Ecological assembly processes of the bacterial and fungal microbiota of wild and domesticated wheat species

Hassani, M. Amine; Özkurt, Ezgi; Franzenburg, Sören; Stukenbrock, Eva H.

doi:10.1101/2020.01.07.896910

Cited by 9 publications

(14 citation statements)

References 29 publications

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“…We observed a stronger selection of bacterial and fungal communities at the later growth stages based on the more distinct clustering of samples at BBCH21. Landraces and ancient lines of wheat clustered more distinctly at later stages, which could indicate a stronger selection during the colonization of ancient lines, as was also observed in a recent study (Hassani et al, 2020).…”

Section: Discussionsupporting

confidence: 83%

“…Rossmann et al (2020) observed stronger interactions in landraces with their soil microbiomes compared to modern wheat. Hassani et al (2020) found a higher stochasticity in the assembly of microbial communities in modern wheat compared to the two ancestors T. boeoticum and T. urartu. With a lower immigration rate, we also expected lower alpha diversity, and indeed, we observed that Tm and Tt had the lowest alpha diversity.…”

Section: Discussionmentioning

confidence: 86%

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Breeding selection imposed a differential selective pressure on the wheat root-associated microbiome

Kinnunen-Grubb

Sapkota

Vignola

et al. 2020

FEMS Microbiology Ecology

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Plants-microbiome associations are the result of millions of years of co-evolution. Due to breeding-accelerated plant evolution in non-native and highly managed soil, plant-microbe links could have been lost. We hypothesized that post-domestication breeding of wheat changed the root-associated microbiome. To test this, we analyzed root-associated fungal and bacterial communities shortly after emergence of seedlings representing a transect of wheat evolution including modern wheat, landraces, and ancestors. Numbers of observed microbial taxa were highest in landraces bred in low-input agricultural systems, and lowest in ancestors that had evolved in native soils. The microbial communities of modern cultivars were different from those of landraces and ancestors. Old wheat accessions enriched Acidobacteria and Actinobacteria, while modern cultivars enriched OTUs from Candidatus Saccharibacteria, Verrucomicrobia and Firmicutes. The fungal pathogens Fusarium, Neoascochyta and Microdochium enriched in modern cultivars. Both bacterial and fungal communities followed a neutral assembly model when bulk soil was considered as the source community, but accessions of the ancient Triticum turgidum and T. monococcum created a more isolated environment in their roots. In conclusion, wheat root-associated microbiomes have dramatically changed through a transect of breeding history.

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Section: Discussionsupporting

confidence: 83%

Section: Discussionmentioning

confidence: 86%

Breeding selection imposed a differential selective pressure on the wheat root-associated microbiome

Kinnunen-Grubb

Sapkota

Vignola

et al. 2020

FEMS Microbiology Ecology

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“…Cereal related grasses show high stochasticity in the assembly of endophytic microbiota [ 2 , 15 ]. Given the high stochasticity of microbial community assembly and the heterogeneous growth habitats of these plants, they are prone to accumulate highly heterogeneous microbiomes.…”

Section: Discussionmentioning

confidence: 99%

“…Wild plants are far more diverse and are grown under a much wider range of conditions than crop plants, entailing that FECs in wild species might be enriched for beneficial taxa. For example, FECs from bread wheat ( Triticum aestivum ) were less diverse than FECs from the closely related Triticum urartu [ 15 ]. To fully evaluate the true potential of wild species FECs for crop improvement, it is necessary to analyze FECs in population of wild species and compare them with those of related crops.…”

Section: Introductionmentioning

confidence: 99%

Stem Endophytic Mycobiota in Wild and Domesticated Wheat: Structural Differences and Hidden Resources for Wheat Improvement

Sun

Kosman

Sharon

2020

JoF

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Towards the identification of entophytic fungal taxa with potential for crop improvement, we characterized and compared fungal endophyte communities (FECs) from domesticated bread wheat and two wheat ancestors, Aegilopssharonensis and Triticumdicoccoides. Data generated by next generation sequencing identified a total of 1666 taxa. The FECs in the three plant species contained high proportions of random taxa with low abundance. At plant species level, the majority of abundant taxa were common to all host plants, and the collective FECs of each of the three plant species had similar diversity. However, FECs from the wild plants in specific sites were more diverse and had greater richness than wheat FECs from corresponding specific fields. The wild plants also had higher numbers of differentially abundant fungal taxa than wheat, with Alternaria infectoria being the most abundant species in wild plants and Candida sake the most abundant in wheat. Network analysis on co-occurrence association revealed a small number of taxa with a relatively high number of co-occurrence associations, which might be important in community assembly. Our results show that the actual endophytic cargo in cultivated wheat plants is limited relative to wild plants, and highlight putative functional and hub fungal taxa with potential for wheat improvement.

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“…According to their model, beta-null deviation values close to zero indicate neutral assembly, and values that are different from zero as niche-based assembly. Furthermore, Tucker et al's framework has been applied in a study that investigated the response of soil microbial communities to an anthropogenic disturbance (10) and in another that explored the role of ecological selection, drift and dispersal in assembling the bacterial communities associated with domesticated and wild wheat species (17).…”

Section: Introductionmentioning

confidence: 99%

Use of null models to compare the assembly of northeast Atlantic bacterial community in the presence of crude oil with either chemical dispersant or biosurfactant

Nikolova

Ijaz

Gutiérrez

2020

Preprint

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The compositions of marine microbial communities in response to crude oil in the presence of biosurfactant or synthetic dispersants have been extensively studied in the last decade. Assembly processes, however, in such communities are poorly understood. In this study, we used seven different but complementing null model approaches, such as elements of metacommunity structure, Raup-Crick beta-diversity, normalised stochasticity ratio, Tucker’s null model, quantitative process estimates, lottery assembly, and phylogenetic dispersion models, to quantify the relative importance of ecological process that drive the community assembly. We found that the presence of chemical dispersant in the oil-amended microcosms induced significant temporal changes in the assembly processes that were different from the oil-only or biogenic dispersant-amended microcosms. The assembly processes in all microcosms were neither purely deterministic nor stochastic, but increasingly deterministic in dispersant-amended microcosms. Furthermore, the relative importance of determinisms varied over time and was strongest during the middle phase of incubation. Tucker’s null model revealed that phylogenetically distinct taxa might have shaped the bacterial community assembly in the different microcosms towards more niche or neutral processes. Moreover, there was faster recruitment of phylogenetically distant species in the dispersant-amended community. Drift, homogenising selection and dispersal limitation were the dominant assembly processes in all microcosms, but variable selection was only important in dispersant-amended microcosms. In conclusion, our study highlights that the assembly processes in marine bacterial communities are not static but rather dynamic, and the chemical dispersant can cause significantly different patterns of community assembly compared to non-amended or biosurfactant-amended microcosms.ImportanceThe null model strategy is designed to intentionally exclude an ecological or evolutionary process of interest and create a beta diversity pattern that would be expected in the absence of this particular process – i.e. the community structure is random in respect to the process being tested. Recent advancements of bioinformatics and statistical tools have made it possible to apply theoretical macroecological concepts to microbial metagenomics in order to better understand and quantify the mechanisms and patterns controlling the complexity of microbial ecology. The conclusions from the null models can help predict the changes in microbial biodiversity and ecosystem services in oil polluted environments and therefore assist in making effective decisions with regards to what would be the best oil spill response option for similar environmental conditions.

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Ecological assembly processes of the bacterial and fungal microbiota of wild and domesticated wheat species

Cited by 9 publications

References 29 publications

Breeding selection imposed a differential selective pressure on the wheat root-associated microbiome

Breeding selection imposed a differential selective pressure on the wheat root-associated microbiome

Stem Endophytic Mycobiota in Wild and Domesticated Wheat: Structural Differences and Hidden Resources for Wheat Improvement

Use of null models to compare the assembly of northeast Atlantic bacterial community in the presence of crude oil with either chemical dispersant or biosurfactant

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