Environmental Microbiome

Drylands represent a significant part of the Earths surface and include essential and vulnerable ecosystems for the global ecological balance. The Caatinga, with its unique biodiversity adapted to the extreme conditions of this semi-arid region, offers a valuable opportunity to expand our knowledge about these ecosystems. Here, this work reveals the high microbial diversity in the soil and rhizosphere of the Caatinga, with the roots presenting more specialized communities. Bacteria such as Bacilli, Alphaproteobacteria and Firmicutes excelled in critical functions such as nutrient cycling. Interplant differences suggested the influence of root exudates. The metagenomic study of interactions between microorganisms in the rhizosphere of selected plants revealed microbial biodiversity and contributed to our understanding of nutrient cycling, plant growth and resistance to water stress. In addition, they demonstrate biotechnological potential to address global challenges such as desertification and food security.

AbstractThe use of plant-derived peptides as resistance inducers provides innovative and potentially environmentally friendly methods to safeguard crop health. Although their use is increasing rapidly, their broader impact, particularly on plant-associated microbiomes, remains underexplored. This study investigated the influence of a promising immunomodulatory peptide derived from the tomato defense protein prosystemin on the tomato phyllosphere microbiome. We applied the peptide via foliar spray biweekly to simulate common agricultural practices from the planting stage to two months post-germination. Using a shotgun metagenomics approach combined with qPCR, we identified bacterial communities of high abundance (up to 4.6 log10 bacterial 16S rRNA copies) and high diversity, mainly comprising Actino-, Alphaproteo- and Gammaproteobacteria, on all tomato leaves. The peptide treatment led to a significant and targeted shift in the bacterial community, characterized by reduced diversity and network complexity and species loss, i.e., Streptomyces. The enrichment was predominantly observed in bacterial genera such as Acinetobacter, Sphingobium, Sphingomonas, Brevundimonas, and Massilia, which are typically associated with improved plant growth and stress resilience. Intriguingly, shifts in both taxonomic and functional profile upon peptide application aligned with patterns typically observed during plant defense activation, involving jasmonic acid and related secondary metabolites. Members of the Sphingomonadaceae family, particularly Sphingobium yanoikuyae, have emerged as potential drivers of such microbial dynamics, likely adapting to plant upregulated defenses and potentially supporting its resilient phenotype. Overall, in addition to its well-established role in combating tomato pests and necrotrophic fungi, the prosystemin-derived peptide paves the way for disentangling peptide-induced resistance and its interplay with the plant microbiota.

The wild legume Lotus japonicus engages in mutualistic symbiotic relationships with arbuscular mycorrhiza (AM) fungi and nitrogen-fixing rhizobia. Using plants grown in natural soil and community profiling of bacterial 16S rRNA genes and fungal internal transcribed spacers (ITS), we examined here the role of the Lotus symbiosis genes RAM1, NFR5, SYMRK, and CCaMK in structuring bacterial and fungal root-associated communities. We found host genotype-dependent community shifts in the root and rhizosphere compartments that were mainly confined to bacteria in nfr5 or fungi in ram1 mutants, whilst symRK and ccamk plants displayed major changes across both microbial kingdoms. We observed in all AM mutant roots an almost complete depletion of a large number of Glomeromycota taxa that was accompanied by a concomitant enrichment of Helotiales and Nectriaceae fungi, suggesting compensatory niche replacement within the fungal community. A subset of Glomeromycota whose colonization is strictly dependent on the common symbiosis pathway was retained in ram1 mutants, indicating that RAM1 is dispensable for intraradical colonization by some Glomeromycoyta fungi. However, intraradical colonization by certain Burkholderiaceae taxa is dependent on AM root infection, thereby revealing a microbial interkingdom interaction. Our findings imply a broad role for Lotus symbiosis genes in structuring the root microbiota.

Heat stress is a major limiting factor for soybean productivity worldwide. Recent studies have highlighted the critical role of the plant microbiome in enhancing plant resilience to heat stress. However, our understanding of the molecular and physiological mechanisms underlying root-microbiome interactions under heat stress remains limited. To elucidate the role of native soil microbes in the heat tolerance of soybean genotypes, we analyzed rhizosphere bacterial and fungal communities via 16S rRNA and ITS sequencing, and characterized root metabolites and anatomical traits in response to microbiome composition and heat stress. Soybean plants were grown under controlled conditions in either natural soil containing native microbiota or in microbiome-disturbed soil (via 3-hour autoclaving), under both optimal and elevated temperature regimes. Alpha and beta diversity analyses revealed significant microbial shifts between treatments. Distinct clustering of bacterial, fungal, and metabolite profiles was observed under high temperature and microbial disturbance. Nodule-forming bacteria such as Rhizobium and Janthinobacterium were markedly suppressed, and belowground traits exhibited sensitivity, with significantly reduced nodule numbers and nodulation efficiency under high temperature and soil microbial perturbation. Non-targeted root metabolomics identified 372 differentially accumulated metabolites. Integrative multi-omics analysis revealed associations between metagenomic profiles, metabolite levels, and nitrogen-fixation traits, implying a coordinated modulation of root physiological processes. These findings contribute to a growing understanding of how heat stress interacts with rhizosphere microbial communities and may support future efforts in breeding climate-resilient soybean cultivars.

BackgroundMicrobial communities in the rhizosphere are key drivers of plant immunity, mediating plant responses to stress. Under specific stresses plants are capable of recruiting beneficial microorganisms into their rhizosphere with the potential to alleviate these stresses. Among these stresses, herbivorous pests remain a major agricultural challenge. Despite this, the impact of leaf herbivory on root-associated microbiomes, and how this impact can shape plant defense phenotypes are still understudied. In this study, our main objective was to determine the extent to which leaf herbivory affects the rhizosphere microbiome, and whether and how these herbivory-induced changes modulate plant defense phenotypes through plant-soil feedback. To that end, we designed a two-phase assay in which we challenged sunflower (Helianthus annuus L.) with Spodoptera exigua and later tested the effect of the microbial legacy after infestation on sunflower defense phenotype, considering resistance and tolerance as major drivers. ResultsWe found that herbivory triggered significant changes in the bacteriome structure and dynamics, and microbiome functional profile, while effects on mycobiome were comparatively less pronounced. Under herbivory, several bacterial taxa and functional groups were enriched, the bacterial co-occurrence network was more complex and assembly processes were slightly more stochastic. Furthermore, after evaluating the plant-soil feedbacks of herbivory-induced microbiomes we observed no effect on plant resistance proxies such as herbivore growth and survival, and leaf phenolic and flavonoid content. We did observe differences on tolerance proxies, while plants grown on herbivore-challenged microbiome were overall smaller, the biomass loss to herbivory was significantly lower while the elemental nutrient content and photosynthetic pigments content was enhanced. ConclusionsOur study demonstrates that insect herbivory by S.exigua reshapes sunflower rhizosphere microbiome and generates a soil legacy that promotes herbivory tolerance on subsequent plant generations. This highlights the broader potential of microbiome-mediated plant-soil feedbacks in shaping plant adaptation to herbivory.

Leaves are primarily responsible for the plants photosynthetic activity. Thus, changes in the phyllosphere microbiota, which includes deleterious and beneficial microbes, can have far reaching effects on plant fitness and productivity. In this context, identifying the processes and microorganisms that drive the changes in the leaf microbiota over a plants lifetime is crucial. In this study we analyzed the temporal dynamics in the leaf microbiota of Arabidopsis thaliana, integrating both compositional changes and changes in microbe-microbe interactions via the study of microbial networks. Field-grown Arabidopsis were used to follow leaf bacterial, fungal and oomycete communities, throughout the plants growing season (extending from November to March), over three consecutive years. Our results revealed the existence of conserved time patterns, with microbial communities and networks going through a stabilization phase (decreasing diversity and variability) at the beginning of the plants growing season. Despite a high turnover in these communities, we identified 19 core taxa persisting in Arabidopsis leaves across time and plant generations. With the hypothesis these microbes could be playing key roles in the structuring of leaf microbial communities, we conducted a time-informed microbial network analysis which showed core taxa are not necessarily highly connected network hubs and hubs alternate with time. Our study shows that leaf microbial communities exhibit reproducible dynamics and patterns, suggesting it could be possible to predict and drive these microbial communities to desired states.

Striga hermonthica (Striga) is a parasitic weed that severely affects sorghum yields in sub-Saharan Africa. Recent studies highlighted the soil microbiomes potential to suppress Striga through interference with specific stages in its life cycle. In this study, meta-analysis of 48 Ethiopian field soils revealed that microbial communities and their interactions with soil physico-chemical properties correlated with Striga field occurrence. Striga infestation of sorghum and soil seedbank levels were negatively correlated with clay content and the nutrients potassium, sulfur, calcium, and carbon. Microbiome analyses indicated that fungal communities were more responsive than bacteria to changes in Striga infestation and seedbank levels, with distinct microbial compositions even in soils where Striga was not detected. Specific fungal and bacterial genera showed both positive and negative correlations with Striga measures, but patterns rarely held across taxonomic levels, highlighting the complexity of microbiome-Striga interactions. To begin to validate these correlations, we tested an isolate from the fungal genus Neocosmospora, which negatively correlated with the Striga seedbank, and showed that this isolate promotes Striga seed germination in vitro, suggesting potential for biological control of Striga. The data and analysis methods are integrated and shared in a public Shiny App for broader analysis and continued research on soil-Striga interactions.

Plant root microbiomes play a central role in plant health, yet their responses to viral infection remain poorly understood. Here, we investigated how Turnip mosaic virus (TuMV) alters root-associated bacterial and fungal communities in two Arabidopsis thaliana genotypes (Col-0 and Mar-12) grown in natural soils. Using 16S and ITS amplicon sequencing, we assessed changes in diversity, taxonomic composition, enriched microbial taxa, and co-occurrence network structure to distinguish between plant-mediated recruitment ("cry-for-help") and pathogen-induced dysbiosis. TuMV infection caused a pronounced reduction in bacterial diversity and a restructuring of bacterial community composition, whereas fungal communities remained largely stable. Viral infection also led to genotype-specific shifts in enriched bacterial genera, with opportunistic and stress-tolerant taxa proliferating differently in each genotype. Despite the initial perturbation, bacterial networks recovered connectivity and, in some cases, reached higher complexity than those of healthy plants, indicating strong microbial resilience. Together, these results reveal that TuMV infection acts as a selective filter on bacterial, but not fungal, root communities and that the surviving taxa can reorganize into functional networks. Our study provides one of the most comprehensive assessments of virus-induced microbiome restructuring and highlights the importance of host genotype in shaping microbial responses to biotic stress.

BackgroundThe association between plants and soil microbes is critical for both soil and plant health. Studies have shown that introducing beneficial microbial inoculants can shape the soil microbiome community for plant health. Among these microbes, mycorrhizal fungi play a well-documented role in enhancing nutrient uptake in plants. Ergothioneine (ERGO), a compound well-known for its anti-inflammatory and antioxidant properties, has been linked to increased longevity in various model systems and its significance for human health. However, neither animals nor plants contain ERGO biosynthetic pathways, which are limited to fungi, including and some species of bacteria, including Actinomyceota, Cyanobacteria, and Methylobacteria. Though the leading dietary sources of ERGO for humans are fungi in the form of mushrooms or fermented foods, biofortification of crops by promoting the production and uptake of ERGO from microbial sources in the soil has promise for enhancing nutritional quality and public health outcomes. ResultsThis study explores the of interaction between soil ERGO application and arbuscular mycorrhizal fungi (AMF) in plant-symbiotic relationships to increase the ERGO content in the staple crop wheat (Triticum aestivum). We investigate how ERGO supplementation, both alone and in combination with AMF, influences the wheat root and soil microbiome in a greenhouse experiments. Our data shows that plants can take up ERGO in absence of AMF fungi. In addition, treatment with pure ERGO and ERGO in combination with AMF altered microbial diversity and community structure in both the rhizosphere and rhizoplane regions of wheat roots. ConclusionsOverall, our work reveals that plants can readily take up ERGO from soil, both with and without AMF presence, highlighting a broader role of ERGO in connecting soil health to human health, a connection that warrants further investigation.

The maize microbiome consists of microbes that are associated with plants, and can be shaped by the host plant, the environment, and microbial partners, some of which can impact plant performance. We used a public dataset to analyze bacteria and fungi in the soil, rhizosphere, roots, and leaves of commercial maize at 30 locations across the US. We found that both tissue type and location had significant effects on community structure and makeup, although the patterns differed in bacteria and fungi based on tissue type. We also found many differences in predicted microbial gene pathways between tissues, with location also shaping predicted functional gene profiles. We found a pattern of potential interaction between fungi and bacteria, and potential intra-kingdom mutualism, in microbiome networks. The robustness of these networks was dependent upon tissue, with endophytes in leaves and roots showing significantly higher natural connectivity. Within a tissue, this connectivity was relatively stable across locations. We identified environment and soil characteristics that may impact tissue specific microbial abundance. Sulfate level in the soil was positively correlated with Proteobacteria abundance, but negatively correlated with Firmicutes abundance in the roots and leafs. Ascomycota appears to be affected by different environmental variables in each tissue. We also identified gene functions and enzymes which may be necessary to allow microbes to transition across compartments and become endophytes.

BackgroundThe root microbiome plays a critical role in nutrient acquisition, stress tolerance and overall plant health. Rice, a staple food for more than half of the worlds population, is commonly cultivated under flooded conditions. Despite its agronomical importance, our current understanding of root-associated microbiomes in rice grown under flooded conditions is limited. On the other hand, nitrogen (N) and phosphorus (P) fertilizers are routinely applied to maximize rice yield. It is also well known that root colonization by arbuscular mycorrhizal (AM) fungi enhances mineral nutrition in plants, but whether mycorrhizal associations influence the composition of the rice root microbiome remains poorly understood. In this study, shotgun metagenomic sequencing was used to characterize the root endosphere and rhizosphere microbiomes in two temperate japonica rice varieties (cv. Bomba and JSendra) grown under flooded conditions. The impact of colonization by the AM fungus Rhizophagus irregularis on the root microbiome was investigated. ResultsRoot-associated compartments harbour distinct microbial communities in rice with bacterial taxa comprising approximately 95% of the total microbia in rice roots. At the Phylum level, the root bacteriome was primarily composed of Pseudomonadota (Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria) followed by Actinomycetota. The fungal microbiome was dominated by Ascomycota (Sordariomycetes, Eurotiomycetes and Dothideomycetes) and Basidiomycota. Not only the root compartment, but also the host genotype can shape the root microbiome. Recruitment of specific microorganism mainly occurs at the species level. Genotype-specific and compartment-specific associations of microbial species in mycorrhizal rice roots were also observed supporting that root colonization by an AM fungus contributes to variations in the root microbiome. Further, key microbial species primarily associated to methane production and nutrient cycling (e.g. Phosphate Solubilizing Bacteria and Nitrogen cycling bacteria) colonizing root compartments in each rice genotype and mycorrhizal condition are described. ConclusionsThe rice genotype, root compartment and mycorrhizal condition markedly influence the microbiome in roots of rice plants growing in flooded rice fields. These findings illustrate the potential of the plant to shape its associated root microbiome, thus, offering valuable insights for the development of microbiome-based strategies to improve growth and performance in rice plants under flooded conditions.

Plant-associated bacteria can improve plant performance under abiotic stress, but beneficial functions in plant microbiomes may depend on defined combinations of microorganisms rather than individual isolates alone. Here, we developed a cube-based screening strategy to identify functional synthetic microbial communities (SynComs) from 135 quinoa-associated bacterial isolates while preserving combinatorial diversity and traceability of isolate-level contributions. The isolates were divided into five 27-isolate sets, each arranged as a 3 x 3 x 3 cube in which each 3 x 3 layer was defined as a 9-isolate SynCom, generating 45 SynComs in total. Screening under 100 mM NaCl identified SynCom DY1 (SCDY1) as a candidate salt stress-mitigating consortium. SCDY1 consisted of nine taxonomically diverse isolates and exhibited a multifunctional profile, including siderophore production, phosphate solubilization, carboxymethyl cellulose degradation, indole compound production, and growth under saline conditions. In Arabidopsis thaliana, SCDY1 promoted primary root elongation and biomass accumulation in a salinity-dependent manner, with the clearest effect under 120 mM NaCl, and at least a subset of constituent bacteria was recoverable from inoculated seedlings. RNA sequencing and targeted RT-qPCR indicated that SCDY1 modulated host gene expression under moderate salinity stress, with responsive genes associated with oxidative stress, water- and oxygen-related processes, phenylpropanoid biosynthesis, glutathione metabolism, and root epidermis-related processes. Root hair phenotyping further showed that SCDY1 enhanced root hair-related traits and shifted visible root hair formation closer to the root apex. These findings identify a quinoa-derived SynCom that improves plant performance under salinity stress and provide a practical, traceable framework for discovering beneficial microbial consortia from plant-associated bacterial collections. Scope statementThis manuscript fits the Research Topic "Harnessing Plant Microbiomes for Climate Resilience: From Ecological Insight to Synthetic Community Design" in Frontiers in Plant Science because it presents a traceable strategy for discovering functional synthetic microbial communities from a stress-adapted plant-associated bacterial collection. We developed a cube-based screening strategy using 135 quinoa-associated bacterial isolates and identified a nine-isolate synthetic microbial community, SCDY1, that promotes Arabidopsis growth under moderate salinity stress. The study integrates microbiological screening, characterization of plant growth-promoting traits, bacterial re-isolation, plant growth phenotyping, RNA-seq, RT-qPCR, and root hair phenotyping. These analyses link SCDY1 treatment to salinity-dependent growth promotion, recoverable bacterial members, stress- and redox-associated transcriptional changes, phenylpropanoid-related responses, and modulation of root epidermal phenotypes. By connecting a defined SynCom with host transcriptional and root epidermal responses, this work advances understanding of beneficial plant-microbe interactions under salt stress. The cube-based design also provides a practical and traceable framework for discovering functional SynComs from large plant-associated bacterial collections, which should be of interest to researchers studying plant symbiosis, microbiome engineering, abiotic stress tolerance, and sustainable crop improvement.

BackgroundPlant-microbe interactions in two root compartments - the rhizosphere and endosphere - play vital roles in maintaining plant health and ecosystem dynamics. The microbial communities in these niches are shaped in complex ways by factors including the plants developmental stage and cultivar, and the compartment where the interactions occur. Different plant cultivars provide distinct nutritional and ecological niches and may selectively enrich specific microbial populations through the secretion of root exudates. This gives rise to complex and dynamic plant-microbe interactions; some cultivars promote the recruitment of beneficial symbionts while others may deter pathogens. To clarify these processes, this work investigated the structure of the endosphere and rhizosphere microbial communities of wild type finger millet and five domesticated cultivars across two plant developmental stages. ResultsOur results showed that the plant developmental stage, compartment, and cultivar have varying degrees of impact on root-associated microbiomes. The dominant bacterial phyla in all samples were Proteobacteria, Actinobacteria, and Bacteroidetes, while the dominant fungal phyla were Ascomycota and Basidiomycota. All of these phyla exhibited pronounced variations in abundance. In general, an increased abundance of Actinobacteria in the endosphere was accompanied by a reduced abundance of Proteobacteria. The most pronounced changes in microbial community structure were observed in the rhizosphere during the flowering stage. Changes in the microbiome patterns of the rhizosphere were driven predominantly by the genus Pseudomonas. Moreover, the host plants developmental stage strongly influenced the microbial communities, suggesting that plants can recruit specific taxa based on their need for particular soil consortia. ConclusionsOur results show that both host developmental stage and domestication strongly affect the assembly and structure of the plant microbiome. Moreover, plant root compartments can selectively recruit specific taxa from associated core microbial communities to fulfill their needs in a manner that depends on both the plants developmental stage and the specific root compartment that is involved. These findings show that deterministic selection pressures exerted by plants during their growth and development can significantly affect their microbial communities and have important implications for efforts to create tools for manipulating the microbiome to sustainably improve primary productivity.

Due to climate change, drought frequencies and severities are predicted to increase across the United States. Plant responses and adaptation to stresses depend on plant genetic and environmental factors. Understanding the effect of those factors on plant performance is required to predict the species responses to environmental change. We used reciprocal gardens planted with distinct regional Andropogon gerardii ecotypes adapted to dry, mesic, and wet environments to characterize their rhizosphere communities using 16S rRNA metabarcode sequencing. Even though the local microbial pool was the main driver of these rhizosphere communities, the significant plant ecotype effect highlighted active microbial recruitment in the rhizosphere driven by ecotype or plant genetic background. Our data also suggest that ecotypes were more successful in recruiting rhizosphere community members unique to their local homesites, supporting the "home field advantage" hypothesis. These unique homesite microbes may represent microbial specialists that are linked to plant stress responses. Further, our data support ecotypic variation in the recruitment of congeneric but distinct bacterial variants, highlighting the nuanced effects of plant ecotypes on the rhizosphere microbiome recruitment. Our results should facilitate expanded studies on understanding the complexity of plant host interactions with local soil microbes and identification of functional potential of recruited microbes. Our study has the potential to aid in predicting ecosystem responses to climate change and the impact of management on restoration practices. ImportanceIn this study, we used reciprocal gardens located across a sharp precipitation gradient to characterize rhizosphere communities of distinct dry, mesic, and wet regional Andropogon gerardii ecotypes. We used16S rRNA amplicon sequencing and focused oligotyping analysis and showed that even though the location was the main driver of the microbial communities, ecotypes could potentially recruit distinct bacterial populations. We showed that different A. gerardii ecotypes were more successful in overall community recruitment and recruitment of microbes unique to the "home" environment, when growing at their "home site". We found evidence for "home field advantage" interactions between the host and associated rhizobiomes, and the capability of ecotypes to recruit specialized microbes that were potentially linked to plant stress responses. Our study provides insights into the understanding of factors effecting the plant adaptation, improving management strategies, and predicting of the future landscape under the changing climate.

Benefits leaf bacterial communities provide to plant hosts are reduced by external stress. Understanding how plant hosts impact phyllosphere community assembly, how microbes influence plant traits, and how this interaction changes under stress will advance our insight into the evolutionary relationship between plants and their microbial communities. We investigated phyllosphere community assembly change over time, between host species, and under drought stress on three native temperate grasses and three non-native tropical grasses. By growing them together, effects of host geography and differences in environmental variables were eliminated allowing us to test evolutionary history on community assembly. We found evidence of phylosymbiosis which increased significantly under drought stress, indicating phyllosphere communities and their response to stress relate to grass species phylogeny. We also show native temperate grasses displayed stronger cophylogenetic relationships between grass hosts and their microbial communities and had increased selection by host species over time compared to non-native tropical hosts. Interestingly, the functional marker gene nifH, though differentially present on all host species was not susceptible to drought. The evidence of shared evolutionary history, presence of functionally important bacteria, and responses to drought suggest that microbial communities are important plant traits that coevolve alongside their plant hosts.

Agricultural soils harbor rich and diverse microbial communities that have a deep influence on soil properties and productivity. Large scale studies have shown the impact of environmental parameters like climate or chemical composition on the distribution of bacterial and fungal species. Comparatively, little data exists documenting how soil microbial communities change between different years. Quantifying the temporal stability of soil microbial communities will allow us to better understand the relevance of the differences between environments and their impact on ecological processes on the global and local scale. We characterized the bacterial and fungal components of the soil microbiota in ten vineyards in two consecutive years. Despite differences of species richness and diversity between the two years, we found a general stability of the taxonomic structure of the soil microbiota. Temporal differences were smaller than differences due to geographical location, vineyard land management or differences between sampling sites within the same vineyard. Using machine learning, we demonstrated that each site was characterized by a distinctive microbiota, and we identified a reduced set of indicator species that could classify samples according to their geographic origin across different years with high accuracy. ImportanceThe temporal stability of the soil microbiota is important to understand the relevance of the differences that are found in response to a variety of environmental factors. By comparing fungal and bacterial microbiota from samples collected in the same sites in two consecutive years, we found a remarkable stability of both components, with characteristic differences between bacteria and fungi. Our work fills an important gap toward the definition of a microbial cartography of agricultural soils.

The plant microbiome protects plants from stresses, including pathogen attacks. However, identifying microbes that provide plant protection remains challenging in complex microbial communities. In this study, we analysed samples from natural A. thaliana populations, including both plants infected with the pathogenic oomycete Albugo laibachii and uninfected plants, over six years. Using machine learning classification models, we achieved high accuracy in distinguishing infected and uninfected plants based on microbiome abundance. We identified 80 key taxa associated with health and disease. Among the health-associated microbes (HCom), we selected bacteria, fungi, and cercozoa that effectively reduced pathogen presence in co-inoculation assays. In comparison, disease-associated microbes (DCom) were less effective in conferring protection. Our findings highlight the complexity of plant-microbe interactions and advance our understanding of microbial roles in plant disease ecology. By integrating ecological insights with machine learning, we take a significant step towards designing robust microbial consortia that enhance plant resilience against pathogens.

Coastal salt flats, locally known as Sabkhas, are hypersaline, alkaline desert ecosystems that impose extreme abiotic stress on microbial and plant life. Despite their ecological significance, plant-associated microbiomes in these habitats remain poorly characterized. In this study, we investigated the bacterial communities of native halophytes across three sabkha sites in southern Morocco using an integrated culture-independent and culture-dependent framework. Soil physicochemical analyses revealed strong gradients in salinity and ionic composition, along with consistently alkaline pH across sites. These conditions strongly structured bacterial assemblage: alpha diversity declined progressively from bulk soil to rhizosphere soil, root and shoot; and beta diversity showed clear compartmental separation driven by environmental factors. Canonical Correspondence Analysis identified electrical conductivity (EC), Na2O, K2O and carbonate fractions as the main abiotic drivers. Across plant species, bacterial communities converged toward a stable halophilic core microbiome dominated by Halomonas, Kushneria and Marinococcus, with 66% of ASVs shared across compartments. Host identity played a secondary role, as environmental filtering overshadawed host-specific associations. Culture-dependent isolation recovered 19 halophilic and halotolerant bacterial strains, mainly, Halomonas, Idiomarina, Marinobacter, Psychrobacter, Planomicrobium and Bac illus, tolerating up to 25% NaCl. The strong concordance between cultured isolates and metabarcoding profile confirms that dominant halophilic lineages are both ecologically robust and readily culturable. Together, these findings demonstrate that sabkha plant microbiomes are primarily shalped by deterministic abiotic filtering and harbor resilient, stress-adapted bacterial communities. Sabkhas thus represent promising reservoirs of halophilic microbes with potential applications in saline agriculture and improving crop resilience under extreme environmental conditions. ImportanceCoastal salt flats (sabkhas) are among the most extreme terrestrial environments, characterized by high salinity, alkalinity, and limited water availability. As soil salinization expands worldwide, understanding how life persists in such habitats is increasingly important for sustainable agriculture. This study shows that sabkha ecosystems impose strong environmental filtering on plant-associated bacterial communities, leading to highly structured microbiomes across soil, root, and shoot compartments. Despite differences among sites and plant species, bacterial communities converged toward a shared halophilic core microbiome, dominated by salt-adapted genera that are resilient to extreme ionic stress. Importantly, many of these dominant bacteria were readily culturable, highlighting sabkhas as accessible reservoirs of stress-tolerant microbes. Our findings demonstrate that abiotic conditions outweigh plant identity in shaping microbiome assembly under extreme stress and reveal sabkha halophytes as valuable natural models for discovering microbes with potential applications in saline agriculture, soil restoration, and crop resilience in salt-affected environments.

Aridification and climate stress threaten global plant productivity, but the survival strategies of desert plants remain only partly understood. In this study, we examined how the microbiome of Citrullus colocynthis, a hardy desert cucurbit valued for its ecological and medicinal benefits, may influence the plants ability to withstand harsh conditions. Using 16S rRNA amplicon sequencing, shotgun metagenomics, and culture-based methods, we analyzed microbiome changes across two regions of the UAE during the rainy and dry seasons. Leaf and root bacterial communities showed clear seasonal shifts, with greater richness in winter and higher evenness in summer, while soil microbiomes remained stable. Dominant bacterial groups, Actinomycetota and Pseudomonadota, varied seasonally, indicating trade-offs between stress tolerance and metabolic flexibility. Fungal communities (mainly Ascomycota and Basidiomycota) were stable at the phylum level but reorganized by order between seasons; archaeal populations showed little change. Among 24 cultured bacterial isolates, including three potential new species, we identified multiple stress tolerance and plant growth-promoting traits. Genomic data revealed biosynthetic clusters for antimicrobial and stress-protective functions, as well as adaptation genes in Pseudomonas orientalis. These results demonstrate that the dynamic, functionally diverse microbiome of C. colocynthis enhances its resilience to desert stress, offering potential for arid-land agriculture.

In a field experiment we investigated the influence of the environmental filters soil type and plant species identity on rhizosphere community assembly of Cercozoa, a dominant group of (mostly bacterivorous) soil protists. The experiment was set up with two plant species, lettuce and potato, grown in an experimental plot system with three contrasting soils. Plant species (14%) and rhizosphere origin (vs. bulk soil) with 13%, together explained four times more variation in cercozoan beta diversity than the three soil types (7% explained variation in beta diversity). Our results clearly confirm the existence of plant species-specific protist communities. Network analyses of bacteria-Cercozoa rhizosphere communities identified scale-free small world topologies, indicating mechanisms of self-organization. While the assembly of rhizosphere bacterial communities is bottom-up controlled through the resource supply from root (secondary) metabolites, our results support the hypothesis that the net effect may depend on the strength of top-down control by protist grazers. Since grazing of protists has a strong impact on the composition and functioning of bacteria communities, protists expand the repertoire of plant genes by functional traits, and should be considered as protist microbiomes in analogy to bacterial microbiomes. HighlightMicrobiomes of rhizosphere protists are plant species-specific and tightly co-evolving with their bacterial prey, thereby extending and modifying the functional repertoire of the bacterial-plant symbiosis.