Nature Microbiology, Published online: 17 September 2026; doi:10.1038/s41564-026-02493-2Functional versatility plays a key role in shaping root microbiota.

Plants and other photosynthetic organisms interact with their environment and surrounding microbiota through specialized associations. A global core microbiota has been proposed at high taxonomic levels, such as the order level. However, it remains unclear which environmental factors and how microbe-microbe interactions drive variation of this core microbiota at lower taxonomic resolution. Here, we leveraged the environmental diversity of 141 sites across the southwest of France to characterize algal populations, and their associated bacterial and fungal microbiota. We then performed a meta-analysis, combining these data with published datasets to formally identify the global core microbiota of terrestrial photosynthetic organisms, which comprises seven bacterial and five fungal orders. We next investigated diversity within this core microbiota and the environmental drivers shaping site-specific community composition. While environmental factors have a low impact on the total relative abundance of core orders, the core microbiota at the ASV-level is impacted by climatic factors, edaphic factors, and plant community descriptors. Using interaction network analysis, we finally explored how microbe-microbe interactions contribute to the assembly of stable core communities. Our results show that core ASVs occupy central positions in algal-associated microbial networks and that distinct core orders drive site-specific variation in core microbiota structure. Together, these findings highlight the importance of both environmental context and microbial interactions in shaping the composition and stability of the core microbiota associated with photosynthetic organisms. ### Competing Interest Statement The authors have declared no competing interest. European Research Council, 951444 – PATHOCOM, erc-stg-948219, EPYC Agence Nationale de la Recherche, ANR-10-LABX-41 Biotechnology and Biological Sciences Research Council, https://ror.org/00cwqg982, BB/ X011054/1, BBS/E/F/000PR13631

Decoding the molecular and cellular basis of plant-microbe interactions. Single-cell and spatial omics of plant immunity. Led by Tatsuya Nobori at TSL, Norwich, UK.

Abstract. The model plant Arabidopsis thaliana hosts diverse microbial communities collectively known as the microbiota. The plant microbiota is generally

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Plants can recruit beneficial microbes to suppress pathogens, offering a route to rational biocontrol beyond empirical screening. Here, the authors use machine learning to identify disease-associated ...

Background Plant roots are hotspots for interactions with soil microbes, where a characteristic bacterial community structure is formed. Plant specialized metabolites often play pivotal roles in this assembly process. However, the molecular basis underlying root microbiota responses to these bioactive compounds, and how such metabolic interactions shape the assembly of host-specific root microbiota, remain largely unknown. Nicotine is a toxic alkaloid predominantly produced by the genus Nicotiana, and the genus Arthrobacter is known as one of the nicotine-degrading bacteria in the tobacco root microbiota. In this study, we used the tobacco–Arthrobacter interaction system as a model and integrated comparative genomics and experimental genetic manipulation assays to uncover the role of bacterial catabolism capacity for host specialized metabolites in shaping host-specific root microbiota. Results Nicotine catabolism genes are uniquely found in the Arthrobacter strains derived from nicotine-containing environments, and this restricted gene distribution is driven by a plasmid-mediated horizontal gene transfer. To assess the ecological consequences of this genomic adaptation in Arthrobacter fitness in tobacco roots, we characterized the nicotine utilization ability of Arthrobacter and conducted adaptation assays under in planta conditions using genetically manipulated Arthrobacter strains and tobacco mutants impaired in nicotine catabolism and biosynthesis, respectively. Nicotine improves Arthrobacter colonization of tobacco roots through a catabolism-dependent mechanism. Bacterial community analysis using a synthetic community approach further demonstrated that this metabolic adaptation enhances Arthrobacter fitness within tobacco root microbiota. Conclusions Our findings illustrated that bacterial catabolic capacity toward host-derived plant specialized metabolites is key for successful root colonization. This metabolic adaptation is driven by plasmid-mediated horizontal gene transfer and ultimately shapes the structure of the root microbiota community. Video Abstract

The Department of Biology at ETH Zurich invites applications for the above-mentioned tenured professorship at the Institute of Biochemistry

Fungal effectors may have evolved from ancient antimicrobials, shaping plant microbiota and immunity during infection.

Gain or loss of a particular domain contributes to functional specialization of a conserved chitinase in beneficial root endophyte towards microbial antagonism or host immune suppression.

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Three new synthetic algal culture media are described that have been used to cultivate ~12,000 diverse strains of (micro)algae, one culture medium for marine and brackish-water algae (ASP-MEL (Artific...