Characteristics and Assembly Mechanisms of Rhizosphere and Root Endosphere Microbial Communities in Davidia involucrata of Different Ages

doi:10.13560/j.cnki.biotech.bull.1985.2025-0823

Abstract

Abstract:

Objective To elucidate the dynamic changes in composition, metabolic functions, and assembly mechanisms of rhizosphere and root endosphere microbial communities associated with Davidia involucrata across distinct ontogenetic stages. Method Utilizing 16S rRNA gene and ITS amplicon sequencing, we characterized the composition, diversity, functional profiles, assembly mechanisms, and associations with soil physicochemical properties of rhizosphere and root endosphere microbial communities in D. involucrata stratified by age: near-mature forest (tree age <50 years), mature forest (tree age=50–100 years), and ancient forest (tree age >100 years). Result No significant age-dependent differences were detected in microbial alpha diversity within either the rhizosphere or root endosphere. However, bacterial beta diversity presented significant compartmentalization. LEfSe analysis identified several biomarker taxa, including Gemmatimonadota, Verrucomicrobiota, Clavulinopsis, Gliophorus, Atractospora, etc. Although microbial community composition showed variations across age groups, Proteobacteria and Actinobacteriota consistently dominated the bacterial phyla, while Ascomycota and Basidiomycota prevailed among fungi. Core bacterial functional potential was centered on metabolism and genetic information processing, whereas fungal communities were predominantly saprotrophic. Secondary functional analysis revealed significant age-related differences in rhizosphere bacteria for xenobiotic metabolism and lipid metabolism, while root endosphere bacteria differed significantly only in glycan biosynthesis and metabolism. Rhizosphere fungal functional guilds exhibited significant variation, particularly for plant pathogens and leaf saprotrophs, whereas root endosphere fungi showed no significant functional shifts. Mantel tests indicated no overarching correlation between the total microbial community and soil physicochemical factors, although dominant phyla including Acidobacteriota and Chloroflexi demonstrated significant associations. Partial Least Squares Path Modeling (PLS-PM) indicated tree age exerted a stronger influence on root endosphere microbial diversity than on rhizosphere diversity. Community assembly analysis demonstrated that stochastic processes governed rhizosphere bacterial assembly, whereas deterministic processes dominated the assembly of both rhizosphere and root endosphere fungal communities. Conclusion Tree age exerts a discernible influence on the microbial communities and their functions within the rhizosphere and root endosphere of D. involucrata. Furthermore, the mechanisms governing microbial community assembly present dynamic shifts with tree age.

Key words: Davidia involucrata, rhizosphere, root endosphere, community structure, functional prediction, community assembly

WANG Yu, WANG Yi-min, GAO Han, CHEN Bang-qing, PENG Gang-zhi, TAN Yan, ZHENG Si-yi, GAO Ben-wang. Characteristics and Assembly Mechanisms of Rhizosphere and Root Endosphere Microbial Communities in Davidia involucrata of Different Ages[J]. Biotechnology Bulletin, 2026, 42(5): 158-173.

Figures/Tables 15

Table 1 Physical and chemical properties of soil in Davidia involucrata

样本 Sample	酸碱度 pH	有机碳 SOC （g/kg）	总氮 TN （g/kg）	有效磷 AP （mg/kg）	速效钾 AK （mg/kg）
A	6.09±0.31a	82.16±7.59b	4.56±0.62b	7.50±0.38c	244.66±29.09a
B	5.97±0.22a	165.64±58.77a	5.72±0.94a	12.52±1.40a	264.46±22.32a
C	5.75±0.30a	158.22±70.75a	6.02±0.76a	9.10±0.81b	248.25±35.25a

Fig. 1 Rarefaction curves of microbial communities of D. involucrataA: Rhizosphere bacteria. B: Root endosphere bacteria. C: Rhizosphere fungi. D: Root endosphere fungi. AS: Rhizosphere soil of near-mature forest. BS: Rhizosphere soil of mature forest. CS: Rhizosphere soil of old ancient forest. AR: Root tissue of near-mature forest. BR: Root tissue of mature forest. CR: Root tissue of ancient forest. The same below

Fig. 2 Venn diagram of ASVs in microbial communities in the rhizosphere and root endosphere of D. involucrataA: Rhizosphere bacteria. B: Root endosphere bacteria. C: Rhizosphere fungi. D: Root endosphere fungi

Fig. 3 Alpha-diversity indices of microbial communities in the rhizosphere and root endosphere of D. involucrata

Fig. 4 Beta-diversity indices of microbial communities in the rhizosphere and root endosphere of D. involucrataA: Rhizosphere bacteria. B: Root endosphere bacteria. C: Rhizosphere fungi. D: Root endosphere fungi

Fig. 5 Relative abundance of bacteria in the rhizosphere and root endosphere of Davidia involucrateA: Rhizosphere bacteria at phylum level. B: Root endosphere bacteria at phylum level. C: Rhizosphere bacteria at genus level. D: Root endosphere bacteria at genus level

Fig. 6 Relative abundance of fungi in the rhizosphere and root endosphere of D. involucrateA: Rhizosphere fungi at phylum level. B: Root endosphere fungi at phylum level. C: Rhizosphere fungi at genus level. D: Root endosphere fungi at genus level

Fig. 7 LEfSe analysis of differential species among different tree ages of D. involucrataA: Rhizosphere bacteria. B: Root endosphere bacteria. C: Rhizosphere fungi. D: Root endosphere fungi

Fig. 8 Functional prediction of bacteria in the rhizosphere and root endosphere of D. involucrataA: L1 functions of rhizosphere bacteria. B: L2 functions of rhizosphere bacteria. C: L1 functions of root endosphere bacteria. D: L2 functions of root endosphere bacteria

Fig. 9 Functional prediction of fungi in the rhizosphere and root endosphere of D. involucrataA: Rhizosphere fungi classified based on Trophic mode; B: Rhizosphere fungi classified based on Guild; C: Root endosphere fungi classified based on Trophic mode; D: Root endosphere fungi classified based on Guild

Fig. 10 Correlation between physicochemical factors and microbial communities in the rhizosphere and root endosphere of D.involucrataA: Bacteria. B: Fungi. *P<0.05; **P<0.01; ***P<0.001, the same below

Fig. 11 Correlation of dominant bacterial phyla with soil physicochemical factors in rhizosphere and root endosphere communities of D. involucrataA: Rhizosphere bacteria. B: Root endosphere bacteria. C: Rhizosphere fungi. D: Root endosphere fungi

Fig. 12 Direct and indirect effects of soil factors on diversity of microbial communities in rhizosphere and root endosphere of D. involucrata

Fig. 13 Assembly processes of microbial communities in the rhizosphere and root endosphere of D. involucrata (based on neutral community model)A: Rhizosphere bacteria. B: Root endosphere bacteria. C: Rhizosphere fungi. D: Root endosphere fungi

Fig. 14 Analysis of modified stochasticity ratio for microbial communities in the rhizosphere and root endosphere of D. involucrataA: Rhizosphere bacteria. B: Root endosphere bacteria. C: Rhizosphere fungi. D: Root endosphere fungi

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