Distinct kin strategies of the legume soybean and the non‐legume balsam by accomplishing different nitrogen acquisition and rhizosphere microbiome composition

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.

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

10.21203/rs.3.rs-87436/v1 ◽

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.

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

Environmental Microbiology ◽

10.1111/1462-2920.12900 ◽

2015 ◽

Vol 17 (8) ◽

pp. 3025-3038 ◽

Cited By ~ 35

Author(s):

Terrence H. Bell ◽

Benoît Cloutier-Hurteau ◽

Fahad Al-Otaibi ◽

Marie-Claude Turmel ◽

Etienne Yergeau ◽

...

Keyword(s):

Microbiome Composition ◽

Rhizosphere Microbiome ◽

Zn Uptake

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

Frontiers in Plant Science ◽

10.3389/fpls.2021.806915 ◽

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

10.21203/rs.3.rs-21333/v1 ◽

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.

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Induced secretion system mutation alters rhizosphere bacterial composition in Sorghum bicolor (L.) Moench

Planta ◽

10.1007/s00425-021-03569-5 ◽

2021 ◽

Vol 253 (2) ◽

Author(s):

Vimal Kumar Balasubramanian ◽

Lavanya Dampanaboina ◽

Christopher Joseph Cobos ◽

Ning Yuan ◽

Zhanguo Xin ◽

...

Keyword(s):

Phenolic Compounds ◽

Sorghum Bicolor ◽

Stress Tolerance ◽

Water Deficit ◽

Plant Root ◽

Secretion System ◽

Secretion Systems ◽

Selective Enrichment ◽

Microbiome Composition ◽

Rhizosphere Microbiome

Abstract Main conclusion A novel inducible secretion system mutation in Sorghum named Red root has been identified. The mutant plant root exudes pigmented compounds that enriches Actinobacteria in its rhizosphere compared to BTx623. Abstract Favorable plant–microbe interactions in the rhizosphere positively influence plant growth and stress tolerance. Sorghum bicolor, a staple biomass and food crop, has been shown to selectively recruit Gram-positive bacteria (Actinobacteria) in its rhizosphere under drought conditions to enhance stress tolerance. However, the genetic/biochemical mechanism underlying the selective enrichment of specific microbial phyla in the sorghum rhizosphere is poorly known due to the lack of available mutants with altered root secretion systems. Using a subset of sorghum ethyl methanesulfonate (EMS) mutant lines, we have isolated a novel Red root (RR) mutant with an increased accumulation and secretion of phenolic compounds in roots. Genetic analysis showed that RR is a single dominant mutation. We further investigated the effect of root-specific phenolic compounds on rhizosphere microbiome composition under well-watered and water-deficit conditions. The microbiome diversity analysis of the RR rhizosphere showed that Actinobacteria were enriched significantly under the well-watered condition but showed no significant change under the water-deficit condition. BTx623 rhizosphere showed a significant increase in Actinobacteria under the water-deficit condition. Overall, the rhizosphere of RR genotype retained a higher bacterial diversity and richness relative to the rhizosphere of BTx623, especially under water-deficit condition. Therefore, the RR mutant provides an excellent genetic resource for rhizosphere-microbiome interaction studies as well as to develop drought-tolerant lines. Identification of the RR gene and the molecular mechanism through which the mutant selectively enriches microbial populations in the rhizosphere will be useful in designing strategies for improving sorghum productivity and stress tolerance.

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