Dataset Information

Dissecting Community Structure in Wild Blueberry Root and Soil Microbiome.

ABSTRACT: A complex network of functions and symbiotic interactions between a eukaryotic host and its microbiome is a the foundation of the ecological unit holobiont. However, little is known about how the non-fungal eukaryotic microorganisms fit in this complex network of host-microbiome interactions. In this study, we employed a unique wild blueberry ecosystem to evaluate plant-associated microbiota, encompassing both eukaryotic and bacterial communities. We found that, while soil microbiome serves as a foundation for root microbiome, plant-influenced species sorting had stronger effect on eukaryotes than on bacteria. Our study identified several fungal and protist taxa, which are correlated with decreased fruit production in wild blueberry agricultural ecosystems. The specific effect of species sorting in root microbiome resulted in an increase in relative abundance of fungi adapted to plant-associated life-style, while the relative abundance of non-fungal eukaryotes was decreased along the soil-endosphere continuum in the root, probably because of low adaptation of these microorganisms to host-plant defense responses. Analysis of community correlation networks indicated that bacterial and eukaryotic interactions became more complex along the soil-endosphere continuum and, in addition to extensive mutualistic interactions, co-exclusion also played an important role in shaping wild blueberry associated microbiome. Our study identified several potential hub taxa with important roles in soil fertility and/or plant-microbe interaction, suggesting the key role of these taxa in the interconnection between soils and plant health and overall microbial community structure. This study also provides a comprehensive view of the role of non-fungal eukaryotes in soil ecosystem.

SUBMITTER: Yurgel SN

PROVIDER: S-EPMC5996171 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Publications

Dissecting Community Structure in Wild Blueberry Root and Soil Microbiome.

Yurgel Svetlana N SN Douglas Gavin M GM Dusault Ashley A Percival David D Langille Morgan G I MGI

Frontiers in microbiology 20180606

A complex network of functions and symbiotic interactions between a eukaryotic host and its microbiome is a the foundation of the ecological unit holobiont. However, little is known about how the non-fungal eukaryotic microorganisms fit in this complex network of host-microbiome interactions. In this study, we employed a unique wild blueberry ecosystem to evaluate plant-associated microbiota, encompassing both eukaryotic and bacterial communities. We found that, while soil microbiome serves as a ...[more]

PMID: 29922264

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Project description:Plant root-associated microbiomes play critical roles in promoting plant health, productivity, and tolerance to biotic/abiotic stresses. Blueberry (Vaccinium spp.) is adapted to acidic soils, while the interactions of the root-associated microbiomes in this specific habitat under various root microenvironments remain elusive. Here, we investigated the diversity and community composition of bacterial and fungal communities in various blueberry root niches (bulk soil, rhizosphere soil, and root endosphere). The results showed that blueberry root niches significantly affected root-associated microbiome diversity and community composition compared to those of the three host cultivars. Deterministic processes gradually increased along the soil-rhizosphere-root continuum in both bacterial and fungal communities. The co-occurrence network topological features showed that both bacterial and fungal community complexity and intensive interactions decreased along the soil-rhizosphere-root continuum. Different compartment niches clearly influenced bacterial-fungal interkingdom interactions, which were significantly higher in the rhizosphere, and positive interactions gradually dominated the co-occurrence networks from the bulk soil to the endosphere. The functional predictions showed that rhizosphere bacterial and fungal communities may have higher cellulolysis and saprotrophy capacities, respectively. Collectively, the root niches not only affected microbial diversity and community composition but also enhanced the positive interkingdom interactions between bacterial and fungal communities along the soil-rhizosphere-root continuum. This provides an essential basis for manipulating synthetic microbial communities for sustainable agriculture. IMPORTANCE The blueberry root-associated microbiome plays an essential role in its adaptation to acidic soils and in limiting the uptake of soil nutrients by its poor root system. Studies on the interactions of the root-associated microbiome in the various root niches may deepen our understanding of the beneficial effects in this particular habitat. Our study extended the research on the diversity and composition of microbial communities in different blueberry root compartment niches. Root niches dominated the root-associated microbiome compared to that of the host cultivar, and deterministic processes increased from the bulk soil to the endosphere. In addition, bacterial-fungal interkingdom interactions were significantly higher in the rhizosphere, and those positive interactions progressively dominated the co-occurrence network along the soil-rhizosphere-root continuum. Collectively, root niches dominantly affected the root-associated microbiome and the positive interkingdom interactions increased, potentially providing benefits for the blueberry.

Project description:Thermal pruning was a common pruning method in the past but has progressively been replaced by mechanical pruning for economic reasons. Both practices are known to enhance and maintain high yields; however, thermal pruning was documented to have an additional sanitation effect by reducing weeds and fungal diseases outbreaks. Nevertheless, there is no clear consensus on the optimal fire intensity required to observe these outcomes. Furthermore, fire is known to alter the soil microbiome as it impacts the soil organic layer and chemistry. Thus far, no study has investigated into the effect of thermal pruning intensity on the wild blueberry microbiome in agricultural settings. This project aimed to document the effects of four gradual thermal pruning intensities on the wild blueberry performance, weeds, diseases, as well as the rhizosphere fungal and bacterial communities. A field trial was conducted using a block design where agronomic variables were documented throughout the 2-year growing period. MiSeq amplicon sequencing was used to determine the diversity as well as the structure of the bacterial and fungal communities. Overall, yield, fruit ripeness, and several other agronomical variables were not significantly impacted by the burning treatments. Soil phosphorus was the only parameter with a significant albeit temporary change (1 month after thermal pruning) for soil chemistry. Our results also showed that bacterial and fungal communities did not significantly change between burning treatments. The fungal community was dominated by ericoid mycorrhizal fungi, while the bacterial community was mainly composed of Acidobacteriales, Isosphaerales, Frankiales, and Rhizobiales. However, burning at high intensities temporarily reduced Septoria leaf spot disease in the season following thermal pruning. According to our study, thermal pruning has a limited short-term influence on the wild blueberry ecosystem but may have a potential impact on pests (notably Septoria infection), which should be explored in future studies to determine the burning frequency necessary to control this disease.

Project description:The input of plant leaf litter has been assumed to be the most important resource for soil organisms of forest ecosystems, but there is increasing evidence that root-derived resources may be more important. By trenching roots of trees in deciduous and coniferous forests, we cut-off the input of root-derived resources and investigated the response of microorganisms using substrate-induced respiration and phospholipid fatty acid (PLFA) analysis. After one and three years, root trenching strongly decreased microbial biomass and concentrations of PLFAs by about 20%, but the microbial community structure was little affected and the effects were similar in deciduous and coniferous forests. However, the reduction in microbial biomass varied between regions and was more pronounced in forests on limestone soils (Hainich) than in those on sandy soils (Schorfheide). Trenching also reduced microbial biomass in the litter layer but only in the Hainich after one year, whereas fungal and bacterial marker PLFAs as well as the fungal-to-plant marker ratio in litter were reduced in the Schorfheide both after one and three years. The pronounced differences between forests of the two regions suggest that root-derived resources are more important in fueling soil microorganisms of base-rich forests characterized by mull humus than in forests poor in base cations characterized by moder soils. The reduction in microbial biomass and changes in microbial community characteristics in the litter layer suggests that litter microorganisms do not exclusively rely on resources from decomposing litter but also from roots, i.e. from resources based on labile recently fixed carbon. Our results suggest that both bacteria and fungi heavily depend on root-derived resources with both suffering to a similar extent to deprivation of these resources. Further, the results indicate that the community structure of microorganisms is remarkably resistant to changes in resource supply and adapts quickly to new conditions irrespective of tree species composition and forest management.

Dataset Information

Dissecting Community Structure in Wild Blueberry Root and Soil Microbiome.

Publications

Dissecting Community Structure in Wild Blueberry Root and Soil Microbiome.

Similar Datasets

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