Phytobiomes Journal

Microbes in floral nectar can impact both their host plants and floral visitors, yet little is known about the nectar microbiome of most pollinator-dependent crops. In this study, we examined the abundance and composition of the fungi and bacteria inhabiting Vaccinium spp. nectar, as well as nectar volume and sugar concentrations, hypothesizing that nectar traits and microbial communities would vary between plants. We compared wild V. myrsinites with two field-grown V. corymbosum cultivars collected from two organic and two conventional farms. Differences in nectar traits and microbiomes were identified between V. corymbosum cultivars but not Vaccinium species. The microbiome of cultivated plants also varied greatly between farms, whereas management regime had only subtle effects, with higher fungal populations detected under organic management. Nectars were hexose-dominant, and sugars were depleted in nectar with higher cell densities. Bacteria were more common than fungi in blueberry nectar, although both were frequently detected and co-occurred more often than would be predicted by chance. Cosmopolitan blueberry nectar microbes that were isolated in all plants, including Rosenbergiella sp. and Symmetrospora symmetrica, were identified. This study provides the first systematic report of the blueberry nectar microbiome, which may have important implications for pollinator and crop health. One-sentence summaryParallel analysis of blueberry crops and a wild relative offers insight into the impacts of management and domestication on the nectar microbiome O_FIG O_LINKSMALLFIG WIDTH=183 HEIGHT=200 SRC="FIGDIR/small/556904v1_ufig1.gif" ALT="Figure 1"> View larger version (62K): org.highwire.dtl.DTLVardef@15f36caorg.highwire.dtl.DTLVardef@63496org.highwire.dtl.DTLVardef@1667a6eorg.highwire.dtl.DTLVardef@eff26e_HPS_FORMAT_FIGEXP M_FIG C_FIG

Premise: Endophytic plant-microbe interactions range from mutualistic relationships that confer important ecological and agricultural traits to neutral or quasi-parasitic relationships. In contrast to root-associated endophytes, the role of environmental and host-related factors for acquiring leaf endophyte communities remains relatively unexplored. Here we assess leaf endophyte diversity to test the hypothesis that membership of these microbial communities is driven primarily by abiotic environment and host phylogeny. Methods: We used a broad geographic coverage of North America in the genus, Heuchera (Saxifragaceae). Bacterial and fungal communities were characterized with 16S and ITS amplicon sequencing, using QIIME2 to call operational taxonomic units and calculate species richness, Shannon diversity, and phylogenetic diversity. We assembled environmental predictors for microbial diversity at collection sites including latitude, elevation, temperature, precipitation, and soil parameters. Results: We find differing assembly patterns for bacterial and fungal endophytes; we found that only host phylogeny is significantly associated with bacteria, while geographic distance alone was the best predictor of fungal community composition. Species richness and phylogenetic diversity are very similar across sites and species, with only fungi showing a response to aridity and precipitation for some metrics. Unlike what has been observed with root-associated microbial communities, in this system microbes show no relationship with pH or other soil factors. Conclusions: Host phylogeny and geographic distance independently influence different microbial communities, while aridity and precipitation determine fungal diversity within leaves of Heuchera. Our results indicate the importance of detailed clade-based investigation of microbiomes and the complexity of microbiome assembly within specific plant organs.

BackgroundOne of the biggest developments of wheat domestication was the development of semi-dwarf cultivars that respond well to fertilisers and produce higher yields without lodging. Consequently, this change has also impacted the wheat microbiome, often resulting in reduced selection of taxa and a loss of network complexity in the rhizospheres of semi-dwarf cultivars. Given the importance of rhizosphere microbiomes for plant health and performance, it is imperative that we understand if and how these changes have affected their function. Here, we use shotgun metagenomics to classify the functional potential of prokaryote communities from the rhizospheres of tall and semi-dwarf cultivars to compare the impact of wheat dwarfing on rhizosphere microbiome functions. ResultsWe found distinct taxonomic and functional differences between tall and semi-dwarf wheat rhizosphere communities and identified that semi-dwarf wheat microbiomes were less distinct from bulk soil communities. Of the 113 functional genes that were differentially abundant between tall and semi-dwarf cultivars, 95 % were depleted in semi-dwarf cultivars and 65 % of differentially abundant reads best mapped to genes involved in staurosporine biosynthesis (antibiotic product), plant cell wall degradation (microbial mediation of plant root architecture, overwintering energy source for microbes) and sphingolipid metabolism (signal bioactive molecules). ConclusionsOverall, our findings indicate that green revolution breeding has developed wheat cultivars with a reduced rhizosphere effect. The consequences of this are likely detrimental to the development of microbiome-assisted agriculture which will require a strong rhizosphere selective environment for the establishment of a beneficial plant root microbiome. We believe our results are of striking importance and highlight that implementation of microbiome facilitated agriculture as part of a sustainable crop production strategy will require an overhaul of wheat breeding programmes to consider plant-microbe interactions, especially in the root environment.

Across diverse ecosystems, bacteria and their host organisms engage in complex relationships having negative, neutral, or positive interactions. However, the specific effects of leaf- associated bacterial community functions on plant growth are poorly understood. To address this gap, we explored the relationships between bacterial community function and host plant growth in the purple pitcher plant (Sarracenia purpurea). The main aim of our research was to investigate how different bacterial community functions affect the growth and nutrient content in the plant. Previous research had suggested that microbial communities may aid in prey decomposition and subsequent nutrient acquisition in carnivorous plants, including S. purpurea. However, the specific functional roles of these bacterial communities in plant growth and nutrient uptake are not well known. In this study, sterile, freshly opened leaves (pitchers) were inoculated with three functionally distinct, pre-assembled bacterial communities and effects examined over 8 weeks. Bacterial community composition and function were measured using physiological assays, metagenomics, and metatranscriptomics. Distinct bacterial functions affected plant traits; a bacterial community enriched in decomposition and secondary metabolite production traits was associated with larger leaves with almost double the biomass of control pitchers. Physiological differences in bacterial communities were supported by metatranscriptomic analysis; for example, the bacterial community with the highest chitinase activity had greater expression of transcripts associated with chitinase enzymes. The relationship between bacterial community function and plant growth observed here indicates potential mechanisms for host-associated bacterial functions to support plant health and growth. ImportanceThis study addresses a gap in understanding the relationships between bacterial community function and plant growth. We inoculated sterile, freshly opened pitcher plant leaves with three functionally distinct bacterial communities to uncover potential mechanisms through which bacterial functions support plant health and growth. Our findings demonstrate that distinct bacterial functions significantly influence plant traits, with some bacterial communities supporting more growth than in control pitchers. These results highlight the ecological roles of microbial communities in plants and thus ecosystems, and suggest potential pathways in which microbes support host plant health. This research provides valuable insights into plant-microbe interactions and effects of diverse microbial community functions.

AimsAnalysis of the microbiota associated with root nodules of five species of drought-tolerant legumes grown in Namibia. These legumes were Lablab purpureus, Vigna radiata, Vigna unguiculata, Macrotyloma uniflorum, and Vigna aconitifolia. Methods16S rRNA gene amplicon sequencing analysis and isolation of rhizobial and non-rhizobial bacterial strains from root nodules was performed. Plant growth-promoting traits were assessed on some isolates and the genomes of four rhizobial strains were sequenced. ResultsThe microbiota analysis revealed Bradyrhizobium as the most prevalent genus in the root nodules, while most of the non-rhizobial community included members of Bacillus genus. In addition, a strain of Variovorax paradoxus was also isolated from V. unguiculata, representing the first documented isolation and characterization report in Namibia. In vitro phenotypic characterization of the non-rhizobial nodule endophytes indicated that they possessed several plant growth-promoting traits. The four rhizobial strains isolated were taxonomically affiliated to the genera Bradyrhizobium and Rhizobium. Genome sequencing revealed that these strains possibly belong to novel species since they share only a limited similarity (dDDH values<70%) to already known species. Impact StatementThis study demonstrated that drought-tolerant legume species harbour microbial diversity from Namibian soil, which allowed us to increase our knowledge on plant-associated bacteria and their possible use in sustainable farming systems, as potential bioinoculants for crop production and for soil revitalization. Utilizing locally isolated bacterial strains as microbial bioinoculants maximizes their compatibility with the local conditions increasing the potential for positive effects on plant health and ecosystem functioning.

O_LIThe plant-associated microbiome has been shown to vary considerably between species and across environmental gradients. The effects of genomic variation on the microbiome within single species are less clearly understood, with results often confounded by the larger effects of climatic and edaphic variation. C_LIO_LIIn this study, the effect of genomic variation on the rhizosphere bacterial communities of maize was investigated by comparing different genotypes grown within controlled environments. Rhizosphere bacterial communities were profiled by metabarcoding the universal bacterial 16S rRNA v3-v4 region. Initially, plants from the inbred B73 line and the Ancho - More 10 landrace were grown for 12- weeks and compared. The experiment was then repeated with an additional four Mexican landraces (Apachito - Chih 172, Tehua - Chis 204, Serrano - Pueb 180 and Hairnoso de Ocho) that were grown alongside additional B73 and Ancho - More 10 genotypes. C_LIO_LIIn both experiments there were significant genotypic differences in the rhizosphere bacteria. Additionally, the bacterial communities were significantly correlated with genomic distance between genotypes, with the more closely related landraces being more similar in rhizosphere bacterial communities. C_LIO_LIDespite limited sampling numbers, here we confirm that genomic variation in maize landraces is associated with differences in the rhizosphere bacterial communities. Further studies that go beyond correlations to identify the mechanisms that determine the genotypic variation of the rhizosphere microbiome are required. C_LI

IntroductionCrop domestication has fundamentally transformed plant phenotypes through artificial selection, yet the consequences of domestication for plant-associated microbial communities across the plant-soil continuum remain poorly understood. Gap StatementWhile recent studies suggest that domestication impacts microbiome structures, the magnitude, mechanisms, and functional implications of such impacts have not been systematically quantified using controlled experimental designs that eliminate environmental confounding factors. AimTo characterize and quantify the effects of crop domestication on microbial community structure and function by comparing maize (Zea mays subsp. mays) and its wild ancestor Balsas teosinte (Zea mays subsp. parviglumis) across multiple plant compartments in an unmanipulated field setting in Mexico, maizes domestication center. MethodologyWe applied a micro-sympatric design in a natural setting to compare microbial communities between maize and Balsas teosinte across five plant compartments: bulk soil, rhizosphere, mucilage, leaves, and seeds. Full-length 16S rRNA gene sequencing was used for taxonomic characterization, Functional Annotation of Prokaryotic Taxa (FAPROTAX) and PICRUSt 2.0 were used to predict functional profiles, and network analysis was used to assess functional connectivity. ResultsCompartment identity explained 72.2% of variation in community structure, with consistent host effects across all niches (9.0%). Teosinte maintained significantly higher microbial diversity than maize across all compartments, with pronounced differences in seeds (32.0 {+/-} 1.9 vs 9.3 {+/-} 1.8 species, P < 0.01) and rhizosphere (60.3 {+/-} 5.8 vs 33.8 {+/-} 10.4 species, P < 0.01). Eighty-nine percent of predicted metabolic functions showed significant changes associated with domestication, with teosinte exhibiting enhanced nitrogen fixation (0.89 {+/-} 0.07 vs 0.44 {+/-} 0.04 in maize mucilage), siderophore production, and pathogen suppression. Network analysis revealed functional fragmentation in maize, with reduced connections (80 to 49) and lower clustering coefficients (0.62 {+/-} 0.03 vs 0.25 {+/-} 0.02, P < 0.001). ConclusionBalsas teosinte domestication fundamentally eroded microbial diversity and functional capacity in maize leading to a "domestication gap" that encompasses taxonomic loss, functional simplification, and network fragmentation, and replaced mutualistic plant-microbe partnerships with simplified microbial assemblages that may compromise crop resilience vis-a-vis a changing climate. Impact statementUnderstanding how plants select their microbial partners is crucial for enhancing agricultural productivity yet distinguishing between environmental and host genetic effects on microbiome assemblage remains challenging. Our study provides compelling evidence for host-driven microbiome assembly by comparing ancestral Balsas teosinte with derived maize growing in a common farm field in Mexico, eliminating environmental variation and experimental manipulation as confounding factors. By characterizing bacterial communities across different plant compartments, from soil to seed, we showed that each hosts genotype shaped divergent microbiome compositions despite growing in common environmental conditions. This research represents a significant step forward in understanding plant-microbe co-evolution during crop domestication and has three key implications. First, it suggests that microbiome traits were likely selected in conjunction with plant (host) traits during domestication and post-domestication selection. Second, it identifies specific bacterial communities that could be targeted for improving crop productivity and resilience. And third, it provides a methodological framework for studying host-microbe interactions in other crop-wild ancestor pairs. Our findings are particularly relevant for developing microbiome-based agricultural technologies and conservation strategies for beneficial plant-microbe interactions for deployment in traditional and modern farming systems. Data summaryThe authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.

Plants host diverse microbial communities that can be influenced by their hosts to mitigate biotic stress. Previous research demonstrated that distinct laboratory cultures of Hyaloperonospora arabidopsidis (Hpa) on Arabidopsis thaliana, consistently harbor nearly identical bacteria. In this study, we analyzed the bacterial phyllosphere communities of laboratory-grown spinach plants infected by the downy mildew pathogen Peronospora effusa (Pe). Using 16S amplicon sequencing, we identified 14 Amplicon Sequence Variants (ASVs), with diverse taxonomies, that were enriched in at least 3 out of 5 investigated Pe cultures. This small set of 14 ASVs occupied on average 6.9% of the total bacterial communities in healthy spinach plants, and 43.1% in Pe-inoculated plants. A specific Rhodococcus and a Paenarthrobacter ASV were particularly prevalent and abundant. To validate these findings outside of the laboratory, we planted a susceptible variety of spinach in 4 agricultural fields and sampled leaves from Pe-infected plants in 2 fields where this pathogen naturally occurred. Comparative microbiome analysis of diseased and healthy plants revealed significant enrichment of 16 and 31 ASVs in these 2 fields, respectively. Among these, the Paenarthrobacter ASV was enriched in one field and the Rhodococcus ASV in the other field, suggesting that disease-associated microbiota that are abundantly detected in Pe laboratory cultures are also associated with Pe-infected field plants. Additionally, we observed an overlap of ASVs that were associated with both Pe and Hpa, indicating that similar bacteria are linked to downy mildew disease across different hosts.

The European hazelnut, Corylus avellana, is one of the most economically important tree nut crops globally. The biotrophic ascomycete pathogen Anisogramma anomala, found naturally associated with wild C. americana, continues to pose a significant threat to European hazelnut production across North America. Here, metagenomics was used to examine the taxonomic and functional features of the rhizosphere microbial communities of hazelnut trees differing in their levels of resistance to A. anomala: highly tolerant Corylus americana, and resistant and susceptible Corylus avellana. No statistically significant differences in microbial alpha diversity or beta diversity were noted between the three rhizosphere groups. Compared to bulk soil, all three rhizosphere groups were enriched for the fungal phylum Basidiomycota and bacterial phylum "Candidatus Rokubacteriota". At the genus level, the bacterial genera Actinospica, Occallatibacter, and "Candidatus Sulfotelmatobacter" were under-represented, while the genus Rhizobacter was over-represented, in the resistant and susceptible C. avellana rhizosphere samples compared to the bulk soil. A total of 45 dereplicated, high-quality metagenome-assembled genomes (MAGs) were generated, corresponding to 41 bacteria and 4 archaea. Many of the MAGs carried multiple biosynthetic gene clusters, including MAGs corresponding to the genera Lysobacter and Actinospica. Overall, the low differentiation of the rhizosphere microbiomes suggest that differences in A. anomala disease expression are likely not associated with differences in the rhizosphere microbiome. Nevertheless, the results shed new light on the rhizosphere communities of two species of hazelnut, and woody perennials more broadly, and identify potential avenues for future research into the development of microbial inoculants for Corylus spp..

BackgroundGrowth-promoting endophytes have great potential to boost crop production and sustainability. There is, however, a lack of research on how differences in the plant host affect an endophytes ability to promote growth. We set out to quantify how different maize genotypes respond to specific growth-promoting endophytes. We inoculated genetically diverse maize lines with three different known beneficial endophytes: Herbaspirillum seropedicae (a gram-negative bacteria), Burkholderia WP9 (a gram-negative bacteria), and Serendipita vermifera Subsp. bescii (a Basidiomycota fungus). Maize seedlings were grown for 3 weeks under controlled conditions in the greenhouse and assessed for various growth promotion phenotypes. ResultsWe found Herbaspirillum seropedicae to increase chlorophyll content, plant height, root length, and root volume significantly in different maize genotypes, while Burkholderia WP9 did not significantly promote growth in any lines under these conditions. Serendipita bescii significantly increased root and shoot mass for 4 maize genotypes, and growth promotion correlated with measured fungal abundance. Although plant genetic variation by itself had a strong effect on phenotype, its interaction with the different endophytes was weak, and the endophytes rarely produced consistent effects across different genotypes. ConclusionsThis genome-by-genome interaction indicates that the relationship between a plant host and beneficial endophytes is complex, and it may partly explain why many microbe-based growth stimulants fail to translate from laboratory settings to the field. Detangling these interactions will provide a ripe area for future studies to understand how to best harness beneficial endophytes for agriculture.

Erwinia amylovora is the causal pathogen of fire blight, a contagious disease that affects apple and pear trees and other members of the family Rosaceae. In this study, we investigated the population dynamics of the pear flower microbiome in an agricultural setting during the naturally occurring infection of E. amylovora. Five potential factors were considered: collection date, the flowers phenological stage, location on the tree, location within the orchard, and pear cultivar. The phenological stage and the collection date were identified as the most important factors associated with pear flower microbiome composition. The location of the tree in the orchard and the flowers location on the tree had a marginal effect on the microbiome composition. The leaf microbiome reflected that of the abundant phenological stage on each date. The flower microbiome shifted towards E. amylovora, dominating the community as time and phenological stages progressed, leading to decreased community diversity. The strain population of E. amylovora remained similar throughout the entire collection period. In contrast, other taxa, including Pseudomonas, Pantoea, Lactobacillus, and Sphingomonas, were represented by dozens of amplicon sequence variants (ASVs), and different succession patterns in their populations were observed. Some of the taxa identified include known antagonists to E. amylovora. Overall, our results suggest that flower physiology and the interaction with the environment are strongly associated with the pear flower microbiome and should be considered separately. Strain succession patterns for the different taxa under E. amylovora spread may help in choosing candidates for antagonist-based treatments for fire blight. ImportanceThe spread of pathogens in plants is an important ecological phenomenon and has a significant economic impact on agriculture. Flowers serve as the entry point for E. amylovora, but members of the flower microbiome can inhibit or slow down the proliferation and penetration of the pathogen. Knowledge about leaf and flower microbiome response to the naturally occurring spread of E. amylovora is still lacking. The current study is the first to describe the flower microbiome dynamics during the naturally occurring infection of E. amylovora. Unlike previous studies, our experiment design enabled us to evaluate the contribution of five important environmental parameters to the community composition. We identified different strain succession patterns across different taxa in the flower consortia throughout the season. These results contribute to our understanding of plant microbial ecology during pathogen spread and can help to improve biological treatments for these diseases.

BackgroundThe plant root microbiome is central to disease resistance and stress resilience. In intensive tomato production, prolonged agrochemical use disrupts microbial communities, reducing their protective functions and enabling pathogen establishment. MethodsWe integrated 16S rRNA amplicon sequencing with culture-dependent isolation to analyze microbiome shifts in tomato plants across healthy, asymptomatic, and symptomatic states in a nematode-infested field. Network analysis and machine learning were used to identify key taxa. Isolates were screened for plant growth-promoting rhizobacteria (PGPR) and nematicidal activity, and selected strains were evaluated in planta under pathogen challenge. ResultsMicrobial diversity and community complexity declined with disease severity. Gaiella occulta emerged as a potential biomarker of plant health. From 223 isolates, 45 strains exhibited PGPR and nematicidal traits. Ten were tested in tomato plants, where treatments conferred systemic resistance to Pseudomonas syringae pv tomato without fitness cost. Four strains, primarily Pseudomonas and Bacillus, triggered immune priming, enhanced root development, and three of them were co-isolated from a single asymptomatic plant. ConclusionsOur findings highlight the potential of targeted bacterial consortia to restore microbiome balance and activate immune responses in tomato. These results support the rational design of synthetic microbial communities (SynComs) for sustainable, microbiome-based crop protection.

Improving wheat yield and performance involves selecting varieties that are well adapted for a regional area. Although host genotype and environment are major factors that impact crop performance and resilience, less is known about the relative contribution and occurrence of wheat seed endophytic fungal communities across spatial and temporal scales. An increased understanding of composition and assembly of beneficial endophytic fungal communities across regional scales provides valuable insight into the stability of the endophytic seed mycobiome. Our aim in this study was to examine the relative contribution and impact of latitude and longitude gradients within North Carolina (NC) on wheat seed fungal community structure of two regionally adapted soft red winter wheat cultivars, Hilliard and USG 3640. We examined the endophytic wheat seed microbiome of the two winter wheat cultivars planted in official variety trials at five geographic locations across NC in 2021 and two geographic locations in 2022. ITS1 sequence-based analysis of surface disinfested wheat seeds was conducted to determine alpha and beta diversity. Species richness is influenced by geographical location, however wheat seed mycobiome community structure is stable across cultivars and years. Latitude and longitude contributed to the observed variation in wheat seed mycobiome structure, in addition to yield, seed moisture, and leaf nutrients. When surveying taxa present within all cultivars, geographical sites and years, Alternaria and Epicoccum spp. exhibited high relative abundance in the wheat seed mycobiome. Our results provide a comprehensive catalog of core fungal taxa well-adapted to diverse environments and conserved across wheat cultivars.

There is interest in understanding the factors behind the biogeography of root-associated bacteria due to the joint effects that plant host, climate, and soil conditions can have on bacterial diversity. For legume crops with remaining wild populations, this is of even more importance, because the effects of cropping on undisturbed root-associated bacterial communities can be addressed. Here, we used a community prediction approach to describe the diversity of the root nodule bacterial communities of rooibos (Aspalathus linearis), an endemic legume crop from South Africa. The goal was to reveal whether patterns of root nodule community composition in paired cultivated and wild rooibos populations could be related to geographical distance, plant traits, and plant population type (i.e. cultivated or uncultivated). We identified a core of dominant and widespread Mesorhizobium ZOTUs that each defined one of 4 different root nodule community classes. Rooibos cultivation impacted root nodule bacterial diversity at regional and local scales, while the geographical origin of the root nodule communities was the strongest predictor of root nodule community structure. Beyond impacts of cultivation on root nodule bacterial diversity, this study suggests a mixture of dispersal limitation and ecological drift regionally, and selection by different plant populations locally, define the biogeography of rooibos root nodule bacterial communities.

Soil cultivation may change the soil microbiome and alter interactions between plants and parasites. The objective of this work was to evaluate temporal changes in plant health, microbiome abundance, bacterial diversity and the plant-parasitic nematode, Meloidogyne enterolobii incidence in two soil fields with different agricultural uses. Soil samples were collected from a commercial tomato production field (agricultural soil) and a single-cultivation strawberry field (native soil). Samples for the second experiment were collected from the same fields the following year. Tomato plants cv. Yearly Girl were grown in a greenhouse and inoculated with M. enterolobii. After 45 days, plants were evaluated for the plant growth parameters, nematode reproduction, and soil bacterial assemblages were assessed using cultivation-independent sequencing methods (V3/V4 region of the rRNA 16S). Overall the average of fruit fresh weight in the second experiment was 2.4-fold to 14-fold higher than the first experiment. Moreover, there was a 80.5% decrease in eggs present per root system from the first experiment to the second. The relative abundance of bacterial assemblages from Experiment 1 to Experiment 2 changed for most of the top phyla (eg. Actinobacteria, Bacteroidetes, and Chloroflexi) and genera (eg. Bacillus, Streptomyces, and Flavisolibacter) and there was no change in microbial diversity between the two experiments. This study suggests that soil management can lead to an overall decrease in nematode reproduction and better crop yield, as well as a shift in the overall bacterial assemblages. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=142 SRC="FIGDIR/small/525929v1_ufig1.gif" ALT="Figure 1"> View larger version (58K): org.highwire.dtl.DTLVardef@2b76b2org.highwire.dtl.DTLVardef@17db6c5org.highwire.dtl.DTLVardef@6a6d69org.highwire.dtl.DTLVardef@1352fb0_HPS_FORMAT_FIGEXP M_FIG C_FIG

The ability to predict plant microbiome assembly will enable new bacterial-based technologies for agriculture. A major step towards this is quantifying the roles of ecological processes on community assembly. This is challenging, in part because individual plants are colonised by different communities of soil bacteria and it is difficult to estimate if the absence of a given species was a) because it was not present in the soil to colonise a given plant or b) it went locally extinct from competition, predation or similar. To minimise this uncertainty, the authors develop a mesocosm system to study bacterial communities of individual plants by replicated transplantation to a recipient host plant population, ensuring new hosts receive a homogenous species pool for colonisation. We sought to understand which factors affected the transplant and, what the main drivers of variation in the model communities were. A nested factorial design was used to investigate the transplantation of cultured or total, root or leaf associated bacterial communities from donor host species to surrogate host species. Specific metrics were developed to quantify colonisation efficiency of communities. The results show the root communities were more effectively transplanted than leaf communities, with leaf communities more susceptible to contamination. For root communities the strongest driver of beta diversity was the donor host species, and for leaves it was the surrogate host species. Overall, the results reveal that root, but not leaf communities are amenable to transplant reflecting their differing ecological drivers. This work provides the basis to develop a plant microbiome transplant system.

O_LICrop tissues harbor microbiomes that can affect host health and yield. However, processes driving microbiome assembly, and resulting effects on ecosystem services, remain poorly understood. This is particularly true of flowering crops that rely on pollinators for yield. C_LIO_LIWe assessed effects of orchard management tactics and landscape context on the flower microbiome in almond, Prunus dulcis. Fourteen orchards (5 conventional, 4 organic, 5 habitat augmentation) were sampled at two bloom stages to characterize bacterial and fungal communities associated with floral tissues. The surveys were complemented by in vitro experiments to assess effects of arrival order and fungicides on nectar microbial communities, and effects of fungicides and microbes on honey bee foraging. Finally, a field trial was conducted to test effects of fungicides and microbes on pollination. C_LIO_LIAs bloom progressed, bacterial and fungal abundance and diversity increased, across all floral tissue types and management strategies. The magnitude by which microbial abundance and diversity were affected varied, with host proximity to apiaries and orchard management having notable effects on bacteria and fungi, respectively. C_LIO_LIExperiments showed immigration history and fungicides affected the composition of nectar microbial communities, but only fungicides affected pollinator foraging through reduced nectar removal. Neither treatment affected pollination services. C_LIO_LISynthesis and applications. Our results shed light on routes through which management practices can shape microbiota associated with flowers of a pollinator-dependent crop. With growing appreciation for the role of floral-associated microbes in affecting biotic interactions at the floral interface, understanding such drivers can potentially inform microbial-derived ecosystem services in agricultural landscapes, including pollination and biocontrol. C_LI

BackgroundDrought is a major abiotic stress that limits agricultural productivity. Previous field-level experiments have demonstrated that drought decreases microbiome diversity in the root and rhizosphere and may lead to enrichment of specific groups of microbes, such as Actinobacteria. How these changes ultimately affect plant health is not well understood. In parallel, model systems have been used to tease apart the specific interactions between plants and single, or small groups of microbes. However, translating this work into crop species and achieving increased crop yields within noisy field settings remains a challenge. Thus, the next scientific leap forward in microbiome research must cross the great lab-to-field divide. Toward this end, we combined reductionist, transitional and ecological approaches, applied to the staple cereal crop sorghum to identify key beneficial and detrimental, root associated microbes that robustly affect drought stressed plant phenotypes. ResultsFifty-three bacterial strains, originally characterized for association with Arabidopsis, were applied to sorghum seeds and their effect on root growth was monitored for seven days. Two Arthrobacter strains, members of the Actinobacteria phylum, caused root growth inhibition (RGI) in Arabidopsis and sorghum. In the context of synthetic communities, strains of Variovorax were able to protect both Arabidopsis and sorghum from the RGI caused by Arthrobacter. As a transitional system, we tested the synthetic communities through a 24-day high-throughput sorghum phenotyping assay and found that during drought stress, plants colonized by Arthrobacter were significantly smaller and had reduced leaf water content as compared to control plants. However, plants colonized by both Arthrobacter and Variovorax performed as well or better than control plants. In parallel, we performed a field trial wherein sorghum was evaluated across well-watered and drought conditions. Drought responsive microbes were identified, including an enrichment in Actinobacteria, consistent with previous findings. By incorporating data on soil properties into the microbiome analysis, we accounted for experimental noise with a newly developed method and were then able to observe that the abundance of Arthrobacter strains negatively correlated with plant growth. Having validated this approach, we cross-referenced datasets from the high-throughput phenotyping and field experiments and report a list of high confidence bacterial taxa that positively associated with plant growth under drought stress. ConclusionsA three-tiered experimental system connected reductionist and ecological approaches and identified beneficial and deleterious bacterial strains for sorghum under drought stress.

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.

Tree diebacks are complex and multi-factorial diseases with suspected biotic and abiotic components. Microbiome effects on plant health are challenging to assess due to the complexity of fungal and bacterial communities. Grapevine wood dieback is the main threat to sustainable production worldwide and no causality with microbial species has been established. Here, we aimed to test the hypothesis that grapevine esca disease progression has reproducible drivers in the fungal species community. For this, we analyzed a set of 21 vineyards planted simultaneously with a single susceptible cultivar to provide replication at the landscape scale. We sampled a total of 496 plants across vineyards in two different years to perform deep amplicon sequencing analyses of the fungal communities inhabiting grapevine trunks. The communities were highly diverse with a total of 4,129 amplified sequence variants assigned to 697 distinct species. Individual plants varied in fungal community composition depending on the year of sampling, vineyard location, and disease status. However, we detect no specific fungal species driving symptom development across the vineyards contrary to long-standing expectations. Our study shows how landscape-scale replicated field surveys allow for powerful hypothesis-testing for complex dieback disease drivers and prioritize future research towards additional factors.