Root surface as a frontier for plant microbiome research

Heijden, Marcel G. A. van der; Schlaeppi, Klaus

doi:10.1073/pnas.1500709112

Cited by 110 publications

(60 citation statements)

References 19 publications

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“…The taxonomic composition of the extraordinarily diverse communities of soil microorganisms associated with plants is partly determined by the plant genotype (van der Heijden & Schlaeppi, 2015; Korkama, Pakkanen, & Pennanen, 2006;Peiffer et al, 2013), although many other environmental factors simultaneously operate affecting these communities Peay et al, 2015;Rincón et al, 2015). The influence of plant genotypes on below-ground microbiota can be attributed to differences in plant growth performance, as well as in the varying amounts of carbon (C) provided to soil through litter and root exudates (van der Heijden & Schlaeppi, 2015;Hugoni et al., 2018;Korkama et al, 2006) and through their symbionts (Gorka et al, 2019;Smith & Read, 2008).…”

Section: Introductionmentioning

confidence: 99%

Plant intraspecific variation modulates nutrient cycling through its below ground rhizospheric microbiome

et al. 2019

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Plant genetic variation, through its phenotypic display, can determine the composition of below ground microbial communities. Variation within a species is increasingly acknowledged to have substantial ecological consequences, particularly through trophic cascades. We hypothesized that the intraspecific genotypic variation of the tree host might impact the phylogenetic composition of its rhizospheric microbial communities, by favouring particular clades, that might be further reflected in ecosystem process rates. We tested whether the intraspecific genotypic variation of Pinus pinaster modulates nutrient cycling by determining the phylogenetic structure of its symbiotic ectomycorrhizal fungi and rhizospheric bacteria. We sequenced fungal and bacterial molecular markers and reconstructed phylogenies in the rhizosphere of P. pinaster trees belonging to three genotypic variants (Mediterranean, Atlantic, African) in three 45‐year‐old common garden experiments, and measured seven soil enzymatic activities. Local effects, based on differences in elevation and soil conditions across sites, were strong predictors of the ectomycorrhizal and bacterial communities thriving in tree’s rhizosphere. Across‐site variation also explained differences in phosphorus cycling. We detected, however, a significant effect of the plant genotype on the phylogenetic structure of the root‐associated microbiota that was consistent across sites. The most productive Mediterranean plant genotype sheltered the most distinct root microbiome, with the dominant Basidiomycetes and Proteobacteria having a strong influence on the phylogenetic microbial community structure and associating with an enhanced hydrolysis of celluloses, hemicelluloses and chitin. Beneath the less productive Atlantic genotype, the less abundant Ascomycetes and up to thirteen bacterial phyla shaped the phylogenetic microbial structure, and predicted the rates of peptidase. Ectomycorrhizal fungi explained the activity of cellulases and protease, and bacteria that of hemicellulases and chitinase, suggesting functional complementarity. Synthesis. This is the first report using three‐replicated long‐term common gardens in mature forests to disentangle plant genotype‐ and site‐specific drivers of the rhizospheric microbiome and its enzymatic potential. We concluded that intraspecific variation in primary producers leaves a phylogenetic signature in mutualists and decomposers that further modulate key steps in carbon and nitrogen cycles. These results emphasize the ecological relevance of plant intraspecific diversity in determining essential plant–soil feedbacks that control ecosystem productivity and performance.

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Section: Introductionmentioning

confidence: 99%

Plant intraspecific variation modulates nutrient cycling through its below ground rhizospheric microbiome

et al. 2019

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“…Plants host diverse microbes that colonize to, on and in their tissues 1 . Based on their habitats, plant-associated microbial communities are referred to as rhizosphere microbiome, rhizoplane microbiome, phyllospher microbiome, and endosphere microbiome, respectively [2][3][4][5] . Different microbiomes interact with host plants and impact plants in various ways.…”

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“…In general, plant-associated microbial organisms can potentially have both positive and negative impacts on plant growth, development, and health 1 . Direct impacts on plant growth and development by microorganisms include improved nutrient accessibility such as nitrogen fixation and phosphate solubilization; altered microenvironments such as changed acidity (pH); and hormonal stimulation (phytohormone production) 3,6 . Microorganisms are also involved in the promotion or suppression of plant diseases either directly (such as antibiotics production) or indirectly (via disease resistance) 7 .…”

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Distinct microbial communities among different tissues of citrus tree Citrus reticulata cv. Chachiensis

et al. 2020

Sci Rep

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Plant microbiota colonize all organs of a plant and play crucial roles including supplying nutrients to plants, stimulating seed germination, promoting plant growth, and defending plants against biotic and abiotic stress. Because of the economic importance, interactions between citrus and microbes have been studied relatively extensively, especially citrus-pathogen interactions. However, the spatial distribution of microbial taxa in citrus trees remains under-studied. In this study, Citrus reticulata cv. Chachiensis was examined for the spatial distribution of microbes by sequencing 16S rRNA genes. More than 2.5 million sequences were obtained from 60 samples collected from soil, roots, leaves, and phloem. The dominant microbial phyla from all samples were Proteobacteria, Actinobacteria and Acidobacteria. The composition and structure of microbial communities in different samples were analyzed by PCoA, CAP, Anosim and MRPP methods. Variation in microbial species between samples were analyzed and the indicator microbes of each sample group were identified. Our results suggested that the microbial communities from different tissues varied significantly and the microenvironments of tree tissues could affect the composition of its microbial community.www.nature.com/scientificreports www.nature.com/scientificreports/ trees 23 . Most previous investigation on citrus-associated microbiomes are analyses on huanglongbing-infected, or specially-treated samples [24][25][26][27][28][29] .Citrus reticulata cv. Chachiensis is an important citrus variety widely cultivated around the world and the orange peel of the fruit was regarded as the valuable material which could be processed as food, tea drinks, and seasoning 30 . Besides, the orange peel owned antioxidant properties and extremely high medicinal value was also used as herb-medicine 31 . In China, C. reticulata cv. Chachiensis has grown in Xinhui District, Jiangmen City, Guangdong Province was considered as one of the most important cash crops for locals and the orange peel named genuine Pericarpium Citri Reticulatae (Guang Chen Pi) was admired as the best Chen pi which possesses the excellent clinical efficacy 32 . Plant-related microorganisms could protect the host from pathogens and pests, help plants use nutrients, and improve plant stress resistance 33 , while the microbial community of C. reticulata cv. Chachiensis remains unknown. In this study, endosphere microbiomes in soils, roots, leaves, and phloem of C. reticulata cv. Chachiensis were systematically investigated by sequencing 16S rRNA genes. The composition and structure of the microbial community in different tissues were performed by PCoA, CAP, Anosim and MRPP methods. Variation in microbial compositions among citrus tissues were analyzed and indicator microbes for different samples were identified. Our results suggested that the microbial community from different tissues of C. reticulata cv. Chachiensis in south china varied significantly. Our results laid a foundation for future studies on microbial comm...

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“…Classical microbiological methods have long offered a spotlight view on microbial diversity. Recent high-throughput molecular techniques have revolutionized the field of microbial ecology by unraveling an enormous microbial diversity in numerous organisms and highlighting the deep impact of microbiomes of their host physiology and behavior (1,2). Truffle fungi are no exception, since they are colonized by a complex microbial community made up of bacteria, yeasts, guest filamentous fungi, and viruses (3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14).…”

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The Role of the Microbiome of Truffles in Aroma Formation: a Meta-Analysis Approach

Vahdatzadeh

Deveau

Splivallo

2015

Appl Environ Microbiol

123

118

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dTruffles (Tuber spp.) are ascomycete subterraneous fungi that form ectomycorrhizas in a symbiotic relationship with plant roots. Their fruiting bodies are appreciated for their distinctive aroma, which might be partially derived from microbes. Indeed, truffle fruiting bodies are colonized by a diverse microbial community made up of bacteria, yeasts, guest filamentous fungi, and viruses. The aim of this minireview is two-fold. First, the current knowledge on the microbial community composition of truffles has been synthesized to highlight similarities and differences among four truffle (Tuber) species (T. magnatum, T. melanosporum, T. aestivum, and T. borchii) at various stages of their life cycle. Second, the potential role of the microbiome in truffle aroma formation has been addressed for the same four species. Our results suggest that on one hand, odorants, which are common to many truffle species, might be of mixed truffle and microbial origin, while on the other hand, less common odorants might be derived from microbes only. They also highlight that bacteria, the dominant group in the microbiome of the truffle, might also be the most important contributors to truffle aroma not only in T. borchii, as already demonstrated, but also in T. magnatum, T. aestivum, and T. melanosporum. Microbes can be found almost everywhere on our planet. They colonize many different types of habitats, among them living organisms, such as plant roots or insect and human guts. Classical microbiological methods have long offered a spotlight view on microbial diversity. Recent high-throughput molecular techniques have revolutionized the field of microbial ecology by unraveling an enormous microbial diversity in numerous organisms and highlighting the deep impact of microbiomes of their host physiology and behavior (1, 2). Truffle fungi are no exception, since they are colonized by a complex microbial community made up of bacteria, yeasts, guest filamentous fungi, and viruses (3-14).Truffles are subterranean ascomycete fungi that form ectomycorrhizas in symbiotic relationship with plant roots (15). Their fruiting bodies are appreciated for their distinctive aroma, which is partially derived from microbes (6,14,16). The aim of this minireview is to synthesize the current knowledge on the composition of the microbial community of truffles and discuss their potential role in truffle aroma formation, specifically focusing on volatiles that are responsible for human-perceived truffle aroma (defined as odorants). TRUFFLE MICROBIOMESTruffles are colonized by microbes at all stages of their life cycle, which include a symbiotic stage in association with a host plant (ectomycorrhiza), a sexual stage (fruiting bodies), and a free-living mycelial stage, which might serve an exploratory purpose in the soil. To date, microbes and microbial communities have been characterized in truffles with culture-dependent and -independent techniques in Ͼ15 papers (3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(17)(18)(19)(20)(21). Various life cycle stages of four...

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Root surface as a frontier for plant microbiome research

Cited by 110 publications

References 19 publications

Plant intraspecific variation modulates nutrient cycling through its below ground rhizospheric microbiome

Plant intraspecific variation modulates nutrient cycling through its below ground rhizospheric microbiome

Distinct microbial communities among different tissues of citrus tree Citrus reticulata cv. Chachiensis

The Role of the Microbiome of Truffles in Aroma Formation: a Meta-Analysis Approach

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