Identifying the Active Microbiome Associated with Roots and Rhizosphere Soil of Oilseed Rape

Gkarmiri, Konstantia; Mahmood, Shahid; Ekblad, Alf; Alström, Sadhna; Högberg, Nils; Finlay, Roger D.

doi:10.1128/aem.01938-17

Cited by 124 publications

(95 citation statements)

References 71 publications

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“…Members of the genus Chaetomium , as dominant cellulose utilizers, are known to degrade lignocellulosic biomass and various carbohydrates (Kramer et al., ; Song, Tian, Fan, & He, ). However, contrast with our results, Mortierella were found to primarily assimilate C from older substrate pools (Gkarmiri et al., ) which might need further studies of the characteristics of Mortierella species. The same classes of Eurotiomycetes, Sordariomycetes and Dothideomycetes but different genera including Talaromyces , Fusarium , Thielavia and Massariosphaeria were the major utilizers at Day 7.…”

Section: Discussioncontrasting

confidence: 99%

Analysis of microbial utilization of rice straw in paddy soil using a DNA‐SIP approach

Guo¹,

Zhang

Ai³

et al. 2020

Soil Science Soc of Amer J

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Considering the close connection between soil microorganisms with carbon (C) cycling, the aim of this study was to identify the specific bacterial and fungal microbes that assimilate 13C from incorporated rice straw and explore their dynamics and characteristics during straw decomposition in paddy soil. Soil microcosms based on 12/13C‐labeled rice straw were incubated with the determination of CO2 production at 1, 3, 7, 14, 28, 56 and 90 days after straw incorporation. Meanwhile, the targeted soil bacterial and fungal communities were characterized using a DNA‐based stable isotope probing (DNA‐SIP) approach combined with Illumina MiSeq sequencing. Rice straw decomposed rapidly in the first 2 weeks, coupled with a large turnover of soil native organic matter. During this process, Actinobacteria including the orders Streptomycetales, Caternulisporales and Corynebacteriales dominated the community utilizing rice straw‐derived C with a succession from Streptomyces, to Kitasatospora, to Catenulispora. At Days 56 to 90, the dominant orders assimilating rice straw‐derived 13C were Micrococcales, Sphingobacteriia, Gammaproteobacteria from phyla Actinobacteria, Bacteroidetes and Proteobacteria, respectively. The fungal orders Onygenales, Capnodiales, Sordariales and Pleosporales showed stronger ability of 13C utilization at late decomposition stage. Taken together, along with stimulation of soil organic matter mineralization after rice straw addition, dynamics of 13C‐assimilating bacterial and fungal groups with various characteristics were identified.

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Section: Discussioncontrasting

confidence: 99%

Analysis of microbial utilization of rice straw in paddy soil using a DNA‐SIP approach

Guo¹,

Zhang

Ai³

et al. 2020

Soil Science Soc of Amer J

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“…This taxon was the second most abundant OTU, accounting, on average, for 15% of the fungal reads in the root endosphere. The Olpidium genus includes different obligate biotrophic root pathogens and has been shown to be abundant in the Brassicaceae root microbiota in terms of DNA‐ and RNA‐based abundance (Tkacz et al ., ; Gkarmiri et al ., ). Our P‐replete conditions specifically promoted root colonization by this potential pathogen, favoring the inclusion of OTU00004 O. brassicae in the fungal community network (Fig.…”

Section: Discussionmentioning

confidence: 97%

Plant‐mediated effects of soil phosphorus on the root‐associated fungal microbiota in Arabidopsis thaliana

et al. 2018

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Summary Plants respond to phosphorus (P) limitation through an array of morphological, physiological and metabolic changes which are part of the phosphate (Pi) starvation response ( PSR ). This response influences the establishment of the arbuscular mycorrhizal ( AM ) symbiosis in most land plants. It is, however, unknown to what extent available P and the PSR redefine plant interactions with the fungal microbiota in soil. Using amplicon sequencing of the fungal taxonomic marker ITS 2, we examined the changes in root‐associated fungal communities in the AM nonhost species Arabidopsis thaliana in response to soil amendment with P and to genetic perturbations in the plant PSR . We observed robust shifts in root‐associated fungal communities of P‐replete plants in comparison with their P‐deprived counterparts, while bulk soil communities remained unaltered. Moreover, plants carrying mutations in the phosphate signaling network genes, phr1 , phl1 and pho2 , exhibited similarly altered root fungal communities characterized by the depletion of the chytridiomycete taxon Olpidium brassicae specifically under P‐replete conditions. This study highlights the nutritional status and the underlying nutrient signaling network of an AM nonhost plant as previously unrecognized factors influencing the assembly of the plant fungal microbiota in response to P in nonsterile soil.

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“…In addition, many microbes can probably not easily proliferate in the nutrient-limited conditions of the phyllosphere. While this possibility has not been explicitly tested, in the root system it is well established through stable isotope profiling that only a fraction of the microbiome measurably proliferates at any point in time 54 . Lastly, there is a possibility that unknown biases in our extraction and sequencing methods could potentially skew the relative abundance of microbiota.…”

Section: The Relationship Between the Presence Of A Single Prolific Tmentioning

confidence: 99%

The relationship between microbial population size and disease in the Arabidopsis thaliana phyllosphere

Karasov

Neumann

Duque‐Jaramillo

et al. 2019

Preprint

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A central goal in microbiome research is to learn what distinguishes a healthy from a dysbiotic microbial community. Shifts in diversity and taxonomic composition are important indicators of dysbiosis, but a full understanding also requires knowledge of absolute microbial biomass. Simultaneous information on both microbiome composition and the quantity of its components can provide insight into microbiome function and disease state. Here we use shotgun metagenomics to simultaneously assess microbiome composition and microbial load in the phyllosphere of wild populations of the plant Arabidopsis thaliana. We find that wild plants vary substantially in the load of colonizing microbes, and that high loads are typically associated with the proliferation of single taxa, with only a few putatively pathogenic taxa achieving high abundances in the field. Our results suggest (i) that the inside of a plant leaf is on average sparsely colonized with an estimated two bacterial genomes per plant genome and an order of magnitude fewer eukaryotic microbial genomes, and (ii) that higher levels of microbial biomass often indicate successful colonization by pathogens. Lastly, our results show that load is a significant explanatory variable for loss of estimated Shannon diversity in phyllosphere microbiomes, implying that reduced diversity may be a significant predictor of microbial dysbiosis in a plant leaf.

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Identifying the Active Microbiome Associated with Roots and Rhizosphere Soil of Oilseed Rape

Cited by 124 publications

References 71 publications

Analysis of microbial utilization of rice straw in paddy soil using a DNA‐SIP approach

Analysis of microbial utilization of rice straw in paddy soil using a DNA‐SIP approach

Plant‐mediated effects of soil phosphorus on the root‐associated fungal microbiota in Arabidopsis thaliana

The relationship between microbial population size and disease in the Arabidopsis thaliana phyllosphere

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