Sex Effects on Rhizosphere Assembly in Dioecious Woody Plants Are Ontogenetically Reversible and Still Correlative

Question: How do sex-specific root exudate profiles in dioecious woody plants shape rhizosphere bacterial and fungal community assembly across plant developmental stages?

Answer

Taken together, the retrieved papers support a narrow but specific position: sex-specific root exudation in dioecious woody plants is chemically real and stage-dependent, and the bacterial and fungal differences that track it reverse direction between juvenile and adult plants, so host sex behaves as an ontogenetically contingent filter rather than a fixed microbiome phenotype. The strong form of that claim rests on a single species, Taxus cuspidata, the only retrieved study that resolves sex, exudate chemistry and both bacterial and fungal rhizosphere communities simultaneously across developmental stages [2]. The surrounding assembly literature supplies the boundary conditions: host chemistry and microbial colonization are mutually modifying rather than unidirectional [21] [19], host genetic filtering operates inside inoculum- and environment-imposed ceilings [7] [15], and bacterial and fungal communities can respond to the same host perturbation with very different sensitivity [5] [10]. Across these papers, sex-specific exudates should be treated as a modulator of assembly within a developmental window, not as a determinant that any retrieved dataset has yet isolated from soil history.

Sex-specific exudate chemistry is real, and the compounds differ qualitatively between juvenile and adult plants

In adult Taxus cuspidata, female plants enriched 2-mercaptoethanesulfonic acid and α-keto-γ-methylthiobutyric acid, whereas males secreted more terpenoids such as α-humulene and the purine intermediate xanthine [2]. In the juvenile stage, females instead showed higher phosphoenolpyruvate and L-valine, while males enriched 5-methylcytosine and tricyclic sesquiterpenoid antibiotics [2]. The metabolite identities reported for the two stages do not overlap, which indicates stage-specific exudate chemistry rather than a constitutively sex-fixed exudate signature [2]. This is not simply an artifact of plant size: root exudate composition and community assembly both shift measurably over short developmental windows, as shown by fine-scale sampling through the first four weeks of tomato development [15].

The direction of the sex effect on microbial diversity reverses between stages

In adult T. cuspidata, bacterial (Proteobacteria) and fungal (Mortierellomycota) abundance and diversity were higher in female than male rhizospheres, while males were enriched in Actinobacteria [2]. In juveniles the pattern inverted: male plants supported greater rhizosphere bacterial and fungal diversity than females, with enrichment of stress-tolerant and decomposing taxa such as Humicola [2]. Stage-gating of this kind is independently documented in host-filtering studies: bacterial communities of Pisum accessions varied in diversity, composition and structure across microhabitats and three growth stages under strong host filtering [16], and early tomato rhizosphere succession involved progressive increases in load, richness, evenness and phylogenetic diversity with a shift from copiotrophic Proteobacteria to Actinobacteria and Acidobacteria [15]. Fungal partners are likewise phenologically partitioned, with edaphophilic nutrient-foraging taxa dominating early and rhizophilic taxa dominating later in the season [11]. Developmental stage is therefore a state variable, not a nuisance covariate, in any sex comparison.

Bacteria and fungi do not track the same host signal with equal fidelity, and alpha diversity is a weak test

Viral infection restructured bacterial root communities and reduced their diversity while fungal communities remained largely stable [5]. In a 48-soil field meta-analysis, fungal communities were more responsive than bacteria to changes in Striga infestation and seedbank level [10]. In avocado rhizosphere under Phytophthora cinnamomi, alpha diversity metrics did not differ significantly between asymptomatic and symptomatic trees, yet beta diversity did, and symptomatic-tree fungal networks were more complex and more connected [3]. Two consequences follow for dioecious systems: the kingdom that carries the sex signal may differ among host species, and reported sex reversals based on alpha diversity alone [2] may understate compositional divergence that beta diversity or network topology would expose [3].

Inoculum, environment and priority effects set ceilings that a sex effect must fit inside

Across seven location-year barley trials, 73% of bacterial and 80% of fungal genera were associated with location-year effects, and a reciprocal transplant attributed 20.7% of community variation to soil and 18.2% to inoculum source [7]. Early rhizosphere assembly trajectories in tomato remained strongly constrained by the initial inoculum, and increasing inoculum complexity drove convergence toward a common compositional centroid in which two Pseudomonas ASVs accounted for 50% of abundance [18]. Seed-applied SynComs colonized only transiently yet imposed priority effects that persisted in community composition into the next seed generation [14]. Host specialization itself is partial rather than wholesale: across six Ericaceae and ectomycorrhizal taxa in fumarole fields, prokaryotic and fungal OTUs rarely showed strong preferences for both habitat and host identity, instead specializing to one niche [1]. A sex-exudate effect should therefore be expected as taxon-specific partial specialization, not as global community divergence.

The causal arrow between exudates and the microbiome runs both ways, and the Taxus design cannot orient it

Inoculating Agrobacterium fabrum onto Medicago truncatula roots modulated root phenolic and flavonoid content, with nearly all A. fabrum-specific genomic regions influencing one or more specialized root metabolites [21]. In an Arabidopsis system permitting simultaneous exudate and community monitoring, colonization by initially dominant Pseudomonas produced a transient increase in glucosinolate exudation [19]. Microbial activity, not abundance, predicted successful root colonization [17]. Because a field-grown female and male tree also differ in the community already assembled around them, an exudate difference measured alongside a community difference is as plausibly a consequence as a cause [21].

Conflicts and gaps

The core empirical claim is unreplicated: only one retrieved study resolves sex, exudates and both microbial kingdoms across stages in a dioecious woody plant [2], so the stage reversal cannot be distinguished from a Taxus-specific or even site-specific result. The Taxus system is also genetically ambiguous — in the congener T. baccata, haplotype-resolved assemblies and resequencing of 100 sexed individuals detected no sex-determining region, raising the possibility of non-genetic sex determination [12] — so sex assignment in T. cuspidata may reflect phenotype rather than a fixed genotype, and "sex-specific" exudates may partly track condition. The two kingdoms' relative sensitivity is genuinely contested, with bacteria more responsive in one system [5] and fungi in another [10]. No retrieved paper partitions variance among sex, stage and soil for any dioecious plant, although the design exists for crop genotypes [7]. Method choice can also generate or erase apparent differences: sampling approach imposed a protocol-specific footprint on rhizosphere bacterial and fungal composition while recovering only ~75% of enriched taxa in common [9], clay-particle systems impeded exudate recovery outright [19], and exudate–microbe links vary at microhabitat scale along a single root system [4].

What would change the answer

A factorial common-garden experiment — sexed individuals of one dioecious tree at juvenile and reproductive adult stages, grown in a common soil with sterile and live-inoculum controls, analysed by variance partitioning [7] — would establish whether sex adds explanatory power beyond soil and stage. Compound-specific addition bioassays using the metabolites already identified as sex-diagnostic (α-humulene, xanthine, L-valine, 2-mercaptoethanesulfonic acid) [2] into standardized soil and synthetic communities, with 16S/ITS and network readouts, would convert correlation into recruitment evidence; reconstruction of disease-suppressive SynComs from dilution-to-extinction metagenomics demonstrates that this causal standard is achievable [20]. Isotope tracing of exudate carbon into taxon-resolved DNA, as implemented with 13C-exudate qSIP in rhizosphere communities [8], would identify which bacteria and fungi actually assimilate sex-specific substrates. Spatial mapping along male and female root systems using RhizoGrid-style hardware would test whether sex effects are root-zone heterogeneities averaged away by bulk sampling [4]. Finally, replicating the design in species with characterized sex-determining regions — the dioecious tree Eurycorymbus cavaleriei [13] or the XY cycad Cycas revoluta [6] — would remove the genotype ambiguity that currently limits interpretation of Taxus [12].

References

[1] Murata, A., Noguchi, M., Hayashi, I., Fukushima, K., Toju, H.. "Environmental filtering and host identity collectively shape root-associated microbiomes of Ericaceae and ectomycorrhizal plants in fumarole fields". bioRxiv. 2026-09-26T00:00:00.000Z. URL: https://doi.org/10.64898/2026.09.25.754363

[2] Wu, g. a., Zhang, Y.. "Sex specificity of root exudates and their effects on rhizosphere microorganisms in a rare and endangered plants, Taxus cuspidata". bioRxiv. 2026-10-19T00:00:00.000Z. URL: https://doi.org/10.64898/2026.10.14.759288

[3] Alfaro-Garcia, R. G., Cisneros-Martinez, A. M., Patino-Conde, V., Rebollar, E. A., Guerrero-Analco, J. A., Mendez-Bravo, A., Reverchon, F.. "Root rot by Phytophthora cinnamomi shifts the composition and structure of avocado rhizosphere fungal communities". bioRxiv. 2026-07-11T00:00:00.000Z. URL: https://doi.org/10.64898/2026.07.10.737851

[4] Handakumbura, P. P., Rivas Ubach, A., Battu, A., Anthony, W. E., Schultz, K., McClure, R., Varga, T., Jansson, C., Egbert, R.. "RhizoGrid: Illuminating Spatial Rhizosphere Dynamics". bioRxiv. 2025-12-13T00:00:00.000Z. URL: https://doi.org/10.64898/2025.12.10.693536

[5] Cobos, A., Barrado, M. R., Udaondo, Z., Gonzalo, I., Castrillo, G., Valli, A. A.. "Turnip mosaic virus drives selective filtering and community reassembly in the Arabidopsis thaliana root microbiome in a genotype-specific manner". bioRxiv. 2026-03-02T00:00:00.000Z. URL: https://doi.org/10.64898/2025.12.11.693707

[6] Sato, M. P., Aoyagi, Y. B., Yoshitake, K., Toyama, Y., Iimura, H., Matsuoka, F., Toyoda, A., Akagi, T., Okuda, S., Ito-Inaba, Y., Shirasawa, K.. "Chromosome-scale genome assembly of Cycas revoluta provides insights into cycad diversification and species diversity". bioRxiv. 2026-07-17T00:00:00.000Z. URL: https://doi.org/10.64898/2026.07.11.737888

[7] Killian, E., Williams, J., Halpin-McCormick, A., Ewing, P., Kantar, M. B., Lachowiec, J., Sherman, J., Eberly, J.. "Environment and plant genetics shape barley rhizosphere microbiome structure across contrasting locations". bioRxiv. 2026-07-21T00:00:00.000Z. URL: https://doi.org/10.64898/2026.07.20.739634

[8] Schaefer, S. R., Blazewicz, S. J., Holland-Moritz, H., Hicks Pries, C., Allen, G. M., Pett-Ridge, J., Lopez, F. M., Grandy, A. S., Wieder, W., Ernakovich, J.. "Shrub and Sedge Rhizosphere Communities Display Distinct Affinities Toward Exudates and Soil Organic Matter Degradation: a Quantitative Stable Isotope Probing Analysis". bioRxiv. 2025-12-02T00:00:00.000Z. URL: https://doi.org/10.64898/2025.12.02.691861

[9] Escudero-Martinez, C., Browne, E. Y., Schwalm, H., Santangeli, M., Brown, M., Brown, L., Roberts, D. M., Duff, A. M., Morris, J., Hedley, P. E., Thorpe, P., Abbott, J. C., Brennan, F., Bulgarelli, D., George, T. S., Oburger, E.. "Evaluation of combined root exudate and rhizosphere microbiota sampling approaches to elucidate plant-soil-microbe interaction". bioRxiv. 2025-10-24T00:00:00.000Z. URL: https://doi.org/10.1101/2025.10.23.683011

[10] Taylor, T., Benti, G., Fernandes Alves Leite, M., Etalo, D., Lombard, L., AriasGiraldo, L.-M., Ryba, D., Sanow, S., Mostert, T., Martinez de la Parte, E., Macia-Vicente, J., Yimer, D., Tsega, U., Daska, J., van Doorn, R., Rosa Leite, R., Tessema, T., Crous, P. W., Kawa, D., Kuramae, E., Raajimakers, J., Brady, S.. "Disentangling the importance of microbiological and physicochemical properties of Ethiopian field soils for the Striga seed bank and sorghum infestations". bioRxiv. 2025-10-06T00:00:00.000Z. URL: https://doi.org/10.1101/2025.10.03.680328

[11] Shulman, H. B., Classen, A. T., Breckheimer, I., Dong, W., Falb, P., Henderson, A., Inouye, D. W., Sorensen, P. O., Shin, E. J., Vought, O. K., Kivlin, S. N.. "Warming winter disrupts mycorrhizal phenology and plant-fungal nutrient cycling.". bioRxiv. 2025-12-12T00:00:00.000Z. URL: https://doi.org/10.64898/2025.12.11.693722

[12] Bross, D., Lazic, D., Mader, M., Mittelbach, J., Pippel, M., Kurtz, S., Pers-Kamczyc, E., Raghavan, V., Schroeder, H., Uelze, L., Winkler, S., Mueller, N. A., Kersten, B.. "Haplotype-resolved genome assemblies and population resequencing reveal no evidence for genetic sex determination in the dioecious conifer Taxus baccata". bioRxiv. 2026-10-16T00:00:00.000Z. URL: https://doi.org/10.64898/2026.02.27.708407

[13] Mai, Y., Zheng, J., Sun, W., Qin, Z., Chen, C., Wei, W., Song, C., Liu, X., Su, X., Wu, F., Wu, Q., Yao, B., Hao, Y., Liu, Y., Zeng, Z., Xu, J., Charlesworth, D., Xia, R.. "A trade-off mechanism underpins the evolution of a young two-gene sex-determining system in plants". bioRxiv. 2025-07-27T00:00:00.000Z. URL: https://doi.org/10.1101/2025.07.26.666942

[14] Arnault, G., Colaert-Sentenac, L., Marais, C., Sarniguet, A., Barret, M., Simonin, M.. "Synthetic Community Inoculation on Seeds Revealed its Transient Colonization Capacity but Legacy Effects on Plant Microbiota Assembly". bioRxiv. 2025-03-31T00:00:00.000Z. URL: https://doi.org/10.1101/2025.03.28.645722

[15] Chaboy-Cansado, R., Cobeta, P., Roscales, G., Rastrojo, A., Aguirre de Carcer, D.. "Early rhizosphere assembly during the onset of photosynthesis reveals inoculum-constrained succession with increased phylogenetic clustering, filtering and diversity". bioRxiv. 2026-06-26T00:00:00.000Z. URL: https://doi.org/10.64898/2026.06.25.734670

[16] Angot, V., Pailler, V., Kebieche, A., Belmonte, E., Bourion, V., Bouchenak-Khelladi, Y.. "Ecophylogenetic patterns of rhizosphere bacterial community assembly in Pisum spp. (Fabaceae, Fabeae) reveal strong plant-mediated ecological filtering". bioRxiv. 2026-02-24T00:00:00.000Z. URL: https://doi.org/10.1101/2025.09.30.679227

[17] Harris, J. E., Bledsoe, R. B., Guha, S., Omari, H., Crandall, S. G., Burghardt, L. T., Couradeau, E. M.. "The activity of soil microbial taxa in the rhizosphere predicts the success of root colonization". bioRxiv. 2024-12-08T00:00:00.000Z. URL: https://doi.org/10.1101/2024.12.07.627353

[18] Chaboy-Cansado, R., Cobeta, P., Roscales, G., Rastrojo, A., Aguirre de Carcer, D.. "Combinatorial community coalescence in early tomato assembly reveals a rhizosphere attractor in composition and abundance architecture". bioRxiv. 2026-07-15T00:00:00.000Z. URL: https://doi.org/10.64898/2026.07.05.736546

[19] Joller, C., Waelchli, J., Schlaepfer, J., Schlaeppi, K.. "Paralleled Dynamics of Arabidopsis Root Exudation and SynCom Assembly in a Controlled Environment". bioRxiv. 2026-01-30T00:00:00.000Z. URL: https://doi.org/10.64898/2026.01.29.702624

[20] Jing, J., Ossowicki, A., Tracanna, V., Schijlen, E., Baak, M. L., Pirovano, W., van IJcken, W., Rybka, D., Gerards, S., Elsayed, S. S., Reitz, Z. L., van Wezel, G., Raaijmakers, J. M., Garbeva, P., Medema, M. H.. "Reconstructing plant beneficial bacterial consortia by integrating dilution-to-extinction microbiome perturbation with genome-resolved synthetic ecology". bioRxiv. 2026-04-10T00:00:00.000Z. URL: https://doi.org/10.64898/2026.04.09.717421

[21] Padilla, R., Vial, L., Dechevre, F., Nguyen, T. H. T., Gaillard, V., Meiffren, G., Comte, G., Nesme, X., Lavire, C., Kerzaon, I.. "Phenolic compounds in Medicago truncatula roots are under the influence of Agrobacterium fabrum through its species specific-genes regions". bioRxiv. 2024-12-27T00:00:00.000Z. URL: https://doi.org/10.1101/2024.12.27.630484

How this survey was made

This survey answers one question: “How do sex-specific root exudate profiles in dioecious woody plants shape rhizosphere bacterial and fungal community assembly across plant developmental stages?”

We keep our own collection of recent preprints and refresh it every day from bioRxiv, medRxiv, arXiv, PsyArXiv, SocArXiv and ChemRxiv. For each survey, we search that collection for recent work and keep the strongest matches: papers that use the same terms as the question, and papers on the same topic in different words.

The text was written from the titles and abstracts of those papers; the full texts were not read. Statements that draw on a particular paper are marked with a number in brackets. The reference list just above is the 21 papers whose work this text draws on, chosen from the 132 papers those searches returned; the rest of the shortlist is not printed. It is not a complete review of everything published on the question.

Treat this as a starting point and a reading list, not a peer-reviewed review. The searches behind this survey ran on October 22, 2026 and covered work from the previous two years.