The plant microbiome explored: implications for experimental botany

Berg, Gabriele; Rybakova, Daria; Grube, Martín; Köberl, Martina

doi:10.1093/jxb/erv466

Cited by 435 publications

(248 citation statements)

References 71 publications

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“…All organisms are inhabited by microorganisms including archaea, bacteria, fungi and viruses; this microbiota presents a key role in host health and development 43, 44. The microbiome associated with plants is considered its second genome.…”

Section: Microbiome Interaction With Its Hostmentioning

confidence: 99%

Microbial interactions: ecology in a molecular perspective

Braga

Dourado

Araújo

2016

Brazilian Journal of Microbiology

283

145

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The microorganism–microorganism or microorganism–host interactions are the key strategy to colonize and establish in a variety of different environments. These interactions involve all ecological aspects, including physiochemical changes, metabolite exchange, metabolite conversion, signaling, chemotaxis and genetic exchange resulting in genotype selection. In addition, the establishment in the environment depends on the species diversity, since high functional redundancy in the microbial community increases the competitive ability of the community, decreasing the possibility of an invader to establish in this environment. Therefore, these associations are the result of a co-evolution process that leads to the adaptation and specialization, allowing the occupation of different niches, by reducing biotic and abiotic stress or exchanging growth factors and signaling. Microbial interactions occur by the transference of molecular and genetic information, and many mechanisms can be involved in this exchange, such as secondary metabolites, siderophores, quorum sensing system, biofilm formation, and cellular transduction signaling, among others. The ultimate unit of interaction is the gene expression of each organism in response to an environmental (biotic or abiotic) stimulus, which is responsible for the production of molecules involved in these interactions. Therefore, in the present review, we focused on some molecular mechanisms involved in the microbial interaction, not only in microbial–host interaction, which has been exploited by other reviews, but also in the molecular strategy used by different microorganisms in the environment that can modulate the establishment and structuration of the microbial community.

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Section: Microbiome Interaction With Its Hostmentioning

confidence: 99%

Microbial interactions: ecology in a molecular perspective

Braga

Dourado

Araújo

2016

Brazilian Journal of Microbiology

283

145

View full text Add to dashboard Cite

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“…Litter therefore appears to be their primary habitat and their occurrence in living leaves just a transient stage. The manifold interactions of endophytic fungi with plant hosts (for reviews see Hyde and Soytong 2008;Porras-Alfaro and Bayman 2011;Debbab et al 2012;Hamilton et al 2012;Hardoim et al 2015;Berg et al 2016;Vacher et al 2016) are therefore probably mostly ascribable to fungal individuals and not to fungal communities.…”

Section: Overlap Of Phyllosphere Mycobiomes and Fungal Litter Communimentioning

confidence: 99%

Transient leaf endophytes are the most active fungi in 1-year-old beech leaf litter

et al. 2017

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The ecological significance of fungi occurring asymptomatically inside living plant leaves is poorly understood. Given the broad saprotrophic potential of many endophytic fungi, we hypothesized that they persist in decaying litter for an extended period of time after leaf abscission. Fungal assemblages were assessed by highthroughput sequencing in autumn leaves of beech (Fagus sylvatica) and in the corresponding leaf litter in 388 samples from 22 beech forest plots in three widely distant regions of Germany. A considerable proportion of the leafendophytic fungi was also found in 1-year-old litter. Cooccurrence networks revealed that the fungi formed unstructured assemblages inside the living leaves, rather than well-structured communities. Previously endophytic fungi constituted an integral part of the fungal litter community and were by far the most active fungi in 1-year-old litter. We therefore consider these endophytic occurrences to represent transient stages. Composition of the aboveground microbiome appears therefore to be closely connected to the process of litter decomposition. Considering the respective linked fungal habitat will facilitate predicting nutrient and carbon cycling and storage in forest ecosystems as well as elucidating the ecology of leaf microbiomes.

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“…Rosellinia, Xylaria (both Xylariales order) and Pyronema (Pezizales order) were isolated exclusively from leaves of sweet cherry. Organ-specific association of endophytic fungi has been described for several plants in the literature (see review by Berg et al [6]). …”

Section: Discussionmentioning

confidence: 99%

Characterization of community structure of culturable endophytic fungi in sweet cherry composite trees and their growth-retarding effect against pathogens

Haddadderafshi

Pósa

Péter

et al. 2016

Acta Biologica Hungarica

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Endophytic fungi have the potential to protect their host plants in stress situations. Characterizing the ecology and complex interaction between these endophytes and their host plants is therefore of great practical importance, particularly in horticultural plants. Among horticultural plants, fruit trees form a special category because of their longevity and because they are composites of rootstock and scion, which often belong to different plant species. Here we present the first characterization of culturable endophytic fungal community of sweet cherry. Samples from the Hungarian cultivar 'Petrus' grafted on 11 different rootstocks were collected in autumn and in spring in a bearing orchard and the dependence of colonization rate and endophyte diversity on rootstock, organ and season was analysed. On the basis of their ITS sequences 26 fungal operational taxonomic units were identified at least down to the genus level. The dominant genus, comprising more than 50% of all isolates, was Alternaria, followed by different Fusarium and Epicoccum species . We observed some organ-specificity amongst endophytes, and organs showed more sizeable differences in colonization rates and endophyte diversity than rootstocks. Most dynamic endophyte populations, strongly influenced by environmental conditions and crop management, were observed in leaves. The potential of selected endophytes to confer protection against Monilinia laxa was also analysed and 7 isolates were found to inhibit the growth of this pathogen in vitro.

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The plant microbiome explored: implications for experimental botany

Cited by 435 publications

References 71 publications

Microbial interactions: ecology in a molecular perspective

Microbial interactions: ecology in a molecular perspective

Transient leaf endophytes are the most active fungi in 1-year-old beech leaf litter

Characterization of community structure of culturable endophytic fungi in sweet cherry composite trees and their growth-retarding effect against pathogens

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