Assembly of plant holobionts is governed by nematode communities and their associated microbiota, conditioned by preceding plants

Heuer et al., 2026

Pants form holobionts by associating with diverse microbiota. Self-organization gives rise to emergent properties of the holobiont, such as increased resistance to pathogens. However, the local factors contributing to the self-organization are not well understood. We hypothesized that nematode communities and their associated microbiota govern the rhizobiome of the model plant holobiont tomato in terms of its suppression of root invasion by the parasite Meloidogyne hapla, and that the soil legacy influences the suppressive potential mediated by these biota. In pot experiments, a resistant tomato holobiont was favored by assembly in the presence of a nematode community conditioned by tomato plants, compared to oilseed rape or fallow soil. Nematode communities conditioned by tagetes could enhance resistance even better than tomato. Microbiota from crushed tomato-conditioned nematode communities increased resistance of the tomato holobiont, compared to microbiota of nematode communities conditioned by maize, or heat-inactivated microbiota. The 0.2 µm-filtered microbiota from crushed nematodes had the same effect, suggesting a role of nematode-associated bacteriophages in holobiont assembly. The results indicate that soil nematodes and their associated microbiota play a role in the local organization and stabilization of plant holobionts. They can influence the resistance of plants that subsequently grow in the same soil. From an applied perspective, crop rotation schemes that alter nematode–microbiota communities could be harnessed to engineer crop holobionts.

https://www.biorxiv.org/content/10.64898/2026.07.02.736003v1.full

Random motility regulation as a generic mechanism of community formation 

Dinelli et al., 2026

The self-organization of microbial ecosystems involves a large variety of mechanisms, ranging from biochemical signaling to population dynamics. Among these, the role of motility regulation has been little studied, despite the importance of active migration processes. Here we show how weak, random motility regulation suffices to induce complex forms of organization in bacterial mixtures comprising a large number of coexisting strains. First, we simulate microscopic models of run-and-tumble bacteria whose self-propulsion speeds are weakly regulated by the local density of each strain, mimicking the impact of weak, random metabolic interactions. Our simulations reveal that, as the heterogeneity of the interaction network increases, the system undergoes a phase transition leading to the emergence of distinct, spatially segregated communities. To account for these results and assess their robustness, we use random-matrix theory to analyze the hydrodynamic description of the bacterial mixture, obtaining a quantitative agreement with our microscopic simulations. Our results hold for a variety of motility-regulation mechanisms and highlight the need to characterize the role of motility regulation in experimentally relevant situations.

https://journals.aps.org/pre/abstract/10.1103/cl1f-mfgp

PrePrint:

https://arxiv.org/abs/2503.12692

The host–microbiome dimension of ecological regime shifts 

Rindi et al., 2026

Regime-shift research has largely overlooked host-associated microbiomes, even though they can buffer stress, speed recovery, and mediate chemical interactions that sustain reinforcing feedbacks and lock in alternative states.

Host–microbiome partnerships bolster stress-tolerance to perturbations and support recovery across marine foundation species.

Combining innovative microbiome manipulations with regime-shift mapping tools can reveal whether altering microbiomes shifts thresholds.

Host-associated microbiome-based indicators may precede host-based metrics and enable earlier, more targeted interventions.

A holobiont lens on regime-shift dynamics may help translate microbiome-assisted restoration into actionable tools for managing ecosystems under accelerating change.

Rising climate and local pressures increase the risk of regime shifts, yet despite progress, thresholds remain difficult to identify early enough to take action. We argue that this shortfall reflects a host-centric view that largely omits host-associated microbiomes, which can shape resilience by modulating stress tolerance, aiding recovery, and stabilizing alternative states through inhibitory chemical interactions. We propose a research agenda that integrates host-associated microbiomes into regime-shift ecology by combining novel microbiome manipulations in laboratory and field settings with regime-shift mapping tools, while simultaneously developing microbiome-based early warning indicators. Reframing regime-shift theory through a host-associated microbiome lens can provide practical tools to anticipate collapse, improve monitoring, and inform timely interventions, thereby supporting more adaptive and robust conservation under accelerating global change.

https://www.cell.com/trends/ecology-evolution/abstract/S0169-5347(26)00148-5

Environmental microbes as modulators of plant volatile landscapes: Implications for plant–insect chemical communication 

Zhang et al., 2026

Free-living environmental microbes at four plant-atmosphere interfaces (leaf, nectar, fruit, and bark surfaces) intercept, biotransform, and augment plant volatile signals, shaping what herbivores, pollinators, and parasitoids detect. This forum article reviews how microbes remodel these signals, the threats posed by climate change and land-use intensification, and priorities for translating microbial volatile ecology into sustainable pest management.

The global phyllosphere spans an estimated 1 billion square kilometres of above-ground plant surface, placing surface-dwelling epiphytes, carposphere colonisers, and nectar inhabitants at the plant-atmosphere boundary. At the plant-atmosphere interface, these microbes occupy a biochemical gatekeeper role: intercepting, consuming, and transforming plant-emitted volatile organic compounds (VOCs) before those signals reach insect receivers. Isoprene monooxygenases in Rhodococcus and Variovorax catalyse the oxidation and biocapture of isoprene emitted from leaf surfaces, while fungal cytochrome P450 monooxygenases, reductases, and Baeyer–Villiger oxidases execute stereoselective biotransformations, including regioselective hydroxylation of inactivated C–-H bonds, enantioselective carbonyl reduction, and lactone-forming oxidations.

Biotransformation can redirect a plant monoterpene into functionally divergent chemical spaces. For example, Aspergillus niger DSM 821 and Corynespora cassiicola DSM 62475 can convert (±)-linalool into furanoid and pyranoid linalool oxides, while A. niger DSM 821 and Botrytis cinerea additionally produce lilac aldehydes and lilac alcohols as byproducts through a pathway postulated to proceed via 8-hydroxylinalool. Furanoid linalool oxide is electroantennographically active in bee pollinators and attracts hoverflies, while lilac aldehyde acts as a repellent to the same hoverfly species. Thus, fungal biotransformations can generate compounds with opposing semiochemical functions within the same receiver community. Plant VOCs, in turn, shape phyllosphere microbial community composition, establishing bidirectional exchanges with direct consequences for herbivore, pollinator, and parasitoid perception.

linkinghub.elsevier.com/retrieve/pii/S0966842X26001605