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32 results for “phyllosphere”
16S gene and ASV sequences of bacteria isolated from soil and the phyllosphere of Arabidopsis thaliana
<p>Data from "Induction of antibiotic specialized metabolism by co-culturing in a collection of phyllosphere bacteria" by Qi et al. </p> <p>- 16S gene sequences of bacteria isolated from soil and the phyllosphere of Arabidopsis thaliana in FASTA format. </p> <p>- Filtered OTU (ASV) table across all samples </p> <p>- ASV sequences</p>
Determinants of the vertical distribution of the phyllosphere differ between microbial groups and the epi- and endosphere
<ul> <li>The assembly of phyllosphere microbial communities is under the control of stochastic and deterministic processes. In neotropical forests, the tree host identity and physiology together with strong heterogeneities of the environment within the canopy and at the leaf scale could potentially drive the assembly of phyllosphere microbial communities.</li> <li>We analyzed the assembly processes shaping the microbial communities living in the endophytic and epiphytic phyllosphere in tree species across vertical environmental gradients present from the top of the canopy to the ground. We used DNA metabarcoding to characterize microbial communities and described the microhabitats along the gradient by measuring morphological and chemical foliar traits of host trees.</li> <li>The results revealed that the assembly of both communities resulted from a balance of deterministic and stochastic effects with strong discrepancies between fungal and bacterial communities. Different effects of the host and of the vertical environmental gradient shaped epiphytic and endophytic communities. If fungal communities were mainly shaped by the host identity, different leaf morphological and chemical leaf traits drove the epi- and endophytic bacterial communities.</li> <li>Taken together, the phyllosphere represent a global selective pressure of the plant on microbial communities but the microhabitat at the leaf scale contribute also significantly to drive the assembly of microbial communities.</li> </ul>
Phyllosphere microbial associations improve plant reproductive success
<p class="western">The above-ground (phyllosphere) plant microbiome is increasingly recognized as an important component of plant health. We hypothesized that phyllosphere bacterial recruitment may be disrupted in a greenhouse setting, and that adding a bacterial amendment would therefore benefit the health and growth of host plants. Using a newly developed synthetic phyllosphere bacterial microbiome for tomato (<em>Solanum lycopersicum</em>), we tested this hypothesis across multiple trials by manipulating microbial inoculation of leaves and measuring subsequent plant growth and reproductive success, comparing results from plants grown in both greenhouse and field settings. We confirmed that greenhouse-grown plants have a relatively depauperate phyllosphere bacterial microbiome, which both makes them an ideal system for testing the impact of phyllosphere communities on plant health and important targets for microbial amendments as we move towards increased agricultural sustainability. We find that the addition of the synthetic microbial community early in greenhouse growth leads to an increase in fruit production in this setting, implicating the phyllosphere microbiome as a key component of plant fitness and emphasizing the role that these bacterial microbiomes likely play in the ecology and evolution of plant communities.</p>
Data from: The phyllosphere microbiome in Tsuga canadensis: Possible relationships with resistance to Adelges tsugae and effects of the pesticide dinotefuran
<p>Eastern hemlock (<em>Tsuga canadensis</em>) is an important forest tree species in North America. It currently faces threats from invasive insects; primarily hemlock woolly adelgid (HWA -<em> Adelges tsugae</em>)<em> </em>and elongate hemlock scale (EHS - <em>Fiorinia externa</em><em>). </em>Both insect species are native to Asia with Tsuga species in the native range typically resistant to the damage they cause. We conducted a study of the phyllosphere microbiome of two hemlock species native to North America and susceptible to HWA (<em>T. canadensis</em> and <em>T. caroliniana</em>), and two species native to Asia and resistant to HWA (<em>T. chinensis</em> and <em>T. diversifolia</em>). The files for this experiment are labelled "Hemlock Microbiome." Since pesticide application is often used to treat North American hemlock species impacted by HWA and EHS, we also examined how the pesticide dinotefuran affected the microbiome and overall plant physiology of <em>T. canadensis</em>. The files for this experiment are labelled "Hemlock Dinotefuran."</p> <p>Included here are zOTU tables for fungi and bacteria and the taxonomic matches for each zOTU from both experiments, as well as the codes used in the programs USEARCH and Cutadapt to generate these data tables. (Note that raw sequence reads are publicly available in the Sequence Read Archive under BioProject number PRJNA1052676.) In addition, R scripts that show 1) how these data were analyzed with PERMANOVA and PERMDISP and visualized with PCoA in the R package vegan, including sequence read normalization in the R package DESeq2, 2) how the relative abundance of the top taxa were graphed in the R package phyloseq, and 3) indicator species analysis in the R package indicspecies are included. Finally, the raw data for plant physiology measurements are also included, along with the R script on how these data were analyzed with ANOVAs.</p>
Continental-scale associations of Arabidopsis thaliana phyllosphere members with host genotype and drought
<p><strong><span>Plants are colonized by distinct pathogenic and commensal microbiomes across different regions of the globe, but the factors driving their geographic variation are largely unknown. Using 16S rDNA and shotgun sequencing, we characterized the associations of the <em>Arabidopsis thaliana</em> leaf microbiome with host genetics and climate variables from 267 populations in the species’ native range across Europe. Comparing the distribution of the 575 major bacterial amplicon variants (phylotypes), we discovered that microbiome composition in <em>A. thaliana</em> segregates along a latitudinal gradient. The latitudinal clines in microbiome composition are predicted by metrics of drought, but also by the spatial genetics of the host. To validate the relative effects of drought and host genotype we conducted a common garden field study, finding 10% of the core bacteria to be affected directly by drought, and 20% to be affected by host genetic associations with drought. These data provide a valuable resource for the plant microbiome field, with the identified associations suggesting that drought can directly and indirectly shape genetic variation in A. thaliana via the leaf microbiome.</span></strong></p>
Wheat phyllosphere metagenome assembled genomes collected in Ringsted, Denmark
<p><span>We present a completely novel </span><span>and comprehensive wheat phyllosphere metagenomic dataset of 211 samples and </span><span>1261 MAGs. This dataset represents a significant contribution to the field, as it </span><span>provides insights into the poorly studied microbial communities associated with </span><span>wheat leaf surfaces, an ecosystem of considerable agricultural importance.</span></p>
Data for: Soil cadmium stress-mediated sexual difference in phyllosphere microbiome and associated pathogen resistance of poplars
<p class="MsoNormal"><span>Phyllosphere associated microorganisms play a crucial role in protecting plants from diseases, while their composition and diversity are strongly influenced by heavy metal contaminants. As dioecious plants exhibited sexual dimorphism in metal accumulation and tolerance between male and female individuals, in this study we used male and female full-sibs of <em>Populus deltoides</em> to investigate whether the two plant sexes will present sexual differences in phyllosphere microbiome structure and associated pathogen resistance against a leaf pathogenic fungus after soil cadmium (Cd) exposure. We found that Cd-treated male plants </span><span>grew better </span><span>and a</span><span>ccumulated more leaf Cd than females. </span><span>Cd stress reduced leaf lesion areas of both plant sexes after leaf pathogen infection, whereas male plants exhibited better resistance than females. More importantly, Cd exposure differentially altered the structure and function of the phyllosphere microbiome of male and female plants, with more abundant ecologically beneficial microbes but decreased pathogenic fungal taxa harbored in male phyllosphere. Further <em>in vitro</em> toxicity tests suggested that such sexual difference in pathogen resistance between the two plant sexes could attribute to direct Cd toxicity and indirect shifts in phyllosphere microbiome. This study provides implication for understanding the underlying mechanism of heavy metals involved in plant-pathogen interactions.</span></p>
Data from the fungal phyllosphere of Mediterranean plant species
<p><span>The phyllosphere is a wide and complex ecosystem that provides key support for microbial diversity. Fungal communities inhabiting the leaf are functionally variable and play important roles on plant performance. Factors conditioning the arrival and colonization of fungal communities will determine the phyllosphere fungal composition. Plant identity, leaf functional traits and host plant phylogeny have been shown to be regulators of the microbial colonization of the leaves and can be considered as biotic filters determining the assembly of phyllosphere fungal communities. By high-throughput sequencing, we analysed the phyllosphere fungal communities from 38 Mediterranean woody plant species in two forests of the south-eastern Iberian Peninsula. We analysed the effect of plant species and site on fungal community composition. We also tested the effect of leaf functional traits and plant phylogeny on plant species differences in their fungal communities, and on the structure of the plant-fungus interaction network. Plant species account for a larger proportion than site in the variability of the composition of phyllosphere fungal communities. Leaf traits and host phylogeny influence the arrival and colonization of phyllosphere fungal communities across plant species. Plants with pubescent leaves and phylogenetically closer harbour more similar communities of decomposers, pathogens and epiphytes. Leaf habit (i.e., evergreen vs. deciduous) also influences the community composition of decomposer and epiphytic fungi. Leaf carbon, leaf water content and leaf mass per area affect differentially each functional guild. Plant-fungus interaction networks present a modular structure in which plants belonging to the same module share more fungal species and are phylogenetically closer. We provide evidence that even though phyllosphere fungal communities are complex ecosystems, fungi with contrasting relationships with the plant (decomposers, epiphytes and pathogens) respond similarly to a common subset of leaf traits that impose physical limitations to the assembly of phyllosphere fungal communities. </span></p>
Phyllosphere microbial associations improve plant reproductive success
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Data for: Soil cadmium stress-mediated sexual difference in phyllosphere microbiome and associated pathogen resistance of poplars
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Data from the fungal phyllosphere of Mediterranean plant species
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Abiotic environments prevail over plant functional traits in shaping phyllosphere fungal communities of temperate grasslands in China
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Raw data and code for: Arbuscular mycorrhizal fungus alters the phyllosphere microbial community of alfalfa and modifies plant defenses against dual pea aphid and pathogen attack
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Data from: Host genotype is an important determinant of the cereal phyllosphere mycobiome
The phyllosphere mycobiome in cereals is an important determinant of crop health. However, an understanding of the factors shaping this community is lacking. Fungal diversity in leaves from a range of cultivars of winter wheat (Triticum aestivum), winter and spring barley (Hordeum vulgare) and a smaller number of samples from oat (Avena sativa), rye (Secale cereale) and triticale (Triticum × Secale) was studied using next-generation sequencing. The effects of host genotype, fungicide treatment and location on fungal communities were explored. In total, 635 251 fungal internal transcribed spacer (ITS) reads were obtained from 210 leaf samples. Visual disease assessments and relative read abundance of Zymoseptoria tritici and Ramularia collo-cygni were strongly positively related. Crop genotype at the species level explained 43% of the variance in the total dataset, followed by fungicide treatment (13%) and location (4%). Indicator species, including plant pathogens, responding to factors such as crop species, location and treatment were identified. Host genotype at both the species and cultivar level is important in shaping phyllosphere fungal communities, whereas fungicide treatment and location have minor effects. We found many host-specific fungal pathogens, but also a large diversity of fungi that were relatively insensitive to host genetic background, indicating that host-specific pathogens live in a 'sea' of nonspecific fungi.
Dataset and R code for phyllosphere microbial diversity during rubber tree leaf senescence
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Data from: Organic farming increases richness of fungal taxa in the wheat phyllosphere
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Data from: Negative plant-phyllosphere feedbacks in native Asteraceae hosts – a novel extension of the plant-soil feedback framework
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Data from: Diversity and abundance of phyllosphere bacteria are linked to insect herbivory
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Data from: Host genotype is an important determinant of the cereal phyllosphere mycobiome
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Data from: The impact of bacteriophages on phyllosphere bacterial abundance and composition
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