Water scarcity significantly threatens cotton productivity, a challenge amplified by climate change and increasing competition for limited water resources. As a major source of natural fiber, cotton’s resilience to drought stress is essential for maintaining productivity and supporting global textile production. However, the mechanisms underlying this resilience, particularly the responses of root-associated microbial communities that may influence plant drought stress responses, remain unclear. Here, we quantified the plasticity of bacterial communities associated with roots of six cotton cultivars grown under water-limiting and well-watered conditions in a hot, arid environment. The highest-yielding cotton cultivars markedly shifted their root bacterial communities between irrigation treatments, whereas low-yielding cultivars were less responsive. Microbiome shifts in high-performing varieties suggest that these plants may leverage symbiotic relationships to cope with water limitation. This study links microbial communities and the performance of cotton and highlights the potential for leveraging these relationships to improve crop resilience in water-limited environments.

We present draft genome sequences for 12 fungal isolates, including two isolates each of Trichoderma, Exophiala, and Cladosporium, and one isolate each of Fusarium, Cladorrhinum, Epicoccum, Chaetomiaceae, Didymellaceae, and Pleosporales, from cyanobacteria-dominated biological soil crusts in the Sonoran Desert (Arizona, USA), sequenced on a NovaSeq 6000 at ≥40× coverage.

Understanding how aerial fungal diversity varies across space, habitat, and disturbance is key to linking local-scale sporocarp (fruiting body) reproduction with continental-scale biogeography. In this study, we combined passive spore trap metabarcoding with macrofungal sporocarp records from 31 plots in eight sites across North America to quantify how site, habitat, and fire history shape aerial macrofungal communities. From 823 samples, we recovered 7572 OTUs, nearly half belonging to macrofungi. Macrofungal aerial DNA abundance and OTU richness varied strongly among sites and increased significantly with both temperature and precipitation. Across sites, forest habitats had significantly greater macrofungal aerial DNA abundance than grassland habitats, while conifer forests supported significantly higher OTU richness than oak forests or grasslands. Burn history, likely due to lags in the sampling time following fire, did not significantly impact macrofungal aerial DNA abundance and OTU richness and also had limited effects on community composition. Aerial macrofungal community similarity declined with geographic distance, with geography explaining the most variation (16%). Functional guild composition varied across habitats, shifting from higher ectomycorrhizal prevalence in forest habitats to higher soil saprotroph prevalence in grassland habitats, although wood saprotrophs were the most abundant guild across all habitats. Integration with iNaturalist sporocarp records indicated a mean effective spore trap input range of ~3 km, consistent with strong local dispersal limitation. Together, these findings demonstrate that aerial macrofungal assemblages exhibit pronounced continental-scale structure yet remain locally heterogeneous, shaped primarily by environmental filtering, functional guild association, and limited dispersal.

Global warming and increasing water scarcity pose major challenges to agriculture, emphasising the need to translate stress-biology insights into the development of drought-resilient cultivars. In this study, we evaluated a panel of six diverse sorghum (Sorghum bicolour) accessions grown under field-imposed drought conditions in central Arizona, integrating physiological, transcriptomic and oxidative stress measurements over a 7-week period. Using network analyses informed by co-expression correlations, transcription factor (TF) binding motif signatures and protein-protein interactions, we identified a drought-associated module strongly correlated with photosynthetic capacity. This module contained a stress-responsive TF, SbDof8 (referred to here as SbCDF2/3-like, or SbCDF2/3L), as a highly connected hub gene, and CDF2/3-associated binding motifs were over-represented in the promoters of co-expressed module members. These co-expressed members were enriched for stress response, metabolic and photosynthesis-related processes, and consistently maintain higher expression under drought in tolerant compared to sensitive accessions. Analysis of an independent sorghum drought time-course dataset comprised of two unique accessions revealed concordant expression patterns of SbCDF2/3L and photosynthesis-associated module genes between drought-tolerant and drought-sensitive genotypes, reinforcing the robustness of this regulatory module. Together, our results highlight a subset of photosystem I (PSI)-related genes, including light-harvesting proteins, PSI subunits and importantly, a potential drought-responsive transcriptional regulator that are collectively upregulated in resilient accessions as a means of coping with drought response. These data highlight promising breeding targets for improving drought resilience and biomass productivity in sorghum under field conditions.

RNA covalent modifications (RCMs) influence RNA stability and translation efficiency, and they thus play critical roles in eukaryotic growth and development. However, their role in regulating plant performance under abiotic stress remains largely unexplored. Here, we integrated multi-omics data in 6 Sorghum bicolor accessions under water-limiting conditions in the field to explore the relationship between RCMs and drought response. Within a stress- and photosynthesis-associated gene co-expression module, we identified SbDUS2, a member of a family of enzymes conserved across eukaryotes, that catalyzes the reduction of uracil to dihydrouridine (DHU) on RNA molecules. DHU-modified transcripts in this module were enriched for photosynthetic functions and showed strong correlation with photosynthetic traits. To elucidate the function of this RCM, we characterized loss-of-function dus2 mutants in Arabidopsis thaliana. Under control conditions, these DHU-deficient mutants exhibited impaired germination and delayed development. Furthermore, under water-limiting or heat conditions, these mutants showed significantly reduced net CO2 assimilation and survival. Using multiple transcriptome-wide RNA stability assays, we demonstrated that transcripts associated with lower DHU levels in a dus2 background generally exhibited increased stability compared to Col-0 controls. Particularly, lack of DUS2 led to the hyperstability of photosynthesis-related transcripts, impeding their turnover and likely preventing proper photosynthetic acclimation during stress. We propose a model where DHU acts as a critical post-transcriptional regulator marking mRNAs for rapid turnover under stress, highlighting an overlooked regulatory layer contributing to plant resilience.

PREMISE:Plants in ex situ conservation nurseries acquire diverse fungal associates that may be moved among nurseries or into the wild during outplanting, including fungal endophytes that contribute to a broad range of functions and occur in leaves, sometimes alongside pathogens. To improve understanding of fungal symbionts in a plant of high conservation concern, we characterized foliar fungal endophytes of Torreya taxifolia, one of the world's most threatened conifers, in an ex situ conservation nursery. METHODS:We used culture-based and culture-free approaches to characterize fungal endophytes in leaves of T. taxifolia over 2 years and evaluated how endophytes varied spatially and as a function of environmental, plant-specific, and edaphic factors. We also contrasted them with fungi in other plants (local species and species cultivated at a regional scale) and with soil fungi. RESULTS:Culture-free methods revealed species-rich and phylogenetically diverse foliar fungal endophytes of T. taxifolia that vary spatially, reflecting symbiont acquisition from nearby plants, environmental factors, and plant stress. Endophyte community composition is subject to both stochasticity and temporal turnover and differs markedly from fungal communities in soils and other plants in the area. CONCLUSIONS:Our study provides novel insights into factors that can shape fungal endophyte communities for a critically endangered tree species. In addition to identifying local determinants of endophytic symbioses, our work illustrates that plants in conservation nurseries host rich foliar fungal communities of potential importance in plant germplasm protection.

Plant functional traits connect biodiversity to ecosystem processes, serving as key metrics for assessing how biota responds to environmental conditions. Functional seed traits are critical because they underpin recruitment and colonization, shaping biodiversity patterns and influencing ecosystem resilience. Yet, seed traits remain underrepresented in major data repositories, with severe gaps in the tropics. Climatic, geological, and historical differences between tropical and temperate regions drive distinct regeneration dynamics, suggesting that the paucity of tropical seed trait data limits our ability to predict regeneration niches and weakens global models largely based on temperate ecosystems. To address this gap, we introduce the Tropical Seed Trait Database (TSTD), an open-access repository spanning the full ecological spectrum of tropical seeds. The TSTD is conceived as a community-driven repository of primary data contributed directly by data owners, rather than as a secondary aggregation of global databases. It was built through contributions from ecologists working across all tropical regions, reached through direct contact, and its first version compiles 78 datasets, totaling 137 583 records across 44 functional traits. Covering 5115 species in 33 countries, with the Neotropics overrepresented, the TSTD marks a crucial step toward more inclusive, globally representative trait databases that can open multiple research avenues.

Many insects damage leaves, a phenomenon that is foundational to their impacts on terrestrial ecosystems. Leaf traits, including chemistry, shape these interactions. In turn, leaf-surface (phylloplane) microbes can act directly or in concert with leaf chemistry to influence leaf choice, especially by insects whose reproductive success is tied to prolonged contact with leaf surfaces. Leafcutter bees (Megachile spp.) cut disks from leaves to line their nests, with leaves and their associated microbes forming the environment in which bees' offspring develop. We hypothesized that phylloplane microbial communities act in concert with leaf chemistry to mediate interactions between the leafcutter bee M. lippiae and the plants they cut. We surveyed phylloplane communities on rose (Rosa × hybrida, Rosaceae) leaflets that were cut versus not cut by wild M. lippiae. Microbial communities differed between cut and non-cut leaflets, with Aspergillus spp. overrepresented on cut leaflets, and Alternaria sp. and Bacillus sp. overrepresented on non-cut leaflets. Then, we inoculated rose leaves in the field to test the effect of these microbial taxa on cutting. When inoculated onto rose leaves, Alternaria and Bacillus had no effect on cutting, but Aspergillus resulted in twice as many cuts as on sham-inoculated leaves. To test whether Aspergillus could protect bee nests against pathogens, we grew Aspergillus with two pathogenic fungi: the generalist insect pathogen Beauveria bassiania and three strains of Ascosphaera that cause chalkbrood disease in bee larvae. Aspergillus did not inhibit the growth of Beauveria, but it markedly slowed the growth of Ascosphaera. To clarify whether these phylloplane microbes reflect differences in leaf chemistry or are instead independent cues that influence leaf cutting, we used liquid chromatography-mass spectroscopy to characterize the metabolome of cut and non-cut leaflets. Chemistry did not differ between cut and non-cut leaflets, nor did it vary as a function of microbial community composition. Our results suggest that Aspergillus, a common member of rose phylloplane communities, mediates interactions between leafcutter bees and roses, potentially affecting the fitness of both partners. This study reveals a previously unexplored role for phylloplane microbes in plant-insect associations.

Plant demography is heavily influenced by individual survival at local scales, with host-specific natural enemies potentially reducing the survival of seeds and seedlings in high density patches near conspecific adults, favoring heterospecific recruitment, and ultimately increasing local plant diversity. Natural enemy pressure should differ 1) between sites directly beneath and away from their hosts' crowns, 2) between sites where their hosts are abundant versus rare, and 3) among potentially competing plant species. Assessing the potential pathways by which natural enemies affect diversity at local scales requires coupling experimental approaches that track plant performance with characterization of their natural enemy communities. Here, we focused on the fate of individuals at the seed stage, a critical demographic bottleneck in the plant life cycle. We tested how seed germination is affected by fungal infection, distance from the adult tree, burial duration, and host tree identity. We conducted a seed burial experiment on Barro Colorado Island, Panama, using four pioneer tree species (Jacaranda copaia, Cecropia insignis, C. peltata and C. longipes). Seeds were buried beneath and 30 m away from adult C. insignis and J. copaia trees and retrieved after 3 and 12 months. We measured germination, cultured seed-infecting fungi, and evaluated fungal communities using a culture-independent approach. Germination rates of all tree species declined with burial time. Germination of seeds buried below versus away from focal trees also did not differ. Fungal isolation frequency and richness increased after burial but did not change with distance or identity of the adult tree. Fungal communities in seeds differed markedly among tree species, but distance, burial duration, and seed viability status had little effect on community composition. Consequently, we found limited evidence that distance from conspecifics drives seed mortality in the soil. Nonetheless, seed exposure to the soil increases fungal infections and decreases seed survival, highlighting the role of fungi in seed demography. We recommend that future research explore the mechanisms by which host-generalist soilborne fungi may drive seed mortality in plant communities.

The plant metabolome wields a strong influence on its associated microbiome, with feedback from the microbiome in turn influencing plant resilience and productivity. The root metabolome represents a key element of the chemical signaling that influences microbiome recruitment to plants. We examined how the root metabolome differs between high- and low-performing genotypes of a drought-resilient cereal, Sorghum bicolor L. Moench, and how these differences relate to the root microbiome in field-grown plants. Overall, lower-performing genotypes exhibited a distinct root metabolome from higher-performing genotypes. In particular, lower-performing genotypes exhibited an accumulation of flavonoids, a class of secondary metabolites involved in plant defense and stress response. Network analyses revealed microbes whose abundance covaried with flavonoid content and suggested that higher levels of flavonoids may hinder root colonization by specific microbes. Higher-performing genotypes further exhibited more discriminating metabolites with distinct levels between watering treatments as compared to lower-performing genotypes, pointing to the potential of higher performing genotypes to better cope with stress by modulating their microbiomes via root chemistry. We discuss how insights into crop performance from the lens of metabolomics can improve our knowledge of how crops may more effectively recruit beneficial plant microbiomes.

Endophytic bacteria were isolated from roots and stems of prickly lettuce (Lactuca serriola L.), a wild relative of cultivated lettuce (Lactuca sativa L.) in Tucson, Arizona, USA. Here, we report draft genome sequences of four strains: Priestia megaterium SY0032, Bacillus velezensis SY1154, Bacillus inaquosorum SY1167, and Bacillus subtilis SY1483, assembled using reads arising from Oxford Nanopore 10.4 flow cells.

Covalent RNA modifications (RCMs) are post-transcriptional changes to the chemical composition of RNA. RCMs influence mRNA stability, regulate transcription and translation efficiency, and play critical roles in the growth and development of eukaryotes. However, their role in plants remains poorly understood, particularly as they relate to performance in the field under stress conditions. In this study, we grew a panel of six diverse sorghum (S. bicolor) accessions in the field during the summer in central Arizona and examined their physiological and molecular responses to drought and heat stress over time. We then explored the molecular features that contributed to plant performance under stress. To do so, we combined genomic, transcriptomic, epitranscriptomic, physiological, and metabolomic data in a systems-level approach. Co-expression network analyses uncovered two modules of interest, one controlled primarily by a single stress-responsive transcription factor, SbCDF3, and the other by an RCM, dihydrouridine. While the CDF3 module largely contained a set of stress response and photosynthesis-associated genes that were positively correlated with plant performance, the dihydrouridine-associated module was largely comprised of photosynthesis and metabolism genes, including SbPPDK1, which is integral to C4 photosynthesis in the grasses. In addition, the transcript encoding the enzyme responsible for this RCM, dihydrouridine synthase (SbDUS2), was also present in this module, and its abundance was positively correlated with photosynthetic traits and SbPPDK1 abundance. Given that this highly conserved RCM has never been characterized in plants, we examined loss of function mutants for the DUS2 enzyme in Arabidopsis, demonstrating decreases in plant growth and performance under heat stress in this background. Our work highlights both a key transcription factor, CDF3, for breeding in the Poaceae. In addition, for the first time in plants, we reveal a role for the RCM dihydrouridine in modifying conserved, core metabolic and photosynthesis-associated transcripts in plants. ### Competing Interest Statement The authors have declared no competing interest.

RNA Covalent Modifications (RCMs) are post-transcriptional chemical alterations that influence RNA stability and translation efficiency, thus play critical roles in eukaryotic growth and development. However, their role in regulating plant performance under abiotic stress remain largely unexplored. Here, we integrated multi-omics data in six Sorghum bicolor accessions under water-limiting conditions in the field to explore the relationship between RCMs and drought response. Within a stress and photosynthesis-associated gene co-expression module, we identified SbDUS2, a member of family of enzymes, conserved across eukaryotes, which catalyzes the reduction of uracil to dihydrouridine (DHU) on RNA molecules. DHU-modified transcripts in this module were enriched for photosynthetic functions and showed strong correlation with photosynthetic traits. To elucidate the function of this RCM, we characterized loss of function dus2 mutants in the genetic model, Arabidopsis thaliana. Under control conditions, these DHU-deficient mutants exhibited impaired germination and delayed development. Furthermore, when exposed to heat or water-limiting conditions, these mutants showed significantly reduced net CO2 assimilation and survival. Using multiple transcriptome-wide RNA stability assays, we demonstrated that transcripts associated with lower DHU level in a dus2 background generally exhibited increased stability compared to Col-0 controls. Particularly, lack of DUS2 led to the hyperstability of photosynthesis-related transcripts, impeding their turnover and likely preventing proper photosynthetic acclimation during stress. We propose a model based on these data where DHU acts as a critical post-transcriptional regulator marking mRNAs for rapid turnover under stress, highlighting an overlooked regulatory layer contributing to plant resilience.

Invasive plants threaten global ecosystems, yet traditional analyses of functional traits cannot fully explain their dominance over co-occurring natives. Metabolomics offers insights into plant invasions, but single-technique studies often miss critical biochemical mechanisms. We employ a multimodal metabolomics approach (¹H NMR, LC MS/MS, FT-ICR-MS, and MALDI-MSI) to investigate the biochemical basis of Lehmann lovegrass (Eragrostis lehmanniana) invasion in semi-arid North America, comparing it with a co-occurring native grass, Arizona cottontop (Digitaria californica). Our analysis reveals three metabolomic traits of Lehmann lovegrass compared to Arizona cottontop: Enhanced nitrogen allocation in shoots, reduced defensive metabolites in root layers; and increased root exudate modulation under stress conditions. These traits suggest Lehmann lovegrass succeeds through adaptation to increasing aridity rather than direct competition, demonstrating adaptation to nutrient-poor environments and high phenotypic plasticity in response to increasing aridity. This integrated metabolomic approach provides new mechanistic insights into invasion ecology and plant adaptation under environmental change.

We present draft genome sequences of five endophytic fungi from Lactuca serriola L., a wild relative of cultivated lettuce: Alternaria postmessia, two Alternaria alternata variants, Fusarium falciforme, and Aspergillus terreus. Isolates were obtained from field-grown plants in Arizona, USA, and whole-genome sequenced using Illumina NovaSeq 6000 at ≥50× coverage.

Plant microbiomes are increasingly acknowledged both as extensions of plant characteristics and as biological factors that influence plant traits important for nutrition and resilience. In the context of global change, manipulation of microbiomes has the potential to complement genetic approaches to enhance crop health and productivity under rising heat and drought stress. Understanding the factors that influence microbial communities and their variation across plant genotypes is essential for developing such capabilities. We employed metabarcoding via the Illumina sequencing platform to investigate microbial communities that occur within healthy leaves and roots of 12 lettuce genotypes (Lactuca sativa L.) grown in a desert agriculture environment. We detected diverse foliar- and root-endophytic fungi and bacteria in field-grown lettuce at the Maricopa Agricultural Center (Arizona, USA). The composition of microbial community structure varied with foliar chemistry and root traits. Notably, levels of zinc and other beneficial nutrients in the leaves were strongly linked with specific endophytes. These results document the lettuce microbiome in desert farming and provide insights into endophytes in lettuce leaves, which are noteworthy because they remain after washing and are regularly ingested.

Nitrogen bioavailability frequently constrains primary production in the Arctic with tundra communities vulnerable to ecological and metabolic disruption from climate variability. Diazotrophs associated with lichens and mosses are the primary source of new nitrogen (N) in the Arctic. We made 526 laboratory measurements of biological nitrogen fixation (BNF) in 272 lichens and 254 bryophytes representing 23 and 39 genera, respectively. These samples were collected from 49 tundra sites across the Arctic. We found 65 % of lichen and 44 % of bryophyte genera analyzed fixed N. We also identified potentially new cryptogam-diazotroph relationships in the lichen genera Asahinea, Nephromopsis and Thamnolia and the bryophyte genera Dicranoweisia and Amphidium. We found that while over 95 % of individual bryophyte samples fixed N within three months of storage, this dropped to less than 15 % after one year at room temperature. Individual lichen samples maintained a stable ~45 % fixation rate over nearly two years of frozen storage. Our experiments highlight the complexity in establishing robust BNF measurements required for model simulations.

Fungal endophytes and epiphytes associated with plant leaves can play important ecological roles through the production of specialized metabolites encoded by biosynthetic gene clusters (BGCs). However, their functional capacity, especially in crops like lettuce (Lactuca sativa L.), remains poorly understood. We sequenced the genomes of nine fungal isolates, representing Fusarium sp., Fulvia sp., Alternaria alternata, and Alternaria postmessia, from leaves of lettuce grown under field conditions in Arizona, USA. We used antibiotics and secondary metabolite analysis shell (antiSMASH) and the database for automated carbohydrate-active enzyme annotation (dbCAN3), to predict BGCs and carbohydrate-active enzymes (CAZymes) for each strain, and then compared them to conspecific strains from other environments and substrates. Foliar lettuce-associated fungi featured 39–95 BGCs per genome, with substantial overlap between isolates occurring in association with lettuce leaves vs. from other substrates. Species identity was a significant determinant of BGC count, while host type, isolation source, and lifestyle were not. Several BGCs, including those for alternariol and 1,3,6,8-Tetrahydroxynaphthalene (T4HN), showed 100

Lorchels, also known as false morels (Gyromitra sensu lato), are iconic due to their brain-shaped mushrooms and production of gyromitrin, a deadly mycotoxin. Molecular phylogenetic studies have hitherto failed to resolve deep-branching relationships in the lorchel family, Discinaceae, hampering our ability to settle longstanding taxonomic debates and to reconstruct the evolution of toxin production. We generated 75 draft genomes from cultures and ascomata (some collected as early as 1960), conducted phylogenomic analyses using 1542 single-copy orthologs to infer the early evolutionary history of lorchels, and identified genomic signatures of trophic mode and mating-type loci to better understand lorchel ecology and reproductive biology. Our phylogenomic tree was supported by high gene tree concordance, facilitating taxonomic revisions in Discinaceae. We recognized 10 genera across two tribes: tribe Discineae (Discina, Maublancomyces, Neogyromitra, Piscidiscina, and Pseudodiscina) and tribe Gyromitreae (Gyromitra, Hydnotrya, Paragyromitra, Pseudorhizina, and Pseudoverpa); Piscidiscina was newly erected and 26 new combinations were formalized. Paradiscina melaleuca and Marcelleina donadinii formed their own family-level clade sister to Morchellaceae, which merits further taxonomic study. Genome size and CAZyme content were consistent with a mycorrhizal lifestyle for the truffle species (Hydnotrya spp.), whereas the other Discinaceae genera possessed genomic properties of a saprotrophic habit. Lorchels were found to be predominantly heterothallic—either MAT1-1 or MAT1-2—but a single occurrence of colocalized mating-type idiomorphs indicative of homothallism was observed in Gyromitra esculenta strain CBS101906 and requires additional confirmation and follow-up study. Lastly, we confirmed that gyromitrin has a phylogenetically discontinuous distribution, having been detected exclusively in two distantly related genera (Gyromitra and Piscidiscina) belonging to separate tribes. Our genomic dataset will facilitate further investigations into the gyromitrin biosynthesis genes and their evolutionary history. With additional sampling of Geomoriaceae and Helvellaceae—two closely related families with no publicly available genomes—these data will enable comprehensive studies on the independent evolution of truffles and ecological diversification in an economically important group of pezizalean fungi.