A Comparative Analysis of Ash Leaf-Colonizing Bacterial Communities Identifies Putative Antagonists of Hymenoscyphus fraxineus

Ulrich, Kristina; Becker, Regina; Behrendt, Undine; Kube, Michael; Ulrich, Andreas

doi:10.3389/fmicb.2020.00966

Cited by 36 publications

(28 citation statements)

References 109 publications

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“…In A. thaliana , there is a taxonomic and functional overlap between bacterial communities in the leaves and roots, and evidence that soil is the main driver of leaf bacterial community structure ( Bai et al , 2015 ). Phyla belonging to Proteobacteria , Actinobacteria , and Bacteroidetes were found to be most abundant in A. thaliana , common ash ( Fraxinus excelsior ), and other tree leaves ( Redford et al , 2010 ; Bodenhausen et al , 2013 ; Bai et al , 2015 ; Griffiths et al , 2020 ; Ulrich et al , 2020 ).…”

Section: Colonizing Leaf Surfacesmentioning

confidence: 99%

Shaping the leaf microbiota: plant–microbe–microbe interactions

Chaudhry

Runge

Sengupta

et al. 2020

Journal of Experimental Botany

158

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The aerial portion of a plant, namely the leaf, is inhabited by pathogenic and non-pathogenic microbes. The leaf's physical and chemical properties, combined with fluctuating and often challenging environmental factors, create surfaces that require a high degree of adaptation for microbial colonization. As a consequence, specific interactive processes have evolved to establish a plant leaf niche. Little is known about the impact of the host immune system on phyllosphere colonization by non-pathogenic microbes. These organisms can trigger plant basal defenses and benefit the host by priming for enhanced resistance to pathogens. In most disease resistance responses, microbial signals are recognized by extra- or intracellular receptors. The interactions tend to be species-specific and it is unclear how they shape leaf microbial communities. In natural habitats, microbe-microbe interactions are also important for shaping leaf communities. To protect resources, plant colonizers have developed direct antagonistic or host manipulation strategies to fight competitors. Phyllosphere-colonizing microbes respond to abiotic and biotic fluctuations and are therefore an important resource for adaptive and protective traits. Understanding the complex regulatory host-microbe-microbe networks is needed to transfer current knowledge to biotechnological applications such as plant-protective probiotics.

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Section: Colonizing Leaf Surfacesmentioning

confidence: 99%

Shaping the leaf microbiota: plant–microbe–microbe interactions

Chaudhry

Runge

Sengupta

et al. 2020

Journal of Experimental Botany

158

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“…In each of the districts (A-D), four pairs of adjacent trees consisting of an affected (K) and a tolerant (P) tree were chosen for sampling. Details of the sampling campaign and sample preparation are described in Ulrich et al (2020). Accordingly, the same leaf samples were used in this study to analyze the fungal community.…”

Section: Study Site and Samplingmentioning

confidence: 99%

“…For high comparability among analyses, the total DNA used to investigate of the bacterial community (Ulrich et al, 2020) was also applied to study the fungal community. For this purpose, the ITS2 region was chosen because it has a lower length variability compared to the ITS1 region combined with higher genetic diversity.…”

Section: Amplicon Sequencing and Analysis Of The Its2 Regionmentioning

confidence: 99%

“…Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) was applied as a reliable method for the dereplication and classification of yeasts in environmental analyses (Chudejova et al, 2017;Huschek and Witzel, 2019). Prior to this measurement, the yeast-like isolates were freshly inoculated on CASO agar (Fluka, Buchs, Switzerland) and cultivated for 24 h at 25 • C. Mass spectra were obtained based on the whole-cell measurement protocol as described by Ulrich et al (2020). The analysis was performed on a microflex TM LT/SH MALDI-TOF mass spectrometer (Bruker Daltonics, Bremen, Germany) using Flex Control 3.4 software.…”

Section: Dereplication and Classification Of Fungal Isolatesmentioning

confidence: 99%

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Analyzing Ash Leaf-Colonizing Fungal Communities for Their Biological Control of Hymenoscyphus fraxineus

et al. 2020

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“…For stem and leaf material, the primer set 799f/1115r [ 53 ] can be selected, as recommended in previous works [ 69 , 70 ]. These chloroplast 16S rRNA gene-discriminating primers are commonly utilized for the identification of phyllosphere associated Bacteria [ 71 , 72 , 73 ] because these primers do not amplify host-plant nor cyanobacterial DNA; cyanobacteria are known to be rare in the phyllosphere [ 74 , 75 ].…”

Section: Amplicon Library Preparationmentioning

confidence: 99%

DNA Metabarcoding for the Characterization of Terrestrial Microbiota—Pitfalls and Solutions

et al. 2021

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Soil-borne microbes are major ecological players in terrestrial environments since they cycle organic matter, channel nutrients across trophic levels and influence plant growth and health. Therefore, the identification, taxonomic characterization and determination of the ecological role of members of soil microbial communities have become major topics of interest. The development and continuous improvement of high-throughput sequencing platforms have further stimulated the study of complex microbiota in soils and plants. The most frequently used approach to study microbiota composition, diversity and dynamics is polymerase chain reaction (PCR), amplifying specific taxonomically informative gene markers with the subsequent sequencing of the amplicons. This methodological approach is called DNA metabarcoding. Over the last decade, DNA metabarcoding has rapidly emerged as a powerful and cost-effective method for the description of microbiota in environmental samples. However, this approach involves several processing steps, each of which might introduce significant biases that can considerably compromise the reliability of the metabarcoding output. The aim of this review is to provide state-of-the-art background knowledge needed to make appropriate decisions at each step of a DNA metabarcoding workflow, highlighting crucial steps that, if considered, ensures an accurate and standardized characterization of microbiota in environmental studies.

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A Comparative Analysis of Ash Leaf-Colonizing Bacterial Communities Identifies Putative Antagonists of Hymenoscyphus fraxineus

Cited by 36 publications

References 109 publications

Shaping the leaf microbiota: plant–microbe–microbe interactions

Shaping the leaf microbiota: plant–microbe–microbe interactions

Analyzing Ash Leaf-Colonizing Fungal Communities for Their Biological Control of Hymenoscyphus fraxineus

DNA Metabarcoding for the Characterization of Terrestrial Microbiota—Pitfalls and Solutions

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