Succession of the fungal endophytic microbiome of wheat is dependent on tissue-specific interactions between host genotype and environment

Latz, M.; Kerrn, Mads Herbert; Sørensen, Helle; Collinge, David B.; Jensen, Birgit; Brown, J. K. M.; Madsen, Anne Mette; Jørgensen, Hans Jørgen Lyngs

doi:10.1016/j.scitotenv.2020.143804

Cited by 68 publications

(53 citation statements)

References 69 publications

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“…In addition, the Venn diagrams directly reflect the very small number of shared taxa between population sites suggesting that fungal endophyte communities in the coralloid roots of cycads may also be dependent on host-related factors as shown previously in other studies [ 41 , 44 ]. Host species identity and phylogenetic signals were reported to play a significant role on foliar and root associated endophytes [ 41 , 68 , 69 ]. An evidence showing the dissimilarity in phyllosphere fungal communities in Mussaenda pubescens was found to be positively correlated with the detected genetic differentiation among its regional populations [ 19 ].…”

Section: Discussionmentioning

confidence: 99%

“…Experiments on Arabidopsis revealed that host genotypes have little effects on the composition of its root endophytic microbes [ 68 ]. Similarly, a recent study showed that the host genotype was found to significantly contribute to the shaping of the root communities of fungal endophytes in wheat cultivars [ 69 ]. In Cycadaceae, the use of ISSR molecular markers in previous studies showed that the degree of genetic variation is high in between populations of the same species [ 33 , 34 , 35 ], indicating a clear plant genetic distance.…”

Section: Discussionmentioning

confidence: 99%

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Diversity, Phylogeny and Antagonistic Activity of Fungal Endophytes Associated with Endemic Species of Cycas (Cycadales) in China

Pecundo

Cruz

Chen

et al. 2021

JoF

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The culture-based approach was used to characterize the fungal endophytes associated with the coralloid roots of the endemic Cycas debaoensis and Cycas fairylakea from various population sites in China. We aim to determine if the assemblages of fungal endophytes inside these endemic plant hosts are distinct and could be explored for bioprospecting. The isolation method yielded a total of 284 culturable fungal strains. Identification based on the analysis of the internal transcribed spacer (ITS) rDNA showed that they belonged to two phyla, five classes, eight orders and 22 families. At least 33 known genera and 62 different species were confirmed based on >97% ITS sequence similarity. The most frequent and observed core taxa in the two host species regardless of their population origin were Talaromyces, Penicillium, Fusarium, Pochonia and Gliocladiopsis. Seventy percent was a rare component of the fungal communities with only one or two recorded isolates. Contrary to common notions, diversity and fungal richness were significantly higher in C. debaoensis and C. fairylakea collected from a botanical garden, while the lowest was observed in C. debaoensis from a natural habitat; this provides evidence that garden management, and to a minor extent, ex-situ conservation practice, could influence fungal endophyte communities. We further selected nineteen fungal isolates and screened for their antagonistic activities via a co-cultivation approach against the phytopathogens, Diaporthe sp. and Colletotrichum sp. Among these, five isolates with high ITS similarity matches with Hypoxylon vinosupulvinatum (GD019, 99.61%), Penicillium sp. (BD022, 100%), Penicillifer diparietisporus (GD008, 99.46%), Clonostachys rogersoniana (BF024, 99.46%) and C. rosea (BF011, 99.1%), which showed exceptional antagonistic activities against the phytopathogenic fungi with a significant inhibition rate of 70–80%. Taken together, our data presented the first and most comprehensive molecular work on culturable fungal endophytes associated with the coralloid roots of cycads. Our study also demonstrated that about 5% of fungal endophytes were not detected by the high-throughput sequencing approach, implying the equal importance of a culture-dependent approach to study fungal communities of cycads. We further highlighted the potential role of endemic and rare plants to discover and isolate unique plant-associated fungal taxa with excellent biocontrol properties.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Diversity, Phylogeny and Antagonistic Activity of Fungal Endophytes Associated with Endemic Species of Cycas (Cycadales) in China

Pecundo

Cruz

Chen

et al. 2021

JoF

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“…Previous studies showed that seeds have low microbial biomass and diversity (Adam et al 2018;Chesneau et al 2020;Rezki et al 2016), especially relative to other plant compartments or soil. Therefore, many studies pool seeds to analyze the aggregated microbiome of many seeds and to get enough microbial biomass for metagenomic DNA extraction (Latz et al 2021;Bergna et al 2018;Wassermann et al 2019;Adam et al 2018;Johnston-Monje and Raizada 2011;Klaedtke et al 2016). Generally, microbiome samples that have low biomass have numerous challenges in sequence-based analysis, as discussed elsewhere (Eisenhofer et al 2019;Bender et al 2018).…”

Section: Discussionmentioning

confidence: 99%

Endophytic microbiome variation at the level of a single plant seed

Bintarti

Sulesky-Grieb

Stopnišek

et al. 2021

Preprint

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Like other plant compartments, the seed harbors a microbiome. The members of the seed microbiome are the first to colonize a germinating seedling, and they initiate the trajectory of microbiome assembly for the next plant generation. Therefore, the members of the seed microbiome are important for the dynamics of plant microbiome assembly and the vertical transmission of potentially beneficial symbionts. However, it remains challenging to assess the microbiome at the individual seed level (and, therefore, for the future individual plant) due to low endophytic microbial biomass, seed exudates that can select for particular members, and high plant and plastid contamination of resulting reads. Here, we report a protocol for extracting metagenomic DNA from an individual seed (common bean, Phaseolus vulgaris L.) with minimal disruption of host tissue, which we expect to be generalizable to other medium- and large- seed plant species. We applied this protocol to quantify the 16S rRNA V4 and ITS2 amplicon composition and variability for individual seeds harvested from replicate common bean plants grown under standard, controlled conditions to maintain health. Using metagenomic DNA extractions from individual seeds, we compared seed-to-seed, pod-to-pod, and plant-to-plant microbiomes, and found highest microbiome variability at the plant level. This suggests that several seeds from the same plant could be pooled for microbiome assessment, given experimental designs that apply treatments at the maternal plant level. This study adds protocols and insights to the growing toolkit of approaches to understand the plant-microbiome engagements that support the health of agricultural and environmental ecosystems.

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“…For example, wild bean accessions had abundant Bacteroidetes, while modern domesticated accessions showed Proteobacteria and Actinobacteria in relatively high abundance [212]. A strong connection between host genotype and associated phylloshperic microbial diversity in different tomato accessions was detected [216]; however, host genetic variations, coupled with environmental factors, were correlated with the endophytic microbial diversity in wheat plants [217]. Thus, it is likely that microbial community shift is linked with modified plant genotypes and altered root morphology.…”

Section: Host Genotype-dependent Microbiome Engineeringmentioning

confidence: 99%

Plant–Microbiome Crosstalk: Dawning from Composition and Assembly of Microbial Community to Improvement of Disease Resilience in Plants

Noman

Ahmed

Ijaz

et al. 2021

IJMS

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Plants host diverse but taxonomically structured communities of microorganisms, called microbiome, which colonize various parts of host plants. Plant-associated microbial communities have been shown to confer multiple beneficial advantages to their host plants, such as nutrient acquisition, growth promotion, pathogen resistance, and environmental stress tolerance. Systematic studies have provided new insights into the economically and ecologically important microbial communities as hubs of core microbiota and revealed their beneficial impacts on the host plants. Microbiome engineering, which can improve the functional capabilities of native microbial species under challenging agricultural ambiance, is an emerging biotechnological strategy to improve crop yield and resilience against variety of environmental constraints of both biotic and abiotic nature. This review highlights the importance of indigenous microbial communities in improving plant health under pathogen-induced stress. Moreover, the potential solutions leading towards commercialization of proficient bioformulations for sustainable and improved crop production are also described.

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Succession of the fungal endophytic microbiome of wheat is dependent on tissue-specific interactions between host genotype and environment

Cited by 68 publications

References 69 publications

Diversity, Phylogeny and Antagonistic Activity of Fungal Endophytes Associated with Endemic Species of Cycas (Cycadales) in China

Diversity, Phylogeny and Antagonistic Activity of Fungal Endophytes Associated with Endemic Species of Cycas (Cycadales) in China

Endophytic microbiome variation at the level of a single plant seed

Plant–Microbiome Crosstalk: Dawning from Composition and Assembly of Microbial Community to Improvement of Disease Resilience in Plants

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