寄主生态位与基因型对豌豆真菌群落多样性及组装过程的影响

doi:10.1016/j.jia.2025.06.018

Journal of Integrative Agriculture ›› 2026, Vol. 25 ›› Issue (2): 529-539.DOI: 10.1016/j.jia.2025.06.018

寄主生态位与基因型对豌豆真菌群落多样性及组装过程的影响

收稿日期:2025-02-20 修回日期:2025-06-10 接受日期:2025-05-12 出版日期:2026-02-20 发布日期:2026-01-06

Effects of host niche and genotype on the diversity and community assembly of the fungal community in peas (Pisum sativum L.)

Yu Wang^{1, 2}, Linying Xu^3#, Liquan Zhang³, Rui Zhang³, Qiong Liu¹, Hongquan Liu⁴, Tao Yang⁵, Haoqing Zhang^{1, 6, 7}, Tida Ge^{1, 6, 7}, Li Wang^{1, 6, 7#}

¹State Key Laboratory for Quality and Safety of Agro-Products/Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs/Zhejiang Key Laboratory of Green Plant Protection, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
²School of Marine Sciences, Ningbo University, Ningbo 315211, China
³Cixi City Agricultural Technology Extension Center, Ningbo 315300, China
⁴College of Horticulture, Hebei Agricultural University, Baoding 071001, China
⁵Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
⁶International Science and Technology Cooperation Base for the Regulation of Soil Biological Functions and One Health of Zhejiang Province, Ningbo University, Ningbo 315211, China
⁷Institute of One Health Science (IOHS), Ningbo University, Ningbo 315211, China

Received:2025-02-20 Revised:2025-06-10 Accepted:2025-05-12 Online:2026-02-20 Published:2026-01-06
About author:Yu Wang, Mobile: +86-19883556249, E-mail: 19883556249@163.com; #Correspondence Li Wang, Mobile: +86-15549062286, E-mail: wangli7@nbu.edu.cn; Linying Xu, Mobile: +86-13858330100, E-mail: 283616641@qq.com
Supported by:
This study was financially supported by the National Key Research and Development Program of China (2023YFD1900902), the Joint Funds of the Zhejiang Provincial Natural Science Foundation of China (LLSSZ24C030001) and the Earmarked Fund for China Agriculture Research System (CARS-08-G-09), and sponsored by the K.C. Wong Magna Fund of Ningbo University, China.

摘要/Abstract

摘要：

真菌在营养吸收、植物生长促进以及增强植物对非生物和生物胁迫的抵御能力等方面扮演起着重要作用。然而，关于豌豆（Pisum sativum L.）相关真菌群落的研究目前仍相对匮乏。在本研究中，我们采用模式识别（β多样性分解）、机制验证（中性群落模型检验）和动态追踪（迁移路径溯源分析）等多尺度研究方法，系统研究了宿主生态位（土壤、根、茎、叶、荚）与基因型对豌豆真菌群落多样性及组成的生态效应。结果表明，不同生态位和基因型地优势门为子囊菌门（Ascomycota）、担子菌门（Basidiomycota）和被孢霉门（Mortierellomycota），且土壤-植物连续体的群落结构主要由豌豆生态位而非基因型决定。β-多样性分解在很大程度上归因于物种替代而非丰富度差异，表明微生境间存在显著的生态位特异性与微生物替代。中性模型分析表明基因型相关群落主要受随机性过程主导，而生态位相关群落主要受确定性过程主导。溯源分析确定了真菌在生态位与生态位之间的迁移，其中白粉菌属（Erysiphe），镰刀菌属（Fusarium），头孢菌属（Cephaliophora），粪盘菌属（Ascobolus），链格孢属（Alternaria）和曲霉属（Aspergillus）是关键属。外生生态位向内生生态位的迁移率较低（1.3-61.5%），而外生生态位间（64.4-83.7%）或内生生态位间（73.9-96.4%）的迁移率更高，表明豌豆表皮在内部定殖之前起到了过滤并富集微生物群落的选择性屏障。本研究为寄主过滤、富集和微生物来源的机制提供了全面的见解，增加了对豌豆相关真菌群落的组装机制的理解。

Abstract:

Fungi play crucial roles in nutrient acquisition, plant growth promotion, and the enhancement of resistance to both abiotic and biotic stresses. However, studies on the fungal communities associated with peas (Pisum sativum L.) remain limited. In this study, we systematically investigated the ecological effects of host niches (soil, root, stem, leaf, and pod) and genotypes on the diversity and composition of fungal communities in peas using a multi-level approach that encompassed pattern recognition (β-diversity decomposition), mechanism validation (neutral community model testing), and dynamic tracking methods (migration pathway source-tracking). The results revealed that the dominant fungal phyla across niches and genotypes were Ascomycota, Basidiomycota, and Mortierellomycota, and the community structures of the soil–plant continuum were primarily determined by the pea niches rather than genotypes. β-diversity decomposition was largely attributed to species replacement rather than richness differences, indicating strong niche specificity and microbial replacement across microhabitats. Neutral model analysis revealed that stochastic processes influenced genotype-associated communities, while deterministic processes played a dominant role in niche-based community assembly. Source-tracking analysis identified niche-to-niche fungal migration, with Erysiphe, Fusarium, Cephaliophora, Ascobolus, Alternaria, and Aspergillus as the key genera. Migration rates from exogenous to endogenous niches were low (1.3–61.5%), whereas those within exogenous (64.4–83.7%) or endogenous (73.9–96.4%) compartments were much higher, suggesting that the pea epidermis acts as a selective barrier that filters and enriches microbial communities prior to internal colonization. This study provides comprehensive insights into the mechanisms of host filtering, enrichment and microbial sourcing, which increases our understanding of the assembly rules of the pea-associated fungal microbiome.

Key words: β-diversity decomposition , fungal community assembly , pea , source-sink relationships , host niche , genotype

Yu Wang, Linying Xu, Liquan Zhang, Rui Zhang, Qiong Liu, Hongquan Liu, Tao Yang, Haoqing Zhang, Tida Ge, Li Wang. 寄主生态位与基因型对豌豆真菌群落多样性及组装过程的影响[J]. Journal of Integrative Agriculture, 2026, 25(2): 529-539.

Yu Wang, Linying Xu, Liquan Zhang, Rui Zhang, Qiong Liu, Hongquan Liu, Tao Yang, Haoqing Zhang, Tida Ge, Li Wang. Effects of host niche and genotype on the diversity and community assembly of the fungal community in peas (Pisum sativum L.)[J]. Journal of Integrative Agriculture, 2026, 25(2): 529-539.

参考文献

Beckers B, Beeck M O D, Weyens N, Boerjan W, Vangronsveld J. 2017. Structural variability and niche differentiation in the rhizosphere and endosphere bacterial microbiome of field-grown poplar trees. Microbiome, 5, 25.

Boakye T A, Li H, Osei R, Boamah S, Min Z, Ni C, Wu J, Shi M, Qiao W. 2022. Antagonistic effect of Trichoderma longibrachiatum (TL6 and TL13) on Fusarium solani and Fusarium avenaceum causing root rot on snow pea plants. Journal of Fungi, 8, 1148.

Calderon R B, D angi S R. 2024. Arbuscular mycorrhizal fungi and rhizobium improve nutrient uptake and microbial diversity relative to dryland site-specific soil conditions. Microorganisms, 12, 667.

Callahan B J, McMurdie P J, Rosen M J, Han A W, Johnson A J A, Holmes S P. 2016. DADA2: High-resolution sample inference from Illumina amplicon data. Nature Methods, 13, 581–583.

Caporaso J G, Kuczynski J, Stombaugh J, Bittinger K, Bushman F D, Costello E K, Fierer N, Peña A G, Goodrich J K, Gordon J I, Huttley G A, Kelley S T, Knights D K, Koenig J E, Ley R E, Lozupone C A, Mcdonald D, Muegge B D, Pirrung M, Reeder J, et al. 2010. QIIME allows analysis of high-throughput community sequencing data. Nature Methods, 7, 335–336.

Chase J M. 2010. Stochastic community assembly causes higher biodiversity in more productive environments. Science, 328, 1388–1391.

Chen X, Krug L, Yang H, Li H, Yang M, Berg G, Cernava T. 2020. Nicotiana tabacum seed endophytic communities share a common core structure and genotype-specific signatures in diverging cultivars. Computational and Structural Biotechnology Journal, 18, 287–295.

Cheng S, Feng C, Chen B, Hofer J, Shi Y, Jiang M, Song B, Cheng H, Lu L, Wang L, Howard A, Bendahmane A, Fouchal A, Moreau C, Sawada C, Lesignor C, Barclay E, Vikeli E, Tsanakas G, Zhao H, et al. 2024. Genomic and genetic insights into Mendel’s pea genes. bioRxiv, 5, 596837.

Cregger M A, Veach A M, Yang Z K, Crouch M J, Vilgalys R, Tuskan G A, Schadt C W. 2018. The Populus holobiont: Dissecting the effects of plant niches and genotype on the microbiome. Microbiome, 6, 31.

Gao M, Xiong C, Gao C, Tsui C K M, Wang M, Zhou X, Zhang A M, Cai L. 2021. Disease-induced changes in plant microbiome assembly and functional adaptation. Microbiome, 9, 187.

Goldford J E, Lu N, Bajić D, Estrela S, Tikhonov M, Sanchez-Gorostiaga A S, Segrè D, Mehta P, Sanchez A. 2018. Emergent simplicity in microbial community assembly. Science, 361, 469–474.

Guo B, Zhang H, Liu Y, Chen J, Li J. 2024. Assembly of cereal crop fungal communities under water stress determined by host niche. Environmental and Experimental Botany, 219, 105650.

Guo Q, Wen Z, Ghanizadeh H, Fan Y, Zheng C, Yang X, Yan X, Li W. 2023. Stochastic processes dominate assembly of soil fungal community in grazing excluded grasslands in northwestern China. Journal of Soils and Sediments, 23, 156–171.

Hao J, Liu Q, Song F, Cui X, Liu L, Fu L, Zhang S, Wu X, Zhang X. 2024. Community diversity of endophytic bacteria in the leaves and roots of pea seedlings. Agronomy, 14, 2030.

Jiya N, Shede P, Sharma A. 2023. Diversity and composition of fungal communities across diverse environmental niches in Antarctica. Polar Science, 38, 100973.

Katoh K, Misawa K, Kuma K, Miyata T. 2002. MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research, 30, 3059–3066.

Lahlali R, Taoussi M, Laasli S E, Gachara G, Ezzouggari R, Belabess Z, Aberkani K, Assouguem A, Meddich A, Jarroudi M E, Barka E A. 2024. Effects of climate change on plant pathogens and host-pathogen interactions. Crop and Environment, 3, 159–170.

Li S, Ren K, Yan X, Tsyganov A N, Mazei Y, Smirnov A, Mazei N, Zhang Y, Rensing C, Yang J. 2023. Linking biodiversity and ecological function through extensive microeukaryotic movement across different habitats in six urban parks. iMeta, 2, e103.

Lv X, Wang Q, Zhang X, Hao J, Li L, Chen W, Li H, Wang Y, Ma C, Wang J, Liu Q. 2021. Community structure and associated networks of endophytic bacteria in pea roots throughout plant life cycle. Plant and Soil, 468, 225–238.

Manici L M, Caputo F, De Sabata D D, Fornasier F. 2024. The enzyme patterns of ascomycota and basidiomycota fungi reveal their different functions in soil. Applied Soil Ecology, 196, 105323.

Nguyen N H, Song Z, Bates S T, Branco S, Tedersoo L, Menke J, Schilling J S, Kennedy P G. 2016. FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild. Fungal Ecology, 20, 241–248.

Ozimek E, Hanak a A. 2021. Mortierella species as the plant growth-promoting fungi present in the agricultural soils. Agriculture, 11, 7.

Pappas M L, Liapoura M, Papantoniou D, Avramidou M, Kavroulakis N, Weinhold A, Broufas G D, Papadopoulou K K, 2018. The beneficial endophytic fungus Fusarium solani strain K alters tomato responses against spider mites to the benefit of the plant. Frontiers in Plant Science, 9, 1603.

Pii Y, Mimmo T, Tomasi N, Terzano R, Cesco S, Crecchio C. 2015. Microbial interactions in the rhizosphere: Beneficial influences of plant growth-promoting rhizobacteria on nutrient acquisition process. A review. Biology and Fertility of Soils, 51, 403–415.

Piñeiro C, Abuín J M, Pichel J C. 2020. Very Fast Tree: Speeding up the estimation of phylogenies for large alignments through parallelization and vectorization strategies. Bioinformatics, 36, 4658–4659.

Qian X, Li H, Wang Y, Wu B, Wu M, Chen L, Li X, Zhang Y, Wang X, Shi M, Zheng Y, Guo L, Zhang D. 2019. Leaf and root endospheres harbor lower fungal diversity and less complex fungal co-occurrence patterns than rhizosphere. Frontiers in Microbiology, 10, 1015.

Remus-Emsermann M N P, Schlechter R O. 2018. Phyllosphere microbiology: At the interface between microbial individuals and the plant host. New Phytologist, 218, 1327–1333.

Schmidt R, Mitchell J, Scow K. 2019. Cover cropping and no-till increase diversity and symbiotroph: Saprotroph ratios of soil fungal communities. Soil Biology and Biochemistry, 129, 99–109.

Shen C, Gunina A, Luo Y, Wang J, He J, Kuzyakov Y, Hemp A, Classen A T, Ge Y. 2020. Contrasting patterns and drivers of soil bacterial and fungal diversity across a mountain gradient. Environmental Microbiology, 22, 3287–3301.

Shenhav L, Thompson M, Joseph T A, Briscoe L, Furman O, David B, Mizrahi I, Pe’er I, Halperin E. 2019. FEAST: Fast exp ectation-maximization for microbial source tracking. Nature Methods, 16, 627–632.

Silva R N, Monteiro V N, Steindorff A S, Gomes E V, Noronha E F, Ulhoa C J. 2019. Trichoderma/pathogen/plant interaction in pre-harvest food security. Fungal Biology, 123, 565–583.

Sloan W T, Lunn M, Woodcock S, Head I M, Nee S, Curtis T P. 2006. Quantifying the roles of immigration and chance in shaping prokaryote community structure. Environmental Microbiology, 8, 732–740.

Wan W, Gadd G M, Gu J, Liu W, Chen P, Zhang Q, Yang Y. 2023. Beyond biogeographic patterns: Processes shaping the microbial landscape in soils and sediments along the Yangtze River. mLife, 2, 89–100.

Xiong C, He J, Singh B K, Zhu Y, Wang J, Li P, Zhang Q, Han L, Shen J, Ge A, Wu C, Zhang L. 2020. Rare taxa maintain the stability of crop mycobiomes and ecosystem functions. Environmental Microbiology, 23, 1907–1924.

Xiong C, Zhu Y, Wang J, Singh B, Han L, Shen J, Li P, Wang G, Wu C, Ge A, Zhang L, He J. 2021. Host selection shapes crop microbiome assembly and network complexity. New Phytologist, 229, 1091–1104.

Yang H, Ye W, Yu Z, Shen W, Li S, Wang X, Chen J, Wang Y, Zheng X. 2023. Host niche, genotype, and field location shape the diversity and composition of the soybean microbiome. Journal of Integrative Agriculture, 22, 2412–2425.

Yang T, Liu R, Luo Y, Hu S, Wang D, Wang C, Pandey M K, Ge S, Xu Q, Li N, Li G, Huang Y, Saxena R K, Ji Y, Li M, Yan X, He Y, Liu Y, Wang X, Xiong C, et al. 2022. Improved pea reference genome and pan-genome highlight genomic features and evolutionary characteristics. Nature Genetics, 54, 1553–1563.

Zhang H, Wu C, Wang F, Wang H, Chen G, Cheng Y, Chen J, Yang J, Ge T. 2022. Wheat yellow mosaic enhances bacterial deterministic processes in a plant–soil system. Science of the Total Environment, 812, 151430.

Zhang L, Zhang M, Huang S, Huang S, Li L, Gao Q, Wang Y, Zhang S, Huang S, Yuan L, Wen Y, Liu K, Yu X, Li D, Zhang L, Xu X, Wei H, He P, Zhou W, Philippot L, Ai C. 2022. A highly conserved core bacterial microbiota with nitrogen-fixation capacity inhabits the xylem sap in maize plants. Nature Communications, 13, 3361.

Zhang Z, Zhang J, Jiao S. 2021. Fungi show broader environmental thresholds in wet than dry agricultural soils with distinct biogeographic patterns. Science of the Total Environment, 750, 141761.

Zhao M, Loreau M, Ochoa-Hueso R, Zhang H, Yang J, Zhang Y, Liu H, Jiang Y, Han X. 2024. Decoupled responses of above- and below-ground beta-diversity to nitrogen enrichment in a typical steppe. Ecology Letters, 27, e14339.

Zhou X R, Dai L, Xu G F, Wang H S. 2021. A strain of Phoma species improves drought tolerance of Pinus tabulaeformis. Scientific Reports, 11, 7637.

Zinger L, Taberlet P, Schimann H, Bonin A, Boyer F, Barba M D, Gaucher P, Gielly L, Giguet-Covex C, Iribar A, Réjou-Méchain M, Rayé G, Rioux D, Schilling V, Tymen B, Viers J, Zouiten C, Thuiller W, Coissac E, Chave J. 2019. Body size determines soil community assembly in a tropical forest. Molecular Ecology, 28, 528–543.

Zhu T, Zhang L, Yan Z, Liu B, Li Y, You X, Chen Mo, Liu T, Xu Y, Zhang J. 2023. Niche-dependent microbial assembly in salt-tolerant tall fescue and its contribution to plant biomass. Industrial Crops and Products, 206, 117736.

Zwirzitz B, Wetzels S U, Dixon E D, Stessl B, Zaiser A, Rabanser I, Thalguter S, Pinior B, Roch F, Strachan C, Zanghellini J, Dzieciol M, Wagner M, Selberherr E. 2020. The sources and transmission routes of microbial populations throughout a meat processing facility. NPJ Biofilms and Microbiomes, 6, 26.

寄主生态位与基因型对豌豆真菌群落多样性及组装过程的影响

Effects of host niche and genotype on the diversity and community assembly of the fungal community in peas (Pisum sativum L.)

PDF

可视化

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 0

编辑推荐

Metrics