was used to soak it in sterile phosphatebuffered saline (PBS; 130 mM NaCl, 7 mM Na 2 HPO 4 , 3 mM NaH 2 PO 4 , pH 7.4).Sterilization and homogeni zation of plant samples are carried out under sterile conditions.Finally, each sample of all homogeneous plant materials (roots, stems, leaves, or fruits) is stored at −80 °C until DNA is extracted.

DNA extraction, PCR amplification, and 16S rRNA sequencing
Soil DNA was extracted using the E.Z.N.A. Soil DNA Kit (Omega Bio-tek, Norcross, GA, USA) according to the manufacturer's instructions.For plant tissue, the first equal portions of homogeneous plant material (1.5 mL) (13,400 rpm, 30 min) were centrifuged to collect all cells.The supernatant was discarded and DNA from the precipitated plant materials was extracted.According to the manufacturer's scheme (Strategic Biomedical AG, Birkenfeld, Germany), DNA was extracted from plant samples using the Invisorb Spin Plant Mini Kit.The V3-V4 hypervariable regions of the bacterial 16S rRNA gene were amplified by PCR using a special primer pair (335F: 5′-CAD ACT CCT ACG GGA GGC-3′, and 769R: 5′-ATC CTG TTT GMT MCC CVC RC-3′), where the barcode comprised a six-base sequence that was unique to each sample.PCR was performed using a protocol similar to the method described by Zheng et al. (27).16S rRNA amplicons were pooled and then sequenced with Illumina Hiseq 2500 (Biomarker Technologies, Beijing, China).The sequences obtained in this study were deposited in the Genome Sequence Archive (GSA) of the National Genomics Data Center, under accession number CRA009115.

Illumina Hiseq sequence processing
Raw sequence data were quality filtered: (i) Trimmatic (version 0.33) was used to filter the quality of raw sequence data and remove the reads whose average quality value is lower than 20 (28); (ii) Cutadapt (version 1.9.1) was used to identify and remove primer sequences (29); and (iii) USEARCH (version 10) was utilized to conduct chimera detection and operational taxonomic units (OTUs) clustering (97% similarity) (30).Taxonomy was identified for each OTU using the RDP classifier (31) trained on the Greengenes (32) and Silva (33) databases for bacterial sequences.In this study, after the quality control of the raw sequence, 1,893,703 clean reads were generated, with an average length of 432 bp.The number of clean reads per sample ranged from 46,616 to 72,362.After the data were standardized, QIIME2 was used to calculate the richness and diversity index (ACE, Chao 1, Simpson, and Shannon Weaver).The rarefaction curve and Shannon curve of bacteria indicate that our sequencing data represent most of the composition (Fig. S1).

Statistical analysis
Whether the distribution of parameters conforms to normal distribution, ANOVA or Kruskal-Wallis rank sum test is used to evaluate the significant difference of variance of parameters (ACE, Chao 1, Simpson, and Shannon index).When P < 0.05, post hoc comparisons were employed by either Tukey's honest significant differences tests or pairwise Wilcoxon rank-sum tests.
Based on the Bray-Curtis distance of OTU abundance, community compositional dissimilarities were estimated.To examine the elevational differences in compositional dissimilarities, principal coordinate analysis (PCoA) and permutational multivariate analysis of variance (PERMANOVA) were performed in R package vegan.Compositional dissimilarities among plant compartments (β-diversity) were partitioned into replace ment (Podani family) and richness difference components (Sørensen dissimilarities) using the R package adespatial (34).
EdgeR (R3.3.0) was used to identify the differential expression of bacteria between the two niches, and the genus with a possibility value (P value) higher than 0.05 was defined as the differential genus.Based on Spearman's correlation coefficient (Spearman's |r| > 0.7 or P < 0.05), MCODE in Cytoscape (v.3.8.2) was used to analyze the network at the bacterial genus level (35), and CytohHubba was used to analyze the core bacterial community of Camellia oleifera (36).The networks were visualized in Cytoscape (v.3.8.2).Functional annotations of prokaryotic taxa were carried out using FAPROTAX (v.1.1).

α-diversity of the bacterial community in each plant compartment
The α-diversity of the bacterial community in plant compartments of Camellia oleifera is lower than that of bulk soil (Fig. 1; Table S1).The bacterial richness (ACE and Chao1 index) and diversity (Simpson and Shannon index) of bulk soil (S) were significantly higher than fruit endosphere (FE), leaf endosphere (LE), and stem endosphere (SE), and slightly higher than root endosphere (RE).The richness and diversity of endophytic bacteria in LE were significantly higher than those in SE and FE.Compared with SE, the diversity index (Simpson: 0.947 ± 0.02, Shannon: 5.82 ± 0.8) was significantly reduced under FE, but the richness (ACE and Chao1 index) showed no significant differences between SE and FE.

β-diversity of the bacterial community in each plant compartment
PCoA based on OTU level shows that there are significant differences in bacterial communities and compositions of different niches of Camellia oleifera (Fig. 2 and Table 1).The analysis using Bray-Curtis distance showed that there were different patterns of bacterial communities related to the two axes, which explained 37.52% and 17.78% of the total variation in each compartment of Camellia oleifera.
PERMANOVA analysis (Bray-Curtis distance) shows that the composition of bacterial communities in different niches is significantly different (Table 1).Compared with bulk soil, the composition of the bacterial community in plant compartments is significantly different, forming an independent individual group (FE and S, R 2 = 0.6309, P < 0.01; LE and S, R 2 = 0. 4449, P < 0.01; RE and S, R 2 = 0.4335, P < 0.01; SE and S, R 2 = 0.6262, P < 0.001).Except for LE and RE, the community structure of endophytic bacteria in different compartments (FE and LE, R 2 = 0.3987, P < 0.01; FE and RE, R 2 = 0.4902, P < 0.01; FE and   To understand the influence of niche on the difference in bacterial community composition of Camellia oleifera, we decomposed β-diversity into species replacement and richness difference.The results of β-diversity decomposition analysis showed that the difference of bacterial community composition in each niche of Camellia oleifera was dominated by the process of species replacement, which contributed 69.90%; however, the impact of the richness difference process on β-diversity is relatively small, which contributed 30.14% (Fig. 3).

Bacterial community composition in each plant compartment
A total of 1,720 OTUs were generated from all samples, with significant differences among plant compartments (Fig. 4).The numbers of OTUs in the S and root compart ments were significantly higher than that in FE, SE, and LE (P < 0.05) (Fig. 4A).Compared with FE, SE, and LE, the S increased by 33.20%, 37.03%, and 18.42%, and the RE increased About 58.32%-90.64% of the 1,720 OTUs obtained are classified at the phylum level.The results of difference analysis showed that 1,269, 833, 1,169, and 860 different OTUs were obtained for FE, LE, SE, and RE, respectively, compared with S (Fig. 5).Among them, 365 OTUs were significantly enriched in at least one compartment.As shown in the "tail" in the MA figure (Fig. 5), LE and RE are similar to S. Compared with depleted OTU, the statistically significant high ratio of enriched OTU suggested the enrichment effect of fruit (795 vs 474).Compared with depleted OTU, the statistically significant high ratio of enriched OTU suggested the enrichment effect of fruit (795 vs 474).By contrast, although the SE enriched many OTUs, it also consumed a larger proportion of OTUs (365 vs 804).
Linear discriminant analysis (LDA) and effect size analysis (LEfSe) were used for the quantitative analysis of biomarkers (Fig. 7; Fig. S2).We detected significant differences in the abundance of bacterial biomarkers from different tissues and identified a total of 548 biomarkers from all samples.As shown in Fig. 7, the important taxa in the fruit belong to Bacteroidetes and Proteobacteria; the significantly rich taxa in the leaf are Firmicutes, Nitrospirae, and Spirochaetes.Important taxa in root belong to Actinobacteria, Degerribac teres, Epsilonbateraeota, Fusobacteria, and Gemmatimonadetes.Important taxa in bulk soil samples belong to Acidobacteria, Armatimonadetes, Chloroflexi, and Verrucomicrobia.

Identification of hub bacteria
To further explore the interaction between microorganisms in the microenvironment of Camellia oleifera, we used the genera with relative abundance (>0.01%) to conduct a co-occurrence network analysis (MCODE: node score cutoff = 0.2, K-core = 2) and visualized the correlation between the genera and each niche of Camellia oleifera (Fig. 8).In the bacterial community, we obtained five modules with obvious differences in species characteristics (Fig. 8).Cluster 1 is dominated by leaf endophytic bacteria community, which contains 229 OTUs distributed in 9 phyla and 70 genera, among which Firmicutes (5.23%), Proteobacteria (3.26%), and Bacteroides (2.11%) are the dominant phyla.Cluster 2 is dominated by soil bacterial communities, and 99 OTUs are distributed in 7 phyla and 19 genera, of which Proteobacteria (15.18%) is the dominant phyla.In Cluster 3, 176 OTUs belong to 23 genera in five phyla, among which Proteobacteria (13.90%) is the dominant phyla.
We use Cytohubba to analyze the sub-network Cluster 1 with the highest score and determine Nitrospira, Haemophilus, Staphylococcus, Ruminiclostridium, and Ochrobactrum as the core bacterial community of camellia oleifera (Table 2).

The diversity of endophytic bacteria community in Camellia oleifera is highly dependent on compartment
The results show that the richness and diversity of the Camellia oleifera bacterial community gradually decreased from the bulk soil to the endophytic compartment (Fig. 1; Table S1).This result is consistent with the general view of endophyte colonization.This is because the rhizosphere soil-root interface acts as a selective barrier, and only a limited number of bacteria can adapt to the endogenous lifestyle and dominate the endogenous combination, thus forming a unique, highly rich, and diverse microbial community (37).Some studies have found that niche differentiation, especially between soil and plant tissue, can lead to changes in bacterial community structure (38,39).In this study, there are significant differences in the bacterial community structure in different niches of Camellia oleifera, especially between bulk soil and plant tissues (Fig. 2).The species replacement process (69.90% contribution rate) is the dominant factor causing this difference (Fig. 3; Table 1).This result is consistent with the view that each plant compartment is a unique niche of microbial entities and has a unique microbial combination compared with other plant tissues (including roots, stems, leaves, flowers, and seeds) (8,40,41).

Each compartment represents the unique niche of Camellia oleifera bacteria
The plant endophytic environment is considered to be a restricted niche.A variety of biological factors (infiltration pathway, plant genotype, strain type, etc.) and abio tic factors (ultraviolet radiation, temperature, dryness, etc.) limit the colonization of endophytic bacteria (7,42,43).In this study, the number of OTUs in fruit, leaves, root, and stem was reduced by an average of 33.33% compared to the bulk soil, indicating that it is the main site of microbial colonization and activity in the soil, which harbors a rich and diverse bacterial population as compared to other plant ecological niches (44).
In addition, 1,269, 833, 860, and 1,169 differential OTUs were obtained from fruit, leaves, root, and stem, respectively, compared to bulk soil samples (Fig. 5).Contrary to stem (up 365 vs down 804), fruit showed obvious enrichment effect (up 795 vs down 474).This result is consistent with the conclusion that the diversity of endophytic bacterial communities in Camellia oleifera is highly dependent on compartment, indicating that only adaptive and non-selective bacterial populations can survive and/or proliferate in the tissues of Camellia oleifera (45).Finally, we found that most OTUs are not shared, especially those found in bulk samples (Fig. 5).These findings are consistent with studies showing plant niche differentiation (11,46).Of these, four OTUs (such as Ruminococcaceae, Chitinophagaceae, and Diplorickettsiaceae) are unique to the root tissue and one (Methylopila) to the leaf tissue.In all, 205 OTUs are unique to the soil of Camellia oleifera forest, with the majority of them belonging to functional groups that participate in nutrient transformation (Candidatus_Xiphinematobacte, HSB_OF53-F07, and FCPS473), promote plant growth (Mucilaginibacter), and decompose organic matter (Candidatus_Udaeobacter, Chthoniobacter, and Pedosphaera) (47)(48)(49)(50)(51)(52).At the species level, Proteobacteria, Actinobacteria, and Bacteroidetes are the common dominant bacteria of Camellia oleifera, watermelon, Arabidopsis, rice, Antarctic vascular plants, Dendrobium, and other plants (2,45,(53)(54)(55).This indicates that the composition of endophytic bacterial communities in plants may be similar at the phyla level.It has been found that Proteobacteria plays a dominant role in endoderm (56,57), leaf (45), and stem (11).In this study, Proteobacteria, Bacteroidetes, and Firmicutes were significantly enriched in the fruit, leaf, root, and stem of Camellia oleifera (Table S2), and Proteobacte ria was the dominant phylum (Fig. 6; Table S2).Sphingomons are a common bacteria associated with each other in different plant tissues (58), which is significantly enriched in Camellia oleifera fruits (21.59%).Sphingomons is not only an important regulator of Arabidopsis thaliana leaf microbiota (59) but also the most characteristic microorganism in rice seed disease resistance phenotype.It plays the role of "extending the immune system" in the "disease triangle, " and can be passed from generation to generation in the microbiome of healthy plant seeds (60).However, the significance of sphingomons expression in Camellia oleifera fruits needs further study.Massilia can colonize in plant tissues such as Alopecurus aequalis Sobol and ryegrass, and degrade polycyclic aromatic hydrocarbons (PAH) compounds (61).In this study, Massilia was significantly enriched in Camellia oleifera fruits (9.12%) and stems (3.57%), indicating that Camellia oleifera may be able to eliminate environmental pollution by degrading PAH through Massilia, providing a new perspective for plants to control PAH absorption through endophytic bacteria and reflect the ecological function of Camellia oleifera forest.In addition, we also found a variety of bacteria with nitrogen fixation potential in Camellia oleifera fruits (Hymenobacter, Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium), leaves (Bacillus, Mesorhizobium, Ochrobacterium, Pantooa, Pseudomonas, Stenotrophomona, etc.), roots (Bradyrhizobium), and stems (Devosia) (Fig. S3).The above results indicate that the specific bacteria in the endophytic bacteria of Camellia oleifera may play an important role in eliminating environmental pollution and obtaining nutrition.

Potential ecological functions of hub microbes in Camellia oleifera
Hub microbes can be important nodes in the community, rich taxonomic groups in the network structure of the microbial community, or microbes significantly related to ecological functions (62).In our study, five cluster modules were identified in the Camellia oleifera bacterial co-occurrence network (Fig. 8).According to the analysis of Cluster 1 with the highest score, the hub bacteria of Camellia oleifera are Nitrospira (0.07%), Haemophilus (0.05%), Staphylococcus (0.17%), Ruminiclostridium (0.04%), and Ochrobactrum (0.14%) (Table 2).Nitrospira is one of the most widely distributed and diverse nitrites oxidizing bacteria, and also a key nitrifying bacteria in natural ecosystems (63,64).Ochrobacterium and Staphylococcus can promote the growth of host plants by generating indole-3-acetic acid (IAA) or cooperating with silicate (65,66).Ruminiclostri dium, as a cellulose-degrading bacterium, its cellulose-degrading products can provide a carbon source for the growth of other microorganisms on the one hand (67), and may play an indirect role in activating plant defense on the other hand (68).Haemophilus is usually related to human pathogens, but it has been found that the genus inhabits plants (69).The hub microbes identified by us are relatively low in abundance, but they are widely colonized in various tissues (fruit, leaf, stem, root, and bulk soil) of Camellia oleifera, and may play an important role in nitrogen cycling, host growth promotion, and plant defense.

Conclusion
In general, in this study, highly diversified and structured nichespecific groups were observed in different sample types of Camellia oleifera.The diversity of endophytic bacterial communities in Camellia oleifera is highly dependent on plant compartments, and each compartment represents a unique niche of the bacterial community.Our study not only confirms the niche differentiation of the microbes at the soil-root interface but also demonstrates the finetuning and adaptation of the endophytic microbiota in the stem, leaf, and fruit compartments.In addition, we have identified the hub bacterial microbes of Camellia oleifera.This study provides a relevant model for the systematic study of the changes in microbial community in the organizational level niche of Camellia oleifera plants.These results fill the knowledge gap of the endophytic bacte rial community of Camellia oleifera and provide a theoretical basis for the subsequent exploration of microbial functions and research on bio-fertilizers.S1 and S2 (Spectrum01335-23-S0001.pdf).Sequencing depth, LDA scores, Faprotax function predictions, α-diversity, enrichment effect.

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by 31 .
72%, 35.63%, and 16.60%, respectively.The OTU number of LE was 18.13% and 22.81% higher than FE and SE, respectively.The shared OTU in different plant compart ments of Camellia oleifera is shown in Fig. 4B.FE, LE, SE, RE, and S share 537 OTUs; FE, LE, SE, and RE share 325 OTUs; LE, SE, RE, and S share 91 OTUs; FE, LE, RE, and S share 82 OTUs; LE, SE, and S share 245 OTUs; and SE and S share 77 OTU.For other groups, the number of shared OTUs is less than 30.The number of unique OTUs in the plant compart ment is as follows: S is 205, RE is 4, and LE is 1.

FIG 3
FIG 3 Triangular plots of beta diversity comparisons (using Sørensen dissimilarity index) for bacterial communities among all samples.Each point represents a pair of niches.Its position is determined by a triplet of values from the S (similarity), Repl (replacement), and RichDiff (richness difference) matrices; each triplet sums to 1.The mean values of S, Repl, and RichDiff are shown.

FIG 4
FIG 4 OTU analysis of the bacterial community in different ecological niches of Camellia oleifera.The values represent the mean ± SD (n = 6).Different letters indicate significant differences (P < 0.05) among each compartment.The FE, LE, SE, RE, and S represent the fruit endosphere, leaf endosphere, stem endosphere, root endosphere, and bulk soil, respectively.

FIG 5
FIG 5 Enrichment and depletion for each plant compartment of Camellia oleifera compared with bulk soil controls as determined by differential abundance analysis.Each point represents an individual OTU, and the position along the x-axis represents the abundance fold change compared with bulk soil.The blue dot represents a significant increase in OTU, and the red dot represents a significant decrease.

FIG 6 FIG 7
FIG 6 Top 10 relative abundances of bacterial communities classified at phylum and genus level in different plant compartments of Camellia oleifera.The FE, LE, SE, RE, and S represent the fruit endosphere, leaf endosphere, stem endosphere, root endosphere, and bulk soil, respectively.

FIG 8
FIG 8 Bacterial co-expression network diagram of Camellia oleifera.Each node represents one genus and an edge is drawn between OTUs if they share a Pearson correlation of greater than or equal to 0.6.The size of the node is proportional to the MCODE score and is color marked at the compartments.

TABLE 1
Permutational multivariate ANOVA results with Bray-Curtis distance matrices implemented to determine the composition of the bacterial community in different niches of Camellia oleifera was significantly different a a The FE, LE, SE, RE, and S represent the fruit endosphere, leaf endosphere, stem endosphere, root endosphere, and bulk soil, respectively.

TABLE 2
The network topology properties of hub bacteria