scholarly journals Linking rhizosphere microbiome composition of wild and domesticated Phaseolus vulgaris to genotypic and root phenotypic traits

2017 ◽  
Vol 11 (10) ◽  
pp. 2244-2257 ◽  
Author(s):  
Juan E Pérez-Jaramillo ◽  
Víctor J Carrión ◽  
Mirte Bosse ◽  
Luiz F V Ferrão ◽  
Mattias de Hollander ◽  
...  
Keyword(s):  
Phaseolus Vulgaris ◽  
Phenotypic Traits ◽  
Microbiome Composition ◽  
Rhizosphere Microbiome

scholarly journals Influence of resistance breeding in common bean on rhizosphere microbiome composition and function

2017 ◽  
Vol 12 (1) ◽  
pp. 212-224 ◽  
Author(s):  
Lucas William Mendes ◽  
Jos M Raaijmakers ◽  
Mattias de Hollander ◽  
Rodrigo Mendes ◽  
Siu Mui Tsai
Keyword(s):  
Common Bean ◽  
Resistance Breeding ◽  
Microbiome Composition ◽  
Rhizosphere Microbiome ◽  
And Function

scholarly journals Rhizosphere Microbiome Regulates the Growth of Mustard under Organic Greenhouse Cultivation

Agriculture ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 987
Author(s):  
Ting-Chung Liu ◽  
Hui-Mei Peng ◽  
Seth Wollney ◽  
Chang-Hui Shen
Keyword(s):  
Soil Microbiome ◽  
Physiochemical Properties ◽  
Tropical Regions ◽  
Microbiome Composition ◽  
Vegetable Growth ◽  
Rhizosphere Microbiome ◽  
Organic Cultivation ◽  
Greenhouse Cultivation ◽  
Next Generation Sequencing Ngs ◽  
The Impact

Organic cultivation can improve soil fertility and biodiversity through the preservation of soil organic matter. Meanwhile, greenhouse cultivation can provide a controlled environment and therefore enables the management of every aspect of plant growth. In recent years, the combination of organic and greenhouse cultivation has slowly become a popular option in tropical regions to prevent the unpredictable impact of weather. Although it is known that organic cultivation significantly increases the density and species of microorganisms, the impact of soil microbiome on short-term vegetable growth under organic greenhouse cultivation is still not elucidated. In this study, we examined soil physiochemical properties as well as the rhizosphere microbiome from healthy and diseased mustard plants under organic greenhouse cultivation. Through next generation sequencing (NGS) analysis, our results revealed that the rhizosphere microbiome structure of healthy mustard plants was significantly different from those of the diseased mustard plants under organic greenhouse cultivation. Our findings suggest that soil microbiome composition can influence the growth of the vegetable significantly. As such, we have shown the impact of soil microbiome on vegetable growth under organic greenhouse cultivation and provide a possible strategy for sustainable agriculture.

scholarly journals Variation of soil microbiome in licorice rhizosphere driven with inoculating dark septate endophytes under drought stress

2020 ◽  
Author(s):  
Chao He ◽  
Wenquan Wang ◽  
Junling Hou ◽  
Xianen Li
Keyword(s):  
Microbial Community ◽  
Drought Stress ◽  
Relative Abundance ◽  
Water Regime ◽  
Am Fungi ◽  
Dark Septate Endophytes ◽  
Rrna Genes ◽  
Soil Microbial Community Structure ◽  
Microbiome Composition ◽  
Rhizosphere Microbiome

Abstract BackgroundDark septate endophytes (DSE) are facultative biotrophic ascomycetes that colonize plant roots either alone or with arbuscular mycorrhizal (AM) fungi. DSE may provide nutrients to their plant hosts and help them adapt to various abiotic and biotic stresses. DSE inoculation under drought stress increased the biomass, root exudates, and AM fungi in the licorice (Glycyrrhiza uralensis Fisch.) rhizosphere. We conducted a pot experiment to establish whether the responses of licorice to DSE inoculation under drought stress are caused by changes in the rhizosphere microbiome. Each pot was inoculated with either Acrocalymma vagum or Paraboeremia putaminum. One set of pots was inoculated with a sterile culture medium. All three DSE-treated and uninoculated pots were subjected either to a well-watered (70% field water capacity, FWC) or drought stress (30% FWC) water regime. Rhizosphere microbiome compositions were measured by Illumina MiSeq sequencing of the 16S and ITS2 rRNA genes.ResultsIn total, 1,278 fungal and 1,583 bacterial operational taxonomic units (OUTs) were obtained at a 97% sequence similarity level. Ascomycota were the predominant fungi and Proteobacteria, Actinobacteria, Chloroflexi and Firmicutes were the predominant bacteria. DSE inoculation and water regime significantly influenced the rhizosphere microbiome composition. However, the effects of DSE on the fungal community were greater than those on the bacterial community. Paraboeremia putaminum exerted a stronger impact on the licorice rhizosphere microbiome than Acrocalymma vagum under drought stress. The observed changes in edaphic factors (water condition, soil organic matter, available N, available P, and available K) caused by DSE inoculation could be explained by the variations in rhizosphere microbiome composition. A network analysis indicated that DSE inoculation augmented the relative abundance of beneficial symbiotrophic fungi and growth-promoting bacteria but diminished the relative abundance of pathogens in the licorice rhizosphere.ConclusionsThe present study showed that the licorice rhizosphere microbial community differed between the DSE-inoculated and uninoculated plants. DSE had a stronger influence on the fungal than on the bacterial rhizosphere community under drought stress. These give us the guidance to develop biofertilizers with DSE consortia to enhance the cultivation of medicinal plants by shaping soil microbial community structure in dryland agriculture.

Early rhizosphere microbiome composition is related to the growth and Zn uptake of willows introduced to a former landfill

2015 ◽  
Vol 17 (8) ◽  
pp. 3025-3038 ◽  
Author(s):  
Terrence H. Bell ◽  
Benoît Cloutier-Hurteau ◽  
Fahad Al-Otaibi ◽  
Marie-Claude Turmel ◽  
Etienne Yergeau ◽  
...  
Keyword(s):  
Microbiome Composition ◽  
Rhizosphere Microbiome ◽  
Zn Uptake

Ecology and Evolution of Plant Microbiomes

2019 ◽  
Vol 73 (1) ◽  
pp. 69-88 ◽  
Author(s):  
Viviane Cordovez ◽  
Francisco Dini-Andreote ◽  
Víctor J. Carrión ◽  
Jos M. Raaijmakers
Keyword(s):  
Life Support ◽  
Current Knowledge ◽  
Wild Plant ◽  
Plant Domestication ◽  
Phenotypic Traits ◽  
Support Functions ◽  
Ecological Processes ◽  
Microbiome Composition ◽  
The Impact ◽  
Plant Microbiome

Microorganisms colonizing plant surfaces and internal tissues provide a number of life-support functions for their host. Despite increasing recognition of the vast functional capabilities of the plant microbiome, our understanding of the ecology and evolution of the taxonomically hyperdiverse microbial communities is limited. Here, we review current knowledge of plant genotypic and phenotypic traits as well as allogenic and autogenic factors that shape microbiome composition and functions. We give specific emphasis to the impact of plant domestication on microbiome assembly and how insights into microbiomes of wild plant relatives and native habitats can contribute to reinstate or enrich for microorganisms with beneficial effects on plant growth, development, and health. Finally, we introduce new concepts and perspectives in plant microbiome research, in particular how community ecology theory can provide a mechanistic framework to unravel the interplay of distinct ecological processes—i.e., selection, dispersal, drift, diversification—that structure the plant microbiome.

scholarly journals Predicting Growth and Carcass Traits in Swine Using Metagenomic Data and Machine Learning Algorithms

2018 ◽  
Author(s):  
Christian Maltecca ◽  
Duc Lu ◽  
Costantino Schillebeeckx ◽  
Nathan P McNulty ◽  
Clint Schwab ◽  
...  
Keyword(s):  
Machine Learning ◽  
Prediction Accuracy ◽  
Carcass Traits ◽  
Live Weight ◽  
Carcass Composition ◽  
Machine Learning Algorithms ◽  
Metagenomic Data ◽  
Gradient Boosting ◽  
Phenotypic Traits ◽  
Microbiome Composition

ABSTRACTIn this paper, we evaluated the power of metagenome measures taken at three time points over the growth test period (weaning, 15 and 22 weeks) to foretell growth and carcass traits in 1039 individuals of a line of crossbred pigs. We measured prediction accuracy as the correlation between actual and predicted phenotypes in a five-fold cross-validation setting. Phenotypic traits measured included live weight measures and carcass composition obtained during the trial as well as at slaughter. We employed a null model excluding microbiome information as a baseline to assess the increase in prediction accuracy stemming from the inclusion of operational taxonomic units (OTU) as predictors. We further contrasted performance of models from the Bayesian alphabet (Bayesian Lasso) as well machine learning approaches (Random Forest and Gradient Boosting) and semi-parametric kernel models (Reproducing Kernel Hilbert space). In most cases, prediction accuracy increased significantly with the inclusion of microbiome data. Accuracy was more substantial with the inclusion of metagenomic information taken at week 15 and 22, with values ranging from approximately 0.30 for loin traits to more than 0.50 for back-fat. Conversely, microbiome composition at weaning resulted in most cases in marginal gains of prediction accuracy, suggesting that later measures might be more useful to include in predictive models. Model choice affected predictions marginally with no clear winner for any model/trait/time point. We, therefore, suggest average prediction across models as a robust strategy in fitting metagenomic information. In conclusion, microbiome composition can effectively be used as a predictor of growth and composition traits, particularly for fatness traits. The inclusion of OTU predictors could potentially be used to promote fast growth of individuals while limiting fat accumulation. Early microbiome measures might not be good predictors of growth and OTU information might be best collected at later life stages. Future research should focus on the inclusion of both microbiome as well as host genome information in predictions, as well as the interaction between the two. Furthermore, the influence of microbiome on feed efficiency as well as carcass and meat quality should be investigated.

scholarly journals Bioactive Diterpenoids Impact the Composition of the Root-Associated Microbiome in Maize (Zea mays)

2020 ◽  
Author(s):  
Katherine M. Murphy ◽  
Joseph Ewards ◽  
Katherine B. Louie ◽  
Benjamin P. Bowen ◽  
Venkatesan Sundaresan ◽  
...  
Keyword(s):  
Zea Mays ◽  
Molecular Mechanisms ◽  
Bacterial Community Composition ◽  
16S Rrna Gene Sequencing ◽  
Chemical Defenses ◽  
Rrna Gene ◽  
Wild Type ◽  
Microbiome Composition ◽  
Rhizosphere Microbiome ◽  
Maize Varieties

Abstract Background : Plants deploy both primary and species-specific, specialized metabolites to communicate with other organisms and adapt to environmental challenges. This includes interactions with soil-dwelling microbial communities, where plants may exchange sugars for important nutrients and protection against environmental perturbations, directly benefitting plant fitness. However, the molecular mechanisms underlying these plant-microbe interactions often remain elusive. Results : In this study, we report that maize ( Zea mays ) specialized diterpenoid metabolites with known antifungal bioactivities also influence rhizosphere bacterial communities. Metabolite profiling showed that dolabralexins, antibiotic diterpenoids that are highly abundant in roots of some maize varieties, can be exuded from the roots. Comparative 16S rRNA gene sequencing determined the bacterial community composition of the maize mutant Zman2 ( anther ear 2 ), which is deficient in dolabralexins and closely related bioactive kauralexin diterpenoids. Under well-watered conditions, the Zman2 rhizosphere microbiome differed significantly from the wild-type sibling with the most significant changes observed for Alphaproteobacteria of the order Sphingomonadales. By contrast, there was no difference in the microbiome composition between the mutant and wild-type was observed under drought stress. Metabolomics analyses support that these differences are attributed to the diterpenoid deficiency of the Zman2 mutant, rather than other metabolome alterations. Conclusions : Together, these findings support physiological functions of maize diterpenoids beyond known chemical defenses, including the assembly of the rhizosphere microbiome.

scholarly journals Domestication Impacts the Wheat-Associated Microbiota and the Rhizosphere Colonization by Seed- and Soil-Originated Microbiomes, Across Different Fields

2022 ◽  
Vol 12 ◽  
Author(s):  
Yulduzkhon Abdullaeva ◽  
Stefan Ratering ◽  
Binoy Ambika Manirajan ◽  
David Rosado-Porto ◽  
Sylvia Schnell ◽  
...  
Keyword(s):  
Host Plant ◽  
Vertical Transmission ◽  
Plant Traits ◽  
Aegilops Tauschii ◽  
Seed Transmission ◽  
Rrna Gene ◽  
Wheat Species ◽  
Microbiome Composition ◽  
Rhizosphere Microbiome ◽  
The Impact

The seed-transmitted microorganisms and the microbiome of the soil in which the plant grows are major drivers of the rhizosphere microbiome, a crucial component of the plant holobiont. The seed-borne microbiome can be even coevolved with the host plant as a result of adaptation and vertical transmission over generations. The reduced genome diversity and crossing events during domestication might have influenced plant traits that are important for root colonization by seed-borne microbes and also rhizosphere recruitment of microbes from the bulk soil. However, the impact of the breeding on seed-transmitted microbiome composition and the plant ability of microbiome selection from the soil remain unknown. Here, we analyzed both endorhiza and rhizosphere microbiome of two couples of genetically related wild and cultivated wheat species (Aegilops tauschii/Triticum aestivum and T. dicoccoides/T. durum) grown in three locations, using 16S rRNA gene and ITS2 metabarcoding, to assess the relative contribution of seed-borne and soil-derived microbes to the assemblage of the rhizosphere microbiome. We found that more bacterial and fungal ASVs are transmitted from seed to the endosphere of all species compared with the rhizosphere, and these transmitted ASVs were species-specific regardless of location. Only in one location, more microbial seed transmission occurred also in the rhizosphere of A. tauschii compared with other species. Concerning soil-derived microbiome, the most distinct microbial genera occurred in the rhizosphere of A. tauschii compared with other species in all locations. The rhizosphere of genetically connected wheat species was enriched with similar taxa, differently between locations. Our results demonstrate that host plant criteria for soil bank’s and seed-originated microbiome recruitment depend on both plants’ genotype and availability of microorganisms in a particular environment. This study also provides indications of coevolution between the host plant and its associated microbiome resulting from the vertical transmission of seed-originated taxa.

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