Leaf samples were collected in spring 2018 from a riparian floodplain forest in central Moravia, Czechia, where Ericales plants were absent. The analyzed trees were Alnus glutinosa, Carpinus betulus, Corylus avellana, Quercus petraea and Q. robur. The investigators also mined the GlobalFungi database for published environmental sequences to assess the occurrence of Exobasidium beyond known host plants.

After filtering, the researchers identified 75 Exobasidium amplicon sequence variants from leaves and insect guts, which clustered into 12 phylotypes. Seven grouped with described species that had publicly available DNA barcodes, including E. arescens, E. bisporum, E. camelliae, E. euryae, E. gracile, E. maculosum and E. miyabei. The other five had less than 94% similarity to sequenced species in the National Center for Biotechnology Information database, indicating possible undescribed or as-yet-unsequenced diversity.

This interpretation remains uncertain because many named Exobasidium species still lack public molecular data. Exobasidium communities differed significantly among host tree species in an analysis of similarity based on Jaccard and Morisita-Horn indices with 9,999 permutations. Quercus petraea had the highest measured alpha diversity, with a mean Shannon index of 0.50 and a mean Simpson index of 0.39, while Q. robur had the lowest values, at 0.32 and 0.17, respectively.

Principal component analysis also separated several tree-associated communities. Phylotype 9 accounted for more than 66% of Exobasidium reads on A. glutinosa and 62% on Q. robur, occurred in more than 30% of leaf samples from every analyzed tree and also dominated several caterpillar-gut communities. Overall, the gut datasets did not differ significantly from one another, and their phylotype proportions broadly reflected those in the corresponding tree phyllospheres.

Phylotype 9 was recovered in pure culture from two Tischeria ekebladella caterpillars and from healthy Tilia cordata leaves collected in Slovakia. All three isolates were genetically identical. Phylogenetic analysis placed them as a sister lineage to E. woronichinii and E. rhododendri.

The isolates differed from E. woronichinii by 3.9% of nucleotides in the ITS region and 1.8% in the LSU region, supporting their recognition as Exobasidium phylloplanum. Its name refers to the phylloplane, the leaf surface. The species produces filamentous colonies with fusiform blastoconidia measuring 8.2 ± 3.0 micrometres long and 1.8 ± 0.2 micrometres wide.

Physiological tests found growth from 6 to 25 °C, with optimal growth between 20 and 25 °C. Salinity of 16% or higher prevented growth. The isolates used all 16 tested carbon sources and grew on glucose without fermenting it.

In the GlobalFungi analysis, 17 of 40 examined Exobasidium species or phylotypes appeared in at least one environmental sample. E. phylloplanum was the most frequently detected lineage, occurring in 841 samples from 52 studies, mainly in European forests and in samples from plant shoots and soil. Its records were concentrated in temperate regions, with an absence in the otherwise well-surveyed boreal and Mediterranean areas.

Known parasites E. arescens, E. vaccinii and E. camelliae were also detected in environmental records, while some environmental phylotypes in the E. bisporum and E. miyabei clades occurred more frequently than the available reference sequences. The researchers could not establish that these environmental phylotypes represented the corresponding parasitic species in the sampled regions. They instead proposed that Exobasidium includes a continuum of life histories, ranging from predominantly parasitic species with short saprotrophic phases to lineages with longer environmental phases and possibly predominantly saprotrophic species.

The genome of E. phylloplanum strain CCF 7021 was assembled into five nuclear scaffolds totaling 17.7 megabases. The assembly had an N50 of 5.8 megabases, 95.5% BUSCO completeness and 7,463 annotated proteins. Comparative analyses found broadly similar numbers of carbohydrate-active enzyme genes and genes associated with pathogen–host interactions among E. phylloplanum and other Exobasidium species.

E. phylloplanum was distinguished by an expanded set of type I polyketide synthases, consistent with its production of red-brown gunacin pigments. The comparison did not identify a genomic feature that explained its apparently different lifestyle. A central limitation is that environmental DNA cannot by itself distinguish actively growing cells from dormant or wind-dispersed propagules.

Nevertheless, the non-random association of phylotypes with host trees, their recovery from healthy leaves and their isolation from insect guts support active surface colonization, although they do not prove a complete saprotrophic life cycle. It remains unresolved whether E. phylloplanum has an unrecognized pathogenic stage, a predominantly saprotrophic lifestyle or another form of ecological flexibility; the study establishes neither outcome. Infection experiments would be required to assess its parasitic potential.

Subject of Research: Environmental, cultural and genomic evidence for saprotrophic diversity in the fungal genus Exobasidium

Article Title: The saprotrophic dimension of Exobasidium ( Exobasidiales , Basidiomycota ): evidence for greater diversity and ecological flexibility than previously recognized

Article References: Veselská, T., Ježková, T., Ngubane, N. P., Wennrich, A., Kostovčík, M., Hařovská, D., Šigut, M., Pyszko, P., Bracewell, R., Drozd, P., Begerow, D., & Kolařík, M. (2026). The saprotrophic dimension of Exobasidium (Exobasidiales, Basidiomycota): evidence for greater diversity and ecological flexibility than previously recognized. IMA Fungus, 17, Article e180524. https://doi.org/10.3897/imafungus.17.180524

Image Credits: AI Generated

DOI: 10.3897/imafungus.17.180524

Keywords: Exobasidium, Exobasidium phylloplanum, saprotroph, environmental DNA, ITS2 metabarcoding, phyllosphere, fungal diversity, phylogenomics, caterpillar gut microbiome, Exobasidiales, saprotrophic, dimension

The study was conducted at the MycoPhylo experimental field in southeastern Estonia, a site specifically designed to integrate plant phylogenetic diversity with various mycorrhizal types. The researchers sampled leaf tissue from 158 plots representing 110 distinct plant species, ensuring that all plants were of similar age and exposed to comparable edaphic and microclimatic conditions. This controlled environment allowed the scientists to test specific hypotheses regarding the influence of host phylogeny, mycorrhizal associations, and leaf phenotypic characters on foliar fungal assemblages. The experimental setup included trees, shrubs, and herbaceous plants, providing a broad representation of plant growth forms.

Using a metabarcoding approach targeting the Internal Transcribed Spacer (ITS) region of the fungal ribosomal RNA, the team generated a high-resolution profile of the fungal communities present on the leaves. The sequencing data revealed that the fungal communities were dominated by the classes Dothideomycetes, Tremellomycetes, and Taphrinomycetes. Functional guild analysis indicated that plant pathogens and saprotrophs were the most abundant ecological groups within these assemblages. The high level of taxonomic diversity observed underscores the complexity of the phyllosphere and the importance of understanding the mechanisms that regulate microbial colonization in this exposed habitat.

The statistical analysis revealed that plant growth form and mycorrhizal association were significant drivers of foliar fungal alpha diversity and community composition. Plant phylogenetic eigenvectors accounted for up to 25.8% of the variation in fungal richness, indicating that evolutionary history plays a substantial role in determining which fungi can successfully colonize a host. Specifically, plants belonging to certain families, such as Grossulariaceae and Cistaceae, harbored relatively higher fungal richness compared to hosts from families like Lauraceae and Betulaceae. This phylogenetic signal suggests that closely related plant species may share similar microbial communities due to conserved leaf traits or shared evolutionary pressures.

Mycorrhizal type emerged as another key factor influencing fungal community structure, although the effect sizes were modest. Ectomycorrhizal plants were notably richer in Taphrinomycetes and Pucciniomycetes compared to arbuscular mycorrhizal and ericoid mycorrhizal hosts. This finding suggests that the belowground symbiotic relationship between the plant and mycorrhizal fungi may indirectly affect the aboveground microbial community, possibly through changes in leaf nutrient allocation or defense chemistry. However, the study noted that mycorrhizal type is often correlated with other host traits, making it difficult to disentangle the direct effects of the symbiosis from the effects of plant taxonomy and growth form.

Leaf functional traits, such as thickness and hairiness, showed a weaker but still significant influence on fungal richness. Thinner-leaved species generally harbored more fungal operational taxonomic units than thick-leaved species, a pattern consistent with previous studies suggesting that tougher leaf structures may limit fungal proliferation. Leaf hairiness, or the presence of trichomes, also had a minor effect on fungal richness, potentially due to the production of chemical compounds by the hairs that inhibit fungal colonization. Despite these correlations, the overall impact of these morphological traits on community composition was less pronounced than that of plant phylogeny and growth form.

The relationship between host phylogeny and fungal community dissimilarity was further examined using Mantel tests, which revealed weak but guild-dependent associations. While total fungal and saprotroph communities showed a positive relationship with host phylogenetic distance, plant pathogenic fungi did not exhibit a significant phylogenetic signal. This distinction highlights the different ecological strategies employed by various fungal groups; pathogens may be more influenced by specific host species identity and immune responses, whereas saprotrophs may be more responsive to broader phylogenetic and structural traits of the host plant. These findings suggest that the assembly of foliar fungi is a complex process involving multiple interacting factors.

The study also found that plant deciduousness significantly affected fungal community composition, even though it did not influence fungal richness. Deciduous plants harbored higher proportions of certain fungal classes, such as Tremellomycetes and Taphrinomycetes, compared to evergreen plants. This difference may be attributed to the structural and chemical properties of deciduous leaves, which are often thinner and shorter-lived, making them more susceptible to fungal colonization. Evergreen leaves, with their thicker cuticles and longer lifespan, may provide a more stable but less permissive environment for many fungal taxa. These results emphasize the importance of considering leaf phenology when studying phyllosphere microbial communities.

Overall, the findings indicate that host phylogeny and plant functional traits contribute to, but do not solely determine, the structure of foliar fungal assemblages under field conditions. The integration of host evolution with functional ecology provides a robust framework for understanding phyllosphere mycobiome variation. By identifying the specific plant characteristics that drive fungal diversity, this research offers valuable insights for managing plant health and resilience in managed ecosystems. Future studies should focus on the temporal dynamics of these communities and the causal mechanisms linking belowground mycorrhizal interactions to aboveground microbial assembly.

Subject of Research: Drivers of foliar fungal community composition in a common garden experiment

Article Title: Impact of plant species, mycorrhizal type, and leaf traits on foliar fungal communities (in a common garden experiment)

Article References: Ariyan, M., Mikryukov, V., Khalil, H., Gohar, D., Hosseyni Moghaddam, M. S., Drenkhan, R., & Tedersoo, L. (2026). Impact of plant species, mycorrhizal type, and leaf traits on foliar fungal communities (in a common garden experiment). IMA Fungus, 17, Article e173358. https://doi.org/10.3897/imafungus.17.173358

Image Credits: AI Generated

DOI: 10.3897/imafungus.17.173358

Keywords: foliar fungi, plant microbiome, mycorrhizal symbiosis, phyllosphere, plant phylogeny, leaf traits, metabarcoding, fungal diversity, common garden, ecological drivers, Impact, plant

The research team, led by Shuang Li and Weixi Zhang of Shenyang Agricultural University and the Chinese Academy of Forestry, focused on four hybrid poplar varieties grown under identical field conditions in the same plantation. These hybrids, derived from crosses involving Populus deltoides and related species, are the backbone of China’s vast Three-North Shelter Forest System, the largest ecological engineering project on Earth, which stretches across the country’s arid northwest, north, and northeast to hold back windblown sand and protect fragile soils. Understanding what lives on the leaves of these trees, and why, has direct consequences for how such plantations are managed and how their microbial resources might one day be harnessed.

To capture the leaf-surface microbiome, the researchers employed a carefully validated extraction protocol. Leaf samples were collected from the upper canopy at heights of six to eight metres, picked from four cardinal directions on each tree using sterile gloves and high-reach shears. Back in the laboratory, ten grams of leaf tissue were placed in a sterile flask with phosphate buffer and subjected to a mild sequence of ultrasonication and shaking, a treatment strong enough to dislodge epiphytic microbes from the waxy leaf surface but gentle enough to avoid rupturing the cells themselves. The resulting suspension was filtered through a sterile nylon membrane, which was then frozen at minus eighty degrees Celsius until DNA extraction.

The genetic material was amplified using primers targeting the 16S rRNA gene for bacteria and the ITS region for fungi, and sequenced on an Illumina NovaSeq platform. After quality filtering and denoising, the team obtained amplicon sequence variants, or ASVs, which serve as precise molecular markers of individual microbial taxa. Good’s coverage values exceeded 0.9996 across all samples, confirming that the sequencing depth was more than sufficient to capture the full diversity present on the leaves.

The results revealed a striking pattern. Across all four poplar varieties, the dominant microbial groups were remarkably stable: fungi belonged overwhelmingly to the phyla Ascomycota and Basidiomycota, while bacteria were dominated by Proteobacteria and Actinobacteria. Yet beneath this conserved core, the richness and composition of the communities differed significantly from one variety to another. Cultivar Y2 harboured the highest fungal species richness, as measured by the Chao1 index, while cultivar Y4 supported the greatest bacterial richness. The Shannon diversity index, which reflects both richness and evenness, did not differ significantly among varieties for either kingdom, suggesting that variety identity primarily regulates how many microbial taxa colonise the leaf rather than how evenly they are distributed once established.

At the genus level, the specificity became even more apparent. The fungal genus Nothophoma was the most abundant across all four varieties, but its relative abundance ranged from 15.56 percent in cultivar Y3 to 41.71 percent in cultivar Y4. The bacterial genus Methylobacterium-Methylorubrum peaked at 27.18 percent in Y1 but dropped to 11.64 percent in Y3, while Curtobacterium reached 33.49 percent in Y2 yet fell to just 4.76 percent in Y3. Linear discriminant analysis effect size, or LEfSe, screening identified distinct sets of indicator taxa enriched in each variety, from Pseudomonas and Rosenbergiella in Y1 to Pantoea in Y4, painting a picture of four chemically distinct leaf habitats each selecting its own microbial suite.

What drives this sorting? The researchers measured five leaf nutrient traits: total carbon, total nitrogen, total phosphorus, soluble sugar, and starch. The four varieties differed significantly in four of the five, with cultivar Y3 consistently showing the highest levels of carbon, nitrogen, phosphorus, and starch, and cultivar Y1 the lowest nitrogen and phosphorus combined with the highest carbon-to-nitrogen ratio. Redundancy analysis, a statistical technique that quantifies how much of the variation in community composition can be explained by environmental variables, revealed that leaf nutrients explained 34.72 percent of the bacterial and 46.78 percent of the fungal community variation. Variance partitioning showed that the macronutrients carbon, nitrogen, and phosphorus independently explained 30.79 percent of bacterial and 52.73 percent of fungal variation, while the carbohydrates soluble sugar and starch contributed almost nothing on their own.

Spearman correlation analysis added mechanistic texture to these statistical patterns. Among the fungi, the genera Cryptocline, Rhodotorula, and Nigrospora showed significant positive correlations with total phosphorus, total nitrogen, and total carbon, indicating that their relative abundances rise as these macronutrients accumulate in the leaf. Cladosporium, by contrast, was significantly negatively correlated with starch, suggesting its abundance is suppressed when leaves store more of that polysaccharide. Among the bacteria, Methylobacterium-Methylorubrum and Hymenobacter declined with increasing total phosphorus, while Rosenbergiella increased with the same nutrient, being positively regulated by phosphorus, nitrogen, and carbon alike. Total phosphorus was also significantly negatively correlated with the Simpson index of bacterial diversity, implying that excessive phosphorus may reduce community evenness by favouring a small number of phosphorus-responsive dominant taxa.

The finding that nitrogen and phosphorus, rather than carbon-based compounds, are the primary bottom-up regulators of phyllosphere community assembly aligns with a broader ecological paradigm. In nutrient-limited habitats, the availability of these two elements often constrains microbial growth more tightly than carbon does, because carbon is typically abundant in leaf exudates while nitrogen and phosphorus are scarcer. Previous work across neotropical tree species and temperate forests has similarly identified leaf nitrogen and phosphorus concentrations, along with host species identity, as major drivers of phyllosphere bacterial structure. The poplar study extends this paradigm to hybrid cultivars growing side by side under identical site conditions, providing unusually clean evidence that host-mediated nutrient filtering operates at the cultivar level even when the environmental sources of microbial inoculum are shared.

The authors argue that these results confirm obvious host specificity in the phyllosphere microbiome of different poplar varieties and identify leaf nutrients as important driving factors regulating community structure. The practical implications are considerable. Because cultivar identity quantitatively reshapes the conserved core microbiome, forest managers selecting poplar varieties for afforestation are, whether they realise it or not, also selecting the microbial communities that will colonise those trees. Understanding which leaf chemical profiles favour which microbial assemblages could open the door to breeding or managing poplar stands that cultivate beneficial microbes, enhance disease resistance, and improve environmental adaptation, turning the invisible ecosystem on the leaf surface into a deliberate component of plantation design rather than an afterthought of the wind.

Subject of Research: Study on phyllosphere microbial community diversity of poplar

Article Title: Study on phyllosphere microbial community diversity of poplar

Article References: Li, S., Zhang, W., Huiyu, S., Ge, Y., Wu, S., Zhu, W., & Ding, C. (2026). Study on phyllosphere microbial community diversity of poplar. Frontiers in Ecology and Evolution, 14, Article 1963202. https://doi.org/10.3389/fevo.2026.1963202

Image Credits: AI Generated

DOI: 10.3389/fevo.2026.1963202

Keywords: phyllosphere, poplar, microbiome, high-throughput sequencing, leaf nutrients, nitrogen, phosphorus, host specificity, afforestation, shelterbelt, Proteobacteria, Ascomycota

Halophila stipulacea is no ordinary newcomer. Originating in the Red Sea and Indian Ocean, this small, fast-growing seagrass is a Lessepsian migrant, meaning it crossed into the Mediterranean Sea through the Suez Canal after its opening in 1869. It was first observed in the Mediterranean in 1894 and later reached the Caribbean Sea, likely transported by boats, with the first Caribbean sighting reported in Grenada in 2002. Today it ranks among only three known invasive seagrass species worldwide, and its tolerance of wide ranges in light, depth, temperature, salinity, and water movement has long been credited with its spread. What has remained unclear is whether its associated microbes contribute to that remarkable ecological flexibility.

To probe that question, a research team led by scientists at the University of Puerto Rico Río Piedras, working with collaborators in Spain, the United States, Cyprus, and Puerto Rico, built on a previously published controlled competition experiment conducted in Cyprus. Intact cores of naturally co-occurring seagrass containing both species were collected by SCUBA from donor beds and transplanted into 24-liter flow-through mesocosms at a marine aquaculture facility in Larnaka. The experiment ran for six weeks under natural conditions and included four treatments with ten mesocosm replicates each: native and invasive grown together at natural densities, both species together at reduced densities, invasive monoculture, and native monoculture. Monocultures were created by selectively removing one species, while reduced-density mixed treatments were established by removing roughly half the shoots of both species while maintaining their co-occurrence.

The team focused on the phyllosphere, the microbial community living on the surface of seagrass leaves, because shoot dynamics had responded strongly to competition in the earlier experiment. At the start and end of the six-week period, researchers scraped epibionts from blades of both species, washed and centrifuged the samples, and extracted DNA using a commercial soil kit. They then sequenced the V4 region of the 16S rRNA gene, the workhorse marker for characterizing bacterial communities, following the Earth Microbiome Project protocol. Sequencing was performed on an Illumina MiSeq platform, and the resulting data were processed with the QIIME 2 microbiome platform using the DADA2 pipeline to denoise sequences and assign them to amplicon sequence variants, or ASVs, which represent distinct bacterial taxa. Taxonomy was assigned with a naive Bayes classifier trained on the SILVA database.

Alongside the microbial work, the researchers measured an array of biochemical and morphological indicators of plant health. They extracted photosynthetic pigments including chlorophyll a, chlorophyll b, and carotenoids from leaf tissue, quantified hydrogen peroxide as a marker of oxidative stress using the potassium iodide method, and measured malondialdehyde, a product of lipid peroxidation that signals cellular damage. Growth was assessed by counting changes in shoot numbers over the experiment, and the team also recorded aboveground and belowground biomass, rhizome internode length, and sediment nitrate and nitrite concentrations. This combination of microbial, biochemical, and morphological data allowed the researchers to look for associations between bacterial communities and the physiological state of each seagrass species under different competitive conditions.

The results revealed a striking asymmetry. In the competition experiment, the invasive H. stipulacea increased by an average of 3.7 shoots, roughly a 59 percent gain, when grown in mixed assemblages with the native seagrass, while the native C. nodosa lost about one shoot, a 29 percent decline, under the same conditions. When density was reduced in mixed treatments, the invader grew by 4.3 shoots, an increase of roughly 150 percent, while the native showed a modest gain of 0.2 shoots. Aboveground biomass followed the same pattern: natives produced significantly more biomass when grown alone than when mixed, whereas the invader maintained or increased its biomass in mixed treatments. Notably, the native seagrass had internode lengths roughly three times longer than the invader, a morphological difference that had not been documented in the earlier work.

Biochemical measurements added another layer of intrigue. Hydrogen peroxide concentrations were more than sevenfold higher in the native C. nodosa, averaging 4.18 micromoles per gram compared with just 0.62 in the invader, indicating substantially greater oxidative stress in the native species. Malondialdehyde levels were also higher in the native seagrass, and the difference varied by treatment. Photosynthetic pigment levels told an opposite story for the two species: the native seagrass had higher pigment concentrations when grown in mixed communities than when alone, while the invader showed the reverse pattern, producing significant treatment-by-species interactions for chlorophyll a, chlorophyll b, and carotenoids. Sediment nitrate and nitrite concentrations, by contrast, did not differ significantly between treatments or species.

On the microbial side, sequencing of 41 libraries yielded 301,907 raw reads, of which 169,068 high-quality reads survived quality control, chimera removal, and filtering. After rarefaction to a standardized depth of 1,500 reads per sample, the final dataset comprised 826 bacterial ASVs with an average of 220 ASVs per sample. Alpha diversity, measured as Shannon diversity and Pielou evenness, did not differ significantly between species or treatments. However, beta diversity analysis using Bray-Curtis dissimilarities revealed significant overall differences in community composition among groups, with group identity explaining 63.7 percent of the variation in a PERMANOVA test. Complementary ANOSIM analysis supported this separation, and tests for homogeneity of multivariate dispersion confirmed that the differences were not driven by unequal within-group variability. Results from an alternative normalization approach, Scaling with Ranked Subsampling, were consistent with the rarefied analyses, strengthening confidence in the findings.

The taxonomic composition of the two seagrass microbiomes diverged sharply. Proteobacteria dominated across all samples, accounting for 72.1 percent of sequence reads, followed by Bacteroidota at 7.7 percent and Planctomycetota at 3.7 percent. The native C. nodosa in monoculture harbored the richest microbiome, with elevated proportions of genera such as Oceanicella, uncultured Microtrichaceae, Hyphomonas, Methylotenera, and Lentimonas. When the native grew alongside the invader, its microbial diversity declined and several taxa associated with nutrient cycling and stress tolerance, including the sulfate-reducing genus Desulfobulbus and the hydrocarbon-degrading genus Bermanella, became strongly associated with monoculture conditions. Conversely, the invader’s microbiome was most abundant in mixed environments: the genus Pseudoalteromonas reached 32.7 percent relative abundance in full mixed density compared with just 6.5 percent in monoculture, and genera such as Vibrio, Photobacterium, Zeaxanthinibacter, and Tenacibaculum were more prevalent when the invader grew with the native. Modeling with MaAsLin 2, which integrates microbial data with experimental covariates while correcting for multiple comparisons, confirmed these associations, and a sensitivity analysis with reduced predictor sets produced qualitatively consistent results.

The authors propose several hypotheses to explain these patterns. One possibility is microbe-mediated allelopathy: the invader may harbor bacterial associates that produce compounds harmful to the native species, a mechanism well documented in terrestrial plants but not yet reported between seagrasses. Supporting this idea, recent work has shown that H. stipulacea produces a distinct volatilome compared with native seagrasses, including allelopathic compounds such as apocarotenoids and isothiocyanates. Another hypothesis is that the invader actively selects beneficial microbes when competing, or alternatively passively acquires its microbiome from environmental sources. The study has limitations: it examined only phyllosphere bacteria, leaving rhizosphere and sediment communities unexplored, and the compositing strategy used to reduce technical variation may have underestimated within-treatment variability. Sequencing depth was also constrained by quality filtering. Nevertheless, the correlative patterns are compelling, and the authors emphasize that future work must determine whether the microbial shifts are a cause or a consequence of competitive success. As climate change is expected to further promote the expansion of H. stipulacea in the Mediterranean, understanding whether these microbes are drivers or passengers of invasion could prove critical for predicting and managing the future of seagrass ecosystems on two continents.

Subject of Research: Microbial communities associated with enhanced growth of the invasive seagrass Halophila stipulacea when mixed with native Mediterranean seagrass Cymodocea nodosa

Article Title: Better together? Microbial communities associated with enhanced growth of the invasive seagrass Halophila stipulacea when mixed with a native Mediterranean seagrass Cymodocea nodosa

Article References: Hoza-Frederick, E., Martínez-Campos, S., Barber, P. H., Vasquez, M. I., Fotopoulos, V., Antoniou, C., Drakou, K., Godoy-Vitorino, F., & Chiquillo, K. L. (2026). Better together? Microbial communities associated with enhanced growth of the invasive seagrass Halophila stipulacea when mixed with a native Mediterranean seagrass Cymodocea nodosa. Frontiers in Marine Science, 13, Article 1871379. https://doi.org/10.3389/fmars.2026.1871379

Image Credits: AI Generated

DOI: 10.3389/fmars.2026.1871379

Keywords: seagrass, invasive species, microbiome, Mediterranean Sea, Halophila stipulacea, Cymodocea nodosa, 16S rRNA, phyllosphere, marine ecology, plant competition, oxidative stress, Frontiers in Marine Science

The research team, led by Songye Pei, Bing Li, Guangze Jin, and Zhili Liu of Northeast Forestry University in Harbin, China, focused on four dominant tree species in a temperate forest, dividing individuals of each species into two size classes based on diameter at breast height, the standard forestry measure taken at roughly 1.4 meters above the ground. Tree size is far more than a cosmetic variable. As trees grow from saplings to canopy giants, their leaf functional traits change systematically, and so do the communities of bacteria and fungi living on the leaf surface—the phyllosphere. What remained unknown until now was whether those size-driven changes carry through into the dead leaf, altering both the litter’s chemistry and its initial microbial passengers, and whether those changes then translate into measurable differences in decomposition on the forest floor.

To find out, the researchers collected freshly fallen leaf litter from small and large trees of the four species, ran a full chemical characterization of each litter type, and used high-throughput DNA sequencing to profile both the bacterial and fungal communities carried in the material. They then deployed the litter in a field decomposition experiment and, after six months on the forest floor, measured how much mass each litter batch had lost. Six months captures the early stage of decomposition, the phase when easily digested compounds disappear first and the recalcitrant skeleton of the leaf—lignin and structural carbohydrates—begins to dominate what remains.

The chemical results revealed a clear ontogenetic signature. As tree size increased, litter concentrations of total carbon, starch, the carbon-to-nitrogen ratio, and the lignin-to-nitrogen ratio all rose, while total nitrogen declined. In other words, leaves from larger trees were, on paper, lower-quality substrate: more carbon-rich, more nitrogen-poor, and proportionally more reinforced with lignin relative to nitrogen, a combination that classically predicts slower decay. Yet when the team measured actual mass loss, the opposite happened. Litter from large trees decomposed faster than litter from small trees, and the factor most closely tied to that acceleration was an unassuming one: starch. This labile, easily metabolized carbon reserve apparently gave microbial decomposers an immediate energy source, overriding the nominally poorer overall chemistry of the large-tree leaves.

The microbial data added a second layer to the story. Using sequencing-based community profiling, the researchers found that microbial community assembly in litter from larger trees was governed more strongly by deterministic processes—the non-random, environmentally driven sorting of species—than in litter from smaller trees, where stochastic processes play a comparatively larger role. Alongside that shift in assembly rules, larger-tree litter hosted altered community compositions, reduced fungal richness, and simpler co-occurrence networks for both bacteria and fungi. Network complexity, often read as a proxy for the number and strength of ecological interactions within a community, thus declined with tree size, suggesting that the decomposer assemblages arriving on large-tree litter were structurally different in kind, not just in species identity.

The most consequential finding emerged when the team formally partitioned the relative contributions of litter chemistry and microbial community traits to variation in decomposition rates. For litter from small trees, initial chemistry explained more of the variation in mass loss, with starch and cellulose standing out as the key chemical predictors. That is the textbook expectation: substrate quality rules early decay. But in litter from large trees, the importance of chemistry diminished, while the relative importance of the microbial community rose, with shifts in fungal community composition taking center stage. The primary control on decomposition, in effect, migrates from the resource to the decomposers as the source trees grow larger.

Why would fungal composition matter more for large-tree litter? The study’s authors connect this to the deterministic assembly and compositional shifts they documented. Fungi are the principal agents of lignin and cellulose degradation, so which fungal species establish first on a litter batch can strongly condition how the tougher structural fractions are attacked. If larger trees consistently export a distinct, more deterministically assembled fungal community with their litter, the identity of that community—not merely the amount of starch or cellulose in the leaf—becomes the variable that best predicts decay. The finding also underscores the role of labile carbon fractions such as starch in regulating the early stages of decomposition, a phase during which microbes are often carbon-limited and respond rapidly to accessible energy sources.

The broader implications reach into carbon cycle modeling and forest management. Global vegetation models typically represent litter decomposition as a function of climate and coarse litter quality indices, without accounting for tree size as a driver of either substrate chemistry or decomposer community structure. If the same size-dependent shift in controls holds across other forests, then stands dominated by large, mature trees may process their litter through fundamentally different microbial pathways than regenerating stands of the same species, altering rates of carbon return to the soil and nutrient availability for regeneration. The result also dovetails with a growing body of work on phyllosphere microbiomes, which recognizes that the leaf surface is not a passive waiting room for decomposers but an active inoculum that shapes what happens after leaf fall.

Methodologically, the study is notable for treating bacteria and fungi as parallel, equally tracked communities rather than folding all microbes into a single category, and for combining chemical assays of carbon fractions, lignin, cellulose, and nitrogen with network-based analyses of microbial co-occurrence. The raw sequencing data have been deposited in the Genome Sequence Archive under accession CRA030649, allowing other researchers to reanalyze the community profiles. The work was supported by the National Natural Science Foundation of China, the Heilongjiang Postdoctoral Fund, the China Postdoctoral Science Foundation, and the China Scholarship Council.

For now, the message is a humbling one for anyone who assumed decomposition could be predicted from leaf chemistry alone. The same species, growing in the same forest, can produce litter whose decay is governed by different rules depending simply on how big the parent tree was. As forests worldwide age, are harvested, or shift in size structure under management and climate change, the hidden hand of tree size on the microbial crews that recycle dead leaves may prove to be a variable that ecosystem science can no longer afford to ignore.

Subject of Research: How tree size alters litter chemistry and microbial communities to control leaf litter decomposition in temperate forests

Article Title: Tree size shifts the relative importance of litter chemical properties and microbial community traits to litter decomposition

Article References: Pei, S., Li, B., Jin, G., & Liu, Z. (2026). Tree size shifts the relative importance of litter chemical properties and microbial community traits to litter decomposition. Plant and Soil. https://doi.org/10.1007/s11104-026-09052-y

Image Credits: AI Generated

DOI: 10.1007/s11104-026-09052-y

Keywords: tree size, litter decomposition, litter chemistry, microbial community, fungal composition, phyllosphere, starch, temperate forest, community assembly, carbon cycling, high-throughput sequencing, Plant and Soil

The phyllosphere, as the leaf environment is called, is a notoriously difficult place to make a living. It is exposed to ultraviolet radiation, fluctuating humidity, temperature swings and scarce nutrients, and it changes dramatically with the seasons. Yet despite these pressures, leaf surfaces host complex communities of bacteria, fungi, oomycetes and other eukaryotes that influence plant health, disease resistance and even ecosystem function. Understanding which interactions hold these communities together has been a long-standing puzzle, because most studies rely on computational predictions of who interacts with whom rather than direct experimental proof of the underlying mechanisms.

To crack the problem, the researchers launched a continental-scale field survey, collecting 347 wild Arabidopsis plants from 15 natural populations spanning Spain, France, Germany and Sweden. They sequenced bacterial, fungal, oomycete and broader eukaryotic marker genes from both whole-leaf samples and surface-sterilized endophytic samples, building a multikingdom picture of who lives where. Network analysis of the resulting data revealed that certain taxa, so-called hub microbes, occupied disproportionately central positions in the microbial community. Among the most prominent were the oomycete genus Albugo and the basidiomycete yeast Dioszegia, both of which scored highly on measures of closeness and betweenness centrality, indicating that they act as connective tissue within the leaf microbiome.

Albugo laibachii is an obligate biotrophic pathogen, meaning it can only survive on living host tissue. Such pathogens typically lose essential metabolic pathways during evolution because they can steal the missing nutrients from their hosts. Albugo’s genome, for example, lacks the entire pathway for making thiamine. But there is a catch: during the earliest stages of infection, before the pathogen has penetrated the plant, the leaf surface offers almost no resources. The researchers hypothesized that other leaf-dwelling microbes might be filling this gap, and that a positive interaction between Albugo and a co-occurring microbe could explain how the pathogen manages to establish itself in nature.

Testing this idea required moving from correlation to causation. The team adapted a gnotobiotic system in which sterile Arabidopsis seedlings are grown in plates and inoculated with defined microbes, allowing them to measure how individual strains affect Albugo colonization. Of twelve candidate interactors predicted from the network analysis, most either inhibited the pathogen or had no effect. One result was particularly instructive: two strains of the yeast Leucosporidium, predicted to interact positively with Albugo, actually suppressed infection, a reminder that computational associations do not always translate into direct functional outcomes. But one strain, a Dioszegia hungarica isolate designated EY, consistently and strongly promoted Albugo infection, exactly as the network had predicted.

The molecular culprit turned out to be a gene called DhPER1, which encodes a membrane permease for thiamine. Comparing the genomes of the Albugo-promoting EY strain and a non-promoting strain from Portugal, the researchers found that DhPER1 carried the highest density of single-nucleotide polymorphisms among all thiamine-related genes, and that its expression was more than twentyfold higher in EY than in the non-promoting strain. Using a newly developed CRISPR-based transformation system for Dioszegia, they knocked out DhPER1 in the EY strain and found that the mutant lost its ability to promote Albugo infection. Complementing the mutant with the EY version of the gene restored the phenotype, confirming that this single permease is the key to the interaction.

Enzyme-linked immunosorbent assays showed that strains expressing DhPER1 secreted thiamine into their surroundings, and adding purified thiamine to the gnotobiotic system boosted Albugo infection by up to 500 percent at low concentrations. Under the microscope, the researchers observed something remarkable: Albugo zoospores, the motile spores that initiate infection, actively swam toward Dioszegia EY cells rather than drifting freely in water, suggesting that the yeast both attracts and feeds the pathogen. Transcriptomic analysis two days after infection revealed that Albugo’s overall gene expression tripled in the presence of the EY strain, with 316 genes upregulated, many involved in metabolism and membrane transport, indicating that the yeast jump-starts the pathogen’s metabolic machinery during the critical early phase of colonization.

Evolutionary analyses added a deeper layer to the story. The DhPER1 gene shows signatures of strong purifying selection in Dioszegia, with a ratio of nonsynonymous to synonymous substitutions among the most conserved of all genes, and the RELAX algorithm revealed intensified selection specifically along the D. hungarica lineage. The EY strain also carries more than twice as many tRNA genes as other D. hungarica strains, and its thiamine-related genes show significantly higher predicted translation efficiency, suggesting that natural selection has optimized the yeast’s protein-production machinery to support the cross-feeding lifestyle. These findings echo the Black Queen Hypothesis, which proposes that leaky production of costly public goods drives stable metabolic dependencies between microbes.

What does the yeast get out of the deal? In long-term co-cultivation experiments lasting 32 days, roughly the span of Arabidopsis’s vegetative growth, Dioszegia populations gradually died out on non-sterile plants when Albugo was absent, overwhelmed by the native microbiome. But when Albugo was present, the yeast populations were rescued, increasing more than a hundredfold, and strains expressing DhPER1 fared significantly better than those without it. The benefit appears to be indirect: Albugo, known from earlier work to suppress plant immunity and inhibit certain competitors, effectively engineers the leaf environment, sheltering its metabolic partner from competitive exclusion. The result is an asymmetric mutualism in which the yeast supplies a vitamin and the pathogen supplies a niche.

The implications reach well beyond Arabidopsis. Vitamin auxotrophy is widespread among bacteria in oceans, soils and the human gut, and obligate plant pathogens such as downy mildews, rusts and arbuscular mycorrhizal fungi all depend on nutrients they cannot make themselves. If the colonization of such organisms depends on nutrient supplies from the microbiome rather than solely from the host, as this study suggests, then manipulating microbial nutrient flows could become a powerful tool. Researchers envision strategies that either starve harmful obligate pathogens by disrupting their microbial supply lines or bolster beneficial symbionts by engineering cross-feeding partners, opening a new frontier in microbiome engineering for agriculture and ecosystem management.

Subject of Research: Thiamine cross-feeding between a leaf yeast and an oomycete pathogen in the Arabidopsis phyllosphere microbiome

Article Title: Thiamine cross-feeding drives microbial coexistence in the leaf microbiome

Article References: Hu, Y., Bode, J., Gómez-Pérez, D., Guerreiro, M. A., Mari, A., Wang, K., Niemann, S., Mahmoudi, M., Kemen, A., Duran, P., Wacker, O., Straub, D., Nahnsen, S., Schwessinger, B., Roux, F., Alonso-Blanco, C., Ågren, J., Hacquard, S., Stukenbrock, E. H., & Kemen, E. (2026). Thiamine cross-feeding drives microbial coexistence in the leaf microbiome. Nature Microbiology. https://doi.org/10.1038/s41564-026-02499-w

Image Credits: AI Generated

DOI: 10.1038/s41564-026-02499-w

Keywords: thiamine, cross-feeding, phyllosphere, microbiome, Arabidopsis thaliana, Albugo laibachii, Dioszegia hungarica, mutualism, keystone taxa, oomycete, plant pathology, microbial ecology

The stakes are considerable. Strawberry is a hybrid of two American species, Fragaria virginiana and F. chiloensis, that was created in Europe and has since become a global crop with a market value projected to exceed 43 billion US dollars by 2028. Yet the modern industry rests on a fragile chemical foundation. Growers may apply up to 36 pesticide treatments per year, roughly 18 kilograms of plant protectants per hectare, and strawberries consistently rank near the top of the so-called Dirty Dozen list of pesticide-contaminated produce. Climate change compounds the problem: warming temperatures are pushing pests and pathogens toward higher latitudes and elevations, and Europe alone recorded 142 novel pathogen introductions between 2012 and 2022, including viruses, bacteria, and fungi.

The review’s central claim is that strawberry’s unusual biology creates an equally unusual microbiome, and that this microbiome can be harnessed for protection. Unlike most dicotyledonous plants, strawberry builds its root system around a compact crown from which short-lived adventitious and lateral roots continuously emerge and die. This rapid root turnover generates a dynamic rhizosphere in which microbial colonization and succession repeat in cycles, potentially producing microbial assemblages distinct from those of other crops. The plant also propagates vegetatively through stolons, the runners that connect mother plants to daughter plants, providing a physical route for microbes to pass between generations.

That stolon pathway cuts both ways. Researchers have documented identical endophytic bacteria, including Pseudomonas fluorescens and Pantoea species, in both stolons and seeds, and the beneficial nitrogen-fixing bacterium Azospirillum brasilense has been shown microscopically to migrate from mother to daughter plants. But pathogens exploit the same corridor: Fusarium oxysporum f. sp. fragariae, the cause of Fusarium wilt, and the bacterium responsible for strawberry marginal chlorosis both move through stolons. Understanding which microbes ride the runners, the authors argue, could be key to establishing stable, disease-resistant microbial communities in the next generation of plants.

The rhizosphere emerges as the front line of this microbial battlefield. Survey data show the strawberry root zone is dominated by Proteobacteria, followed by Actinobacteria, Bacteroidetes, Acidobacteria, and Firmicutes, with fungal communities dominated by Ascomycota. A landmark 2015 study identified a South Korean field that had maintained remarkably low Fusarium wilt incidence despite fifteen years of continuous strawberry monoculture. The secret lay in the soil: a high relative abundance of Actinobacteria, and in particular a Streptomyces strain designated S4-7, which produces a thiopeptide antibiotic called conprimycin that disrupts cell wall biosynthesis in the Fusarium pathogen by targeting its cell wall remodeling kinase PKC1 and the Golgi transporter SBE2.

Subsequent work has shown that pathogen attack itself reshapes the root community in ways that depend on the plant’s genetic background. Inoculation with the charcoal rot pathogen Macrophomina phaseolina reduced microbial diversity, while Verticillium dahliae increased it. Cultivars resistant to Verticillium consistently enriched Actinobacteria such as Arthrobacter, Nocardioides, and Gaiella, alongside Acidobacteria, taxa presumed to suppress the fungus through antifungal compounds and cell wall-degrading enzymes like chitinase. Even airborne infections leave fingerprints below ground: foliar challenge with the gray mold pathogen Botrytis cinerea enriched Actinobacteria in the rhizosphere, while Colletotrichum infection depleted beneficial genera including Streptomyces, Bacillus, Azospirillum, and Trichoderma. Whether these shifts represent a plant-driven recruitment of defenders or pathogen-mediated sabotage remains an open question the review highlights as a research priority.

Beneficial microbes can also be introduced deliberately, and the evidence suggests they work as ecosystem engineers rather than simple replacements. When researchers applied a consortium of plant growth-promoting rhizobacteria comprising Bacillus subtilis, Bacillus amyloliquefaciens, and Pseudomonas monteilii to field-grown strawberries, the treatment selectively enriched functional taxa involved in nitrogen fixation, nutrient cycling, and pathogen suppression, even though overall diversity measures barely changed. Similarly, a commercial fermented soil amendment called VESTA increased the abundance of Betaproteobacteria involved in nitrogen and sulfur cycling, yet most of the enriched taxa were not even present in the formulation, indicating the product rewired existing microbial networks through plant-microbe interactions rather than displacing the native community.

Above ground, the phyllosphere tells a story of movement and exchange. A core bacterial community dominated by Sphingomonas, Pseudomonas, Bacillus, Methylobacterium, and Flavobacterium persists across cultivars, but its composition varies with genotype. More strikingly, the aerial surfaces of strawberry plants function as ecological crossroads with insects. Predatory mites introduced to greenhouse crops enriched Sphingomonas, Methylobacterium, and Pseudomonas on the leaves, while pollinating bees delivered the bacterial genera Snodgrasella and Gilliamella. In one remarkable case documented in Nature Communications, the beneficial bacterium Streptomyces globisporus SP6C4, first found in the strawberry phyllosphere, spreads among plants via pollinator movement, suppresses fungal diseases, and even protects bees from entomopathogenic fungi, forming a bacteria-plant-insect tripartite alliance. Leaf microbes, meanwhile, are transferred to developing fruit at rates of 38 to 80 percent for bacteria and 50 to 99 percent for fungi, making the phyllosphere a key reservoir for fruit health and postharvest quality.

The practical payoff comes in the form of biological control agents, and the review catalogs an impressive arsenal. Bacillus velezensis strains reduced Fusarium wilt incidence by up to 69.2 percent in field conditions, while a bioorganic fertilizer containing Bacillus licheniformis and B. methylotrophicus suppressed the disease by 80 percent. The microalga Chlorella fusca cut disease severity by 70.4 percent, and combinations of Pseudomonas fluorescens strains producing the antimicrobials 2,4-diacetylphloroglucinol and phenazine-1-carboxylic acid reduced Phytophthora root rot by up to 80 percent. Against foliar anthracnose, Paenibacillus polymyxa TP3 induced systemic resistance that reduced lesion size by 56.8 percent, and, notably, the defense priming was transmitted through stolons to daughter plants, suggesting induced immunity can persist across clonal generations. For postharvest gray mold, the yeast Rhodotorula glutinis cut disease incidence by more than 94 percent, and the mycoparasitic fungus Clonostachys rosea reduced flower and fruit infection rates by roughly 80 percent under field conditions.

Looking forward, the authors outline a roadmap that moves beyond single-strain biocontrol. Synthetic microbial communities, or SynComs, composed of complementary strains for growth promotion, resistance induction, and pathogen inhibition represent the next generation of microbiome manipulation, but their design is hampered by a shortage of high-resolution, function-oriented metagenomic data for strawberry. Artificial intelligence and explainable machine learning could identify keystone taxa and model the interactions within these consortia, while precision agriculture tools such as wearable volatile sensors, hyperspectral imaging, and LED-modulated lighting could create closed-cycle production systems tailored to microbiome health. The authors also propose microbiome-assisted breeding that selects for the plant’s ability to recruit beneficial microbes, a trait they frame through the plant social networking system model, and even raise the provocative possibility that strawberry-associated microbes such as Pseudomonas, Sphingomonas, and Methylobacterium, which have been detected in the human gut at low abundances, may make the fruit not just a source of nutrients but an ecologically meaningful microbial carrier. If the holobiome concept delivers on its promise, the future of strawberry farming may be written less in pesticide labels than in the grammar of microbial communities.

Subject of Research: The strawberry holobiome and its role in biotic stress tolerance and disease suppression

Article Title: Protective holobiome promotes strawberry tolerance of biotic stresses

Article References: Son, J.-S., Lee, S. Y., Sang, M. K., Spinelli, F., & Ryu, C.-M. (2026). Protective holobiome promotes strawberry tolerance of biotic stresses. Stress Biology, 6(1), Article 23. https://doi.org/10.1007/s44154-026-00294-5

Image Credits: AI Generated

DOI: 10.1007/s44154-026-00294-5

Keywords: strawberry, holobiome, microbiome, biological control, plant pathogens, rhizosphere, phyllosphere, induced systemic resistance, SynComs, Fusarium wilt, Botrytis cinerea, sustainable agriculture

The story begins with rice, one of the world’s most important staple crops, and one of its persistent enemies: Rhizoctonia solani, the soil-borne fungus responsible for sheath blight, a disease that can inflict serious yield losses across rice-growing regions. Researchers set out to understand why some rice cultivars withstand the pathogen better than others. By sterilizing the leaves of three representative rice varieties with differing levels of resistance to R. solani, the team made a crucial observation: once the native microbial community was removed, the cultivar-specific resistance disappeared. This result underscored that the plants’ apparent disease resistance was not solely an intrinsic property of their own cells, but depended critically on the microscopic partners living on their leaf surfaces.

To pinpoint which microbes were responsible, the researchers sequenced the phyllosphere microbiome of the rice varieties in the absence of pathogen inoculation. A clear pattern emerged: the abundance of fungi belonging to the genus Aspergillus correlated positively with the degree of disease resistance. This correlation led the team to a specific hypothesis, namely that particular metabolites produced by these Aspergillus fungi were the source of the protective effect. The hypothesis gained strong support when metabolites derived from one species, Aspergillus cvjetkovicii, were shown to suppress R. solani infection in laboratory assays.

The next step was a chemical detective story. Using metabolomic profiling combined with bioassay-guided fractionation, a technique in which candidate molecules are separated and tested step by step for biological activity, the researchers identified the active compound: 2,4-Di-tert-butylphenol, abbreviated as 2,4-DTBP. This small molecule, secreted by the phyllosphere-associated fungus, proved capable of suppressing R. solani on its own. Remarkably, the protective effect was not confined to rice. In experiments extending to other crops, including cucumber, maize, soybean, and tomato, 2,4-DTBP provided protection against the pathogen, and the benefits persisted even under real-world field conditions. That broad-spectrum activity, demonstrated outside the greenhouse, is what sets the finding apart from many earlier laboratory-only microbiome studies.

But how does a single fungal metabolite disarm such a formidable pathogen? The answer emerged from transcriptomic analyses of R. solani exposed to 2,4-DTBP. The researchers observed a significant downregulation of a gene called AMT1, which encodes an ammonium transporter. Follow-up experiments showed that overexpressing RsAMT1 in the pathogen promoted hyphal growth, sclerotia formation, the compact resting structures that help the fungus survive harsh conditions, and overall pathogenicity. In other words, AMT1 acts as a positive regulator of the pathogen’s virulence machinery. When 2,4-DTBP suppresses this gene, the fungus loses much of its offensive capability.

The mechanism runs even deeper, into the chemistry of cellular stress. The team found that 2,4-DTBP reduces the accumulation of reactive oxygen species, or ROS, within R. solani cells. Conversely, when the fungus was treated with hydrogen peroxide, a common reactive oxygen species, AMT1 expression was upregulated, and the same response was observed in another fungal pathogen, Fusarium fujikuroi. Taken together, these results suggest an elegant signaling chain: the fungal metabolite lowers ROS levels inside the pathogen, which dampens AMT1 expression, which in turn weakens hyphal growth, sclerotial development, and ultimately the pathogen’s ability to cause disease. It is a rare example of interspecies chemical signaling in the phyllosphere being traced all the way from molecule to mechanism to field-level protection.

The discovery also feeds into a broader conceptual shift in plant pathology. For decades, crop improvement programs have concentrated on disease resistance genes, known as R genes, which typically encode receptor-like proteins that act as molecular switches. These receptors sense isolate-specific pathogen effectors and trigger robust immune responses. The trouble with R genes is that their protection tends to be race-specific, effective against particular pathogen isolates but not others, and their activation often comes with a growth-immunity tradeoff, meaning plants that invest heavily in defense frequently sacrifice yield. Breeders have long wrestled with this dilemma, trying to stack resistance without penalizing harvests.

This is where the concept of microbiome-shaping genes, or M genes, enters the picture. The composition and structure of the plant microbiome are shaped by plant genotype, developmental stage, and nutrient uptake, reflecting the plant’s adaptation to its environment and influencing traits such as disease resistance beyond what innate immunity alone can achieve. M genes are defined as the genetic basis by which plants manipulate and reshape their associated microbial communities, selectively recruiting beneficial microbes that can then provide direct protection against pathogens. Because this strategy works through the microbiome rather than through costly internal immune signaling, M-gene-mediated resistance may mitigate the growth-defense tradeoff that plagues conventional R-gene approaches. In principle, it offers a route to broad-spectrum, durable disease resistance without compromising crop yield, a combination that has eluded breeders for generations.

Importantly, the new study demonstrated that the rice M gene is dispensable for the beneficial function of Aspergillus itself. In practical terms, this means that Aspergillus can be deployed on crops regardless of whether they carry the M gene, and indeed the researchers showed that the fungus confers disease resistance across multiple crop species. This opens two complementary avenues for disease management. One is biological: applying Aspergillus or its metabolite 2,4-DTBP directly, as a bioagent or a fungicide-like treatment, to reinforce plant defenses from the outside. The other is genetic: breeding or engineering crops whose M genes enrich protective phyllosphere microbes such as A. cvjetkovicii, so that the plant cultivates its own bodyguards. Future breeding programs could integrate both strategies, combining M-gene-mediated microbiome shaping with R-gene-mediated immunity to capture the advantages of each.

Significant questions remain before this vision becomes routine agricultural practice. Microbial communities vary enormously across environments, and future investigations will need to determine how different microbial communities are manipulated by M genes, and how those shifts translate into either broad-spectrum or species- and cultivar-specific resistance. Because the rice cultivars examined in the study exhibit stable resistance under various field conditions, identifying the causal microbes and probing the functional redundancy orchestrated by plant M genes should yield deeper insight into the genetic and ecological foundations of microbiota-driven disease suppression. Researchers have also proposed several hypothetical models of M gene action, ranging from one-to-one regulation of specific microbial species, to single genes with broad-spectrum regulatory reach, to networks of multiple M genes acting additively or redundantly on key microbial partners. Untangling which model prevails in different crops and tissues will be essential for translating the science into the field. Still, the trajectory is clear. By revealing how a leaf-dwelling fungus, a single small molecule, and the plant’s own microbiome-shaping genes converge to fend off one of rice’s worst pathogens, this line of research is turning the phyllosphere from an overlooked frontier into a designable platform for sustainable agriculture, one in which farmers might one day fight disease not with chemicals alone, but by cultivating the right microbial allies on every leaf.

Subject of Research: Phyllosphere microbiome engineering using Aspergillus metabolites and plant microbiome-shaping genes for sustainable crop disease resistance

Article Title: Harnessing Aspergillus and host M genes for sustainable phyllosphere microbiome engineering

Article References: Wang, Z., Yin, J., & Tsuda, K. (2025). Harnessing Aspergillus and host M genes for sustainable phyllosphere microbiome engineering. Crop Health, 3(1), Article 6. https://doi.org/10.1007/s44297-025-00046-3

Image Credits: AI Generated

DOI: 10.1007/s44297-025-00046-3

Keywords: phyllosphere, plant microbiome, Aspergillus cvjetkovicii, 2,4-DTBP, Rhizoctonia solani, rice, M genes, R genes, plant immunity, disease resistance, sustainable agriculture, microbiome engineering

The conceptual heart of the review is the plant holobiont, the idea that a plant and its associated microbiota should be understood as a single functional unit. This includes the rhizosphere, the teeming microbial zone surrounding the roots; the phyllosphere, the leaf and stem surfaces exposed to air and insects; and the endophytes, microorganisms that live entirely inside plant tissues. Traditional models of herbivore resistance treat the plant as a solitary defender, deploying its own chemical and structural weapons against attackers. The holobiont framework insists that this picture is incomplete, because a substantial portion of what looks like plant defence is actually produced, modulated or amplified by microbial partners that conventional breeding programmes never select for.

The authors organize the evidence for microbiome-based regulation into three principal routes. The first is direct chemical warfare: soil and root-associated microbes can produce insecticidal metabolites, including toxic secondary compounds and volatile organic molecules that repel or kill herbivores outright. The second route is immunological priming. Beneficial microbes can place the plant’s own signalling machinery on high alert, sensitizing the jasmonic acid, salicylic acid and ethylene pathways that govern responses to chewing insects, sap-suckers and pathogens respectively. A plant whose defences have been primed by its microbiome responds faster and more strongly when an insect begins feeding, often before the attacker has inflicted serious damage. The third route is perhaps the most surprising: microbes can attack the attacker from within, disrupting the gut microbiota of insect herbivores and thereby impairing their digestion, development and survival.

Each of these mechanisms is well supported by experimental evidence, and the review is careful to say so. Mycorrhizal fungi, for example, have been shown to prime the accumulation of antiherbivore compounds in tomato and to increase herbivore mortality, while arbuscular mycorrhizal colonization can reshape the phyllosphere community and alter plant defences during simultaneous attack by aphids and pathogens. Root-associated microbes have been repeatedly linked to improved plant tolerance of insect damage, a conclusion reinforced by recent systematic reviews and meta-analyses. The soil-borne legacy, in which a previous crop’s microbiome shapes the defence chemistry of the next generation growing in the same soil, adds a further layer of complexity and opportunity.

Yet the review’s central argument is not a celebration of these findings but a diagnosis of their fragility. Mechanisms that perform beautifully in growth chambers and greenhouses routinely fail or underperform in the field, and the authors contend that this lab-to-field gap, rather than any shortage of mechanistic discovery, is now the binding constraint on the entire field. The reason is that microbiome-mediated resistance is governed by a web of interacting variables that controlled experiments deliberately hold constant. Plant genotype shapes which microbes colonize the roots and leaves. Soil chemistry determines nutrient availability and microbial competition. Climate variability alters both the plant’s physiology and the composition of its microbial partners. Agricultural management, from fertilization to tillage to crop rotation, reshuffles the community yet again. Crucially, these factors do not simply add up; they interact non-additively, meaning that a microbial consortium that confers strong resistance under one combination of conditions may confer none under another.

The review reconciles several apparently contradictory findings on this point. Nitrogen nutrition, for instance, can regulate plant defence against herbivores in ways that either amplify or suppress microbiome effects depending on dose and timing. Soil moisture has been shown to mediate plant-microbe-herbivore interactions, so a treatment that works in a wet season may fail in a dry one. Agricultural intensification, with its high inputs and simplified rotations, tends to degrade the very rhizosphere diversity that underpins natural defence, which helps explain why microbiome-based approaches often show more promise in less intensive systems. Even the insects themselves carry microbiomes that exchange and interact with plant-associated communities, adding a second layer of ecological contingency to every field trial.

Where the field has advanced most rapidly, the authors argue, is in measurement and prediction rather than delivery. Multi-omics approaches, combining genomics, transcriptomics, metabolomics and proteomics, can now identify resistance-associated taxa with increasing precision and predict community function with growing confidence. Machine-learning models trained on these datasets can sift through thousands of microbial candidates and flag the combinations most likely to protect a given crop. Synthetic community experiments, in which researchers assemble defined mixtures of microbes and test them under controlled conditions, have demonstrated that protective community patterns can be identified systematically rather than by trial and error. Microbiome-assisted breeding, which treats the microbial partners as heritable components of crop performance, is emerging as a parallel strategy.

But predictive power has not yet translated into consistent field performance, stable formulations or regulatory clarity. Live microbial products are notoriously difficult to manufacture, store and deploy; a consortium that thrives in a laboratory flask may collapse on a seed coating or in a bag of granular inoculant. Once released into a field, introduced strains face competition from resident communities that may exclude them before they can establish. Regulators, meanwhile, still lack clear frameworks for evaluating live microbial pest-control products whose effects depend on context rather than on a single active ingredient. The review suggests that closing these translational gaps will require field-scale experimentation designed around ecological realism, not more greenhouse papers.

The stakes are rising. Climate change is expected to increase crop losses to insect pests as warming accelerates insect metabolism and expands the range of many species, and shifting precipitation patterns will further destabilize the microbial communities on which the holobiont approach depends. The authors argue that this makes the microbiome not a luxury but a necessity for climate-resilient integrated pest management: a plant whose microbial partners help buffer it against variable conditions is inherently more robust than one relying on a single engineered trait or a scheduled spray. In their view, the plant holobiont could become a pillar of sustainable agriculture, but only if the discipline redirects its energy from discovering yet more mechanisms to explaining, predicting and stabilizing performance across the messy gradient of real-world environments.

For farmers, the message is cautiously optimistic. The biology is real, the mechanisms are documented, and the analytical tools to exploit them are maturing fast. What remains is the hardest part of translational science: converting elegant interactions observed in controlled settings into dependable, affordable and regulatable products that work across soils, seasons and management systems. If the field takes the review’s diagnosis seriously, the invisible communities surrounding every root may yet become one of agriculture’s most powerful allies against its oldest enemies.

Subject of Research: Microbiome-mediated regulation of plant defence against insect herbivores

Article Title: Microbiome based regulation of plant insect interactions

Article References: Krishnan, K., Selvaraj, S., Krishnamoorthy, A., & Madhu, B. (2026). Microbiome based regulation of plant insect interactions. Plant Biosystems, 160(4), Article 236. https://doi.org/10.1007/s44473-026-00245-y

Image Credits: AI Generated

DOI: 10.1007/s44473-026-00245-y

Keywords: plant holobiont, microbiome, insect herbivory, jasmonic acid, salicylic acid, rhizosphere, phyllosphere, endophytes, multi-omics, machine learning, integrated pest management, sustainable agriculture