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"study-abstract": "Plant-inhabiting microorganisms interact directly with each other, forming complex microbial interaction networks. These networks may be disrupted by the arrival of a new species, such as a pathogen infecting the plant. Here we decipher intra-kingdom and cross-kingdom interactions involving a pathogen species, by using a Bayesian method of network inference. We use this method to highlight the most likely interactions between Erysiphe alphitoides, the causal agent of oak powdery mildew, and other foliar microorganisms of pedunculate oak (Quercus robur L.). Our results showed that infection by E. alphitoides is accompanied by drastic changes in the foliar fungal community composition but no significant change in the bacterial community composition. Our analyses highlighted 13 fungal Operational Taxonomic Units (OTUs) and 13 bacterial OTUs that are likely to interact directly with E. alphitoides. Four of the fungal OTUs were phyllosphere yeasts. The fungal endophytes Mycosphaerella punctiformis and Monochaetia kansensis were highlighted as potential antagonists of E. alphitoides. These potential interactions will have to be validated experimentally. The study of the temporal dynamics of microbial networks during the course of infection also appears to be a promising research avenue, that will undoubtedly give deeper insights into the ecology of this disease. Overall, we showed that combining metagenomics and network ecology may improve biological control of plant diseases, by highlighting potential antagonists of pathogen species.",
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"secondary-accession": "SRP132042",
"centre-name": "University of Georgia",
"public-release-date": null,
"study-abstract": "Sequencing of bacterial populations on maize leaves to identify the community structure and how the genetics of the maize plant impact its microbial communities.",
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"last-update": "2020-05-21T23:44:41",
"secondary-accession": "ERP116553",
"centre-name": "EMG",
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"study-abstract": "The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB19522. This project includes samples from the following biomes: root:Host-associated:Plants:Phylloplane.",
"study-name": "EMG produced TPA metagenomics assembly of the PRJEB19522 data set (Is there foul play in the leaf pocket? The metagenome of floating fern Azolla reveals endophytes that do not fix N 2 but may denitrify.).",
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"type": "studies",
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"bioproject": "PRJEB19522",
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"secondary-accession": "ERP021566",
"centre-name": "UTRECHT UNIVERSITY",
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"study-abstract": "Dinitrogen fixation by Nostoc azollae residing in specialized leaf pockets supports prolific growth of the floating fern Azolla filiculoides. To evaluate contributions by further microorganisms, the A. filiculoides microbiome and nitrogen metabolism in bacteria persistently associated with Azolla ferns were characterized. A metagenomic approach was taken complemented by nitrogen isotope determinations of fern biomass and detection of N2O released. Ribosomal RNA genes in sequenced DNA of natural ferns, their enriched leaf pockets and water filtrate from the surrounding ditch established that bacteria of A. filiculoides differed entirely from surrounding water and revealed species of the order Rhizobiales. Analyses of seven cultivated Azolla species confirmed persistent association with Rhizobiales. Two distinct near full-length Rhizobiales genomes were identified from leaf-pocket enriched samples from ditch grown A. filiculoides. Annotation revealed genes for denitrification but not N2-fixation. 15N2 incorporation was active in ferns with N. azollae but not in ferns without. N2O was not detectably released from surface sterilized ferns with the Rhizobiales. N2-fixing N. azollae, we conclude, dominated the microbiome of Azolla ferns. The persistent but less abundant heterotrophic Rhizobiales bacteria possibly contributed to lowering O2 levels in leaf pockets but did not release detectable amounts of the strong greenhouse gas N2O.",
"study-name": "Is there foul play in the leaf pocket? The metagenome of floating fern Azolla reveals endophytes that do not fix N 2 but may denitrify.",
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"last-update": "2019-11-30T12:45:13",
"secondary-accession": "SRP186503",
"centre-name": "University of California, Merced",
"public-release-date": null,
"study-abstract": "Bacterial endophytes of tree species belonging to the family Pinaceae. Tree species were collected along the native range of Pinus flexilis",
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"bioproject": "PRJEB21613",
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"is-private": false,
"last-update": "2017-07-10T08:58:36",
"secondary-accession": "ERP023884",
"centre-name": "HASSELT UNIVERSITY",
"public-release-date": null,
"study-abstract": "Structure and function of epispheric microbial communities from Warszawa, Białowieża and Bóbrka",
"study-name": "Structure and function of epispheric microbial communities from Warszawa, Białowieża and Bóbrka",
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"last-update": "2017-04-20T13:27:42",
"secondary-accession": "ERP022236",
"centre-name": "KYUNG HEE UNIVERSITY",
"public-release-date": null,
"study-abstract": "This study is the first to describe bacterial community composition and diversity on broccoli leaf surfaces in-depth using 454 pyrosequencing of 16S rRNA genes. This study suggested variability of bacterial communities associated with geography of farming sites, and alterations by host growth and host health conditions. In a global view of fresh produce, this study delineated bacterial community composition specific for broccoli, which is more similar to ground vegetables than tree fruits and vegetables.",
"study-name": "Geographic and host-associated variations in bacterial communities on the leaf surfaces of field-grown broccoli",
"data-origination": "SUBMITTED"
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"id": "MGYS00001360",
"attributes": {
"accession": "MGYS00001360",
"bioproject": "PRJEB8107",
"samples-count": 48,
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"last-update": "2017-01-05T10:20:55",
"secondary-accession": "ERP009145",
"centre-name": "TUGRAZ",
"public-release-date": null,
"study-abstract": "Bananas (Musa spp.) belong to the most important global food commodities, and their cultivation represents the world''s largest monoculture. Although the plant-associated microbiome has substantial influence on plant growth and health, there is a lack of knowledge of the banana microbiome and its influencing factors. We studied the impact of (i) biogeography, and (ii) agroforestry on the banana-associated gammaproteobacterial microbiome analyzing plants grown in smallholder farms in Nicaragua and Costa Rica. Profiles of 16S rRNA genes revealed high abundances of Pseudomonadales, Enterobacteriales, Xanthomonadales, and Legionellales. An extraordinary high diversity of the gammaproteobacterial microbiota was observed within the endophytic microenvironments (endorhiza and pseudostem), which was similar in both countries. Enterobacteria were identified as dominant group of above-ground plant parts (pseudostem and leaves). Neither biogeography nor agroforestry showed a statistically significant impact on the gammaproteobacterial banana microbiome in general. However, indicator species for each microenvironment and country, as well as for plants grown in Coffea intercropping systems with and without agri-silvicultural production of different Fabaceae trees (Inga spp. in Nicaragua and Erythrina poeppigiana in Costa Rica) could be identified. For example, banana plants grown in agroforestry systems were characterized by an increase of potential plant-beneficial bacteria, like Pseudomonas and Stenotrophomonas, and on the other side by a decrease of Erwinia. Hence, this study could show that as a result of legume-based agroforestry the indigenous banana-associated gammaproteobacterial community noticeably shifted.",
"study-name": "Agroforestry leads to shifts within the gammaproteobacterial microbiome of banana plants cultivated in Central America",
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{
"type": "studies",
"id": "MGYS00001359",
"attributes": {
"accession": "MGYS00001359",
"bioproject": "PRJEB7828",
"samples-count": 160,
"is-private": false,
"last-update": "2017-01-05T10:20:01",
"secondary-accession": "ERP008802",
"centre-name": "UNIV-WUE",
"public-release-date": null,
"study-abstract": "Eukaryote-associated microbiomes interact with their hosts in multiple manners, thereby affecting the hosts? phenotype, physical condition and behaviour. In plants, bacteria have numerous functions, with variable net effects, both in natural and agricultural systems. However, information about the composition and diversity of the bacterial communities associated with different aboveground plant organs, particularly flowers, is lacking. In addition, the relative effects of microhabitat and environmental conditions on community establishment require further attention. Here, using culture-independent methods, we determine that leaves and three floral microhabitats of Metrosideros polymorpha (Myrtaceae), a tree endemic to Hawai?i, host unique indicator communities composed of relatively abundant bacterial taxa. These indicator communities are accompanied by a large number of ubiquitous or rare bacteria with lower abundances. In our study system, the strong effect of microhabitat filtering on plant-associated community composition and bacterial richness and diversity strongly exceeds the influence of environmental effects such as precipitation, altitude, substrate age and geographic distance. Thus, the bacterial richness of aboveground plant organs is strongly underestimated when only one microhabitat, e.g., leaves, is considered. Our study represents a first step towards a comprehensive characterisation of the distribution, composition, and underlying factors, of plant bacterial communities, with implications for future basic and applied research on plant health, pollination and reproduction.",
"study-name": "Meterosideros Flower Microbiota",
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"type": "studies",
"id": "MGYS00001357",
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"study-abstract": "The surface of plant leaves, also termed the phyllosphere, is a selective habitat for microbes. From this phyllosphere microbiome, the bacterial composition seems to depend on plant host species, leaf characteristics, season, climate, and geographic distance between the plant hosts. In this study, we investigated the effect of an urban environment and air pollution on the bacterial composition of phyllosphere communities. We performed a passive biomonitoring experiment in which leaves were sampled from Ivy (Hedera sp.), a common evergreen climber species in the area under study. The bacterial community composition was determined using 16S rRNA gene sequencing on the Illumina MiSeq platform. In addition, exposure to anthropogenic particulate matter was estimated using leaf biomagnetic analyses. We found that the phyllosphere microbial communities of Ivy were greatly different between urban and more rural locations, as we observed a shift in several of the dominant taxa Beijerinckia, Hymenobacter, Methylocystaceae and Methylobacterium. Interestingly, the communities also showed greater variability in the urban area than at the less urbanized locations where we measured lower levels of air pollution. These results indicate that an urban environment and local air pollution can greatly affect the local phyllosphere community composition.",
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"study-abstract": "Spartina anglica phyllosphere was investigated using metagenomics and metaproteomics in order to investigate bacterial Dimethylsulphide degradation associated with Spartina anglica in more detail. DNA from Spartina anglica phyllosphere was extracted and used for metagenomics using the Nextera XT Kit (Illumina). Sequencing was carried out on the Illumina MiSeq. (2 x 301 bp paired end reads)",
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