Crop management system and carrot genotype affect endophyte composition and Alternaria dauci suppression

Abdelrazek, Sahar; Šimon, Petr; Colley, Micaela; Mengiste, Tesfaye; Hoagland, Lori

doi:10.1371/journal.pone.0233783

Cited by 21 publications

(10 citation statements)

References 117 publications

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“…The results of this study suggest that plant-soil microbe interactions are influenced by trait breeding in organic carrot. This aligns with previous findings that carrot genotypes host distinct root-associated microbiomes that potentially differ in their functionality (Triviño et al 2023, Abdelrazek et al 2020. Moreover, we show that root exudation patterns were distinct across genotypes.…”

Section: Discussionsupporting

confidence: 92%

Root exudation and rhizosphere microbial recruitment are influenced by novel plant trait diversity in carrot genotypes

Anderson,

Cagle,

Majumder

et al. 2024

Preprint

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Root exudate composition can influence rhizosphere microbial recruitment and is tightly controlled by plant genetics. However, little research has profiled root exudate in vegetable crops or determined their role in rhizosphere microbial community and metabolite composition. It is also not well understood how root exudates and resulting rhizosphere dynamics shift across plant trait diversity and with the development of novel crop genotypes. To address these knowledge gaps, this study paired metabolomics and microbiome analyses to evaluate associations between the composition of exudates, soil bacterial and fungal communities, and soil metabolites across four genotypes of organically produced carrot of differential breeding histories, including two experimental genotypes. Plant genotypes modified soil microbial diversity and composition, and differentially recruited bacterial taxa with demonstrated potential for plant-growth related functions including ammonia oxidation, nitrogen fixation, and phytohormone production. Bacterial rhizosphere recruitment from bulk soil was genotype and root exudate-mediated, while fungal recruitment was not. Moreover, root exudate composition was distinct in an heirloom genotype and a novel nematode resistant genotype, compared to other genotypes tested. Root exudate and rhizosphere metabolite composition was decoupled, and soil metabolites strongly associated with fungal, but not bacterial communities. Taken together, the results of this study suggest that novel crop trait diversity and breeding histories hold consequences for the functional potential of soils through the diversification of root exudate mediated plant-microbe interactions.

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Section: Discussionsupporting

confidence: 92%

Root exudation and rhizosphere microbial recruitment are influenced by novel plant trait diversity in carrot genotypes

Anderson,

Cagle,

Majumder

et al. 2024

Preprint

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“…40°17′21″ N. long. 86°53′02″), located approximately 10 miles south of Lafayette, IN during summer 2015 48 . Soil at this site is classified in the Drummer soil series, which typically contain approximately 3.2% organic matter and a neutral pH.…”

Section: Methodsmentioning

confidence: 99%

Changes in the core endophytic mycobiome of carrot taproots in response to crop management and genotype

Abdelrazek

Choudhari

Thimmapuram

et al. 2020

Sci Rep

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Fungal endophytes can influence production and post-harvest challenges in carrot, though the identity of these microbes as well as factors affecting their composition have not yet been determined, which prevents growers from managing these organisms to improve crop performance. consequently, we characterized the endophytic mycobiome in the taproots of three carrot genotypes that vary in resistance to two pathogens grown in a trial comparing organic and conventional crop management using Illumina sequencing of the internal transcribed spacer (ITS) gene. A total of 1,480 individual operational taxonomic units (OTUs) were identified. Most were consistent across samples, indicating that they are part of a core mycobiome, though crop management influenced richness and diversity, likely in response to differences in soil properties. There were also differences in individual OTUs among genotypes and the nematode resistant genotype was most responsive to management system indicating that it has greater control over its endophytic mycobiome, which could potentially play a role in resistance. Members of the Ascomycota were most dominant, though the exact function of most taxa remains unclear. Future studies aimed at overcoming difficulties associated with isolating fungal endophytes are needed to identify these microbes at the species level and elucidate their specific functional roles. Carrot (Daucus carota L. subsp. sativus (Hoffm.) Arcang.) is one of the most important vegetable crops in the world, providing a good source of beta-carotene, fiber, Vitamin A and other vitamins and minerals to the human diet 1,2. Carrot taproots are often consumed raw, with per person consumption averaging 3.8 kg in 2015 3. Organic carrot production now accounts for 14% of the U.S. market 4 , and price premiums average 15% 4 , representing an opportunity for growers to transition to organic production. However, both organic and conventional carrot growers face many challenges to produce quality crops while protecting the environment. For example, while carrots are considered a nitrogen (N) scavenging crop, a substantial amount of N fertilizers are lost to the environment 5,6. Carrots are also subject to attack by many pests and diseases including Alternaria dauci 7 , and root knot nematodes 8 , as well as those that contribute to post-harvest storage losses 9. Endophytes, which are now commonly defined as microbes that spend at least part of their life cycle living inside plant tissues 10 , are one component of the plant microbiome that could help address these challenges. These microbes have been demonstrated to help plants acquire nutrients 11-13 , withstand abiotic stress 14,15 , and possibly even enhance the nutritional quality of crops. For example, some endophytes can produce or stimulate production of secondary metabolites 16,17 , indicating that they could play a role in the nutritional quality and organoleptic properties of plants 18. In addition, many endophytic taxa, especially fungi, have been shown to reduce disease caused by ...

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“…Another factor that could enhance the survival and efficacy of beneficial microbial inoculants is varietal or genotype selection. For example, we have previously demonstrated that both tomato (Jaiswal et al., 2020) and carrot (Abdelrazek et al., 2020) genotypes vary in their capacity to benefit from beneficial microbial inoculants. In this trial, we also observed a genotypic response, with fewer deaths in the tomato cultivar W55, but not Corbarino, because of inoculation with T‐22 (Figure 3).…”

Section: Discussionmentioning

confidence: 99%

Leaf mold compost reduces waste, improves soil and microbial properties, and increases tomato productivity

Richardville

Egel

Flachs

et al. 2022

Urban Agric & Regnl Food Sys

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Soils in urban settings are often degraded, which can prevent growers from optimizing the health and productivity of their crops. In this study, we investigated whether amending soil with a locally made leaf-mold compost could (a) improve soil chemical and biological properties, (b) increase survival of a microbial inoculant with plant growth promoting and disease suppressive capabilities, and (c) enhance the yield and quality of a tomato crop. Results were promising, with dramatically greater concentrations of active soil organic matter (SOM) and marketable fruit in plots receiving the amendment in both years of the study. Foliar disease severity was also lower in compost-amended plots in the second year of the trial. Inoculating tomato (Solanum lycopersicum L.) transplants with Trichoderma harzianum T-22 reduced deaths that are due to transplant stress in one of the cultivars evaluated, and the compost supported greater populations of this microbe in soil demonstrating that it is possible to enhance the efficacy of beneficial microbial inoculants in field settings using targeted practices. These results indicate that urban farmers can improve the productivity of their farms by amending soils with leaf mold compost, which will help ensure the long-term sustainability of urban farming initiatives. However, all composts should be tested to ensure they do not contain toxic levels of heavy metals or pathogens, and farmers should avoid overapplication since this can reduce crop health and lead to environmental challenges.

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Crop management system and carrot genotype affect endophyte composition and Alternaria dauci suppression

Cited by 21 publications

References 117 publications

Root exudation and rhizosphere microbial recruitment are influenced by novel plant trait diversity in carrot genotypes

Root exudation and rhizosphere microbial recruitment are influenced by novel plant trait diversity in carrot genotypes

Changes in the core endophytic mycobiome of carrot taproots in response to crop management and genotype

Leaf mold compost reduces waste, improves soil and microbial properties, and increases tomato productivity

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