Studying Seed Microbiomes

Wassermann, Birgit; Rybakova, Daria; Adam, Eveline; Zachow, Christin; Bernhard, Maria Ludwika; Müller, Maria; Mancinelli, Riccardo; Berg, Gabriele

doi:10.1007/978-1-0716-1040-4_1

Cited by 11 publications

(5 citation statements)

References 37 publications

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“…Recent studies have shown the importance of the seed microbiome on germination and initial plant performance (Wassermann et al . 2021). Since seeds were not sterilized prior to sowing, their microbiome could have affected the expected legacy effects.…”

Section: Discussionmentioning

confidence: 99%

Soil legacies of tree species richness in a young plantation do not modulate tree seedling response to watering regime

Dhiedt,

Baeten,

De Smedt

et al. 2023

Plant Biol J

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Trees have a strong and species‐specific influence on biotic and abiotic properties of the soil. Even after the vegetation is removed, the effect can persist to form so‐called soil legacies. We investigated the effects of soil legacies of tree species richness on the emergence and growth of tree seedlings, and how these legacy effects modulate the seedling responses to irrigation frequency. We used a 9‐year‐old tree plantation on former agricultural land in Belgium, which is part of a biodiversity‐ecosystem functioning experiment (FORBIO). Soil originating from monocultures and four‐species plots, with different species combinations, was translocated to a greenhouse. Five tree species (Betula pendula, Fagus sylvatica, Pinus sylvestris, Quercus robur, and Tilia cordata) were sown and grown for one growing season in these soils. We performed a watering treatment (low and high irrigation frequency) to measure any potential interaction effects between the soil legacies and irrigation frequency. There was no evidence for soil legacy effects of species richness on plant performance or their response to the irrigation frequency. However, the effect of irrigation frequency was dependent on species identity of the tree seedlings. Despite the lack of clear legacy effects, performance measures did show correlated responses that are likely due to species composition effects. We ascribe these patterns to the young age of the forest and the agricultural past land use. At this early stage in forest development, the land‐use history likely has a more important role in shaping soil characteristics that affect plant growth and their response to drought, than species diversity.

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Section: Discussionmentioning

confidence: 99%

Soil legacies of tree species richness in a young plantation do not modulate tree seedling response to watering regime

Dhiedt,

Baeten,

De Smedt

et al. 2023

Plant Biol J

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“…Therefore, to target the native endophytic seed microbiome without also allowing for the plant’s potential selection for or filtering against particular members, it is important to use dormant seeds and also to minimally disrupt the seed compartment during extraction. Notably, many protocols have opted to first germinate seeds and, therefore, study the outcome of any plant selection prior to analyzing the seed microbiome (Wassermann et al 2021; Bergna et al 2018; López-López et al 2010).…”

Section: Discussionmentioning

confidence: 99%

“…Therefore, to target the native endophytic seed microbiome without also allowing for the plant's potential selection for or filtering against particular members, it is important to use dormant seeds and also to minimally disrupt the seed compartment during extraction. Notably, many protocols have opted to first germinate seeds and, therefore, study the outcome of any plant selection prior to analyzing the seed microbiome (Wassermann et al 2021;Bergna et al 2018;López-López et al 2010). Taking all of these methodological aspects into consideration, this study presents a protocol and analysis pipeline for endophyte microbiome DNA extraction from a single dormant seed that experiences minimal tissue disruption in the extraction process, includes both positive and negative sequencing controls, and includes bioinformatic steps to identify contamination and remove host signal from the marker gene amplification.…”

Section: Discussionmentioning

confidence: 99%

Endophytic microbiome variation at the level of a single plant seed

Bintarti

Sulesky-Grieb

Stopnišek

et al. 2021

Preprint

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Like other plant compartments, the seed harbors a microbiome. The members of the seed microbiome are the first to colonize a germinating seedling, and they initiate the trajectory of microbiome assembly for the next plant generation. Therefore, the members of the seed microbiome are important for the dynamics of plant microbiome assembly and the vertical transmission of potentially beneficial symbionts. However, it remains challenging to assess the microbiome at the individual seed level (and, therefore, for the future individual plant) due to low endophytic microbial biomass, seed exudates that can select for particular members, and high plant and plastid contamination of resulting reads. Here, we report a protocol for extracting metagenomic DNA from an individual seed (common bean, Phaseolus vulgaris L.) with minimal disruption of host tissue, which we expect to be generalizable to other medium- and large- seed plant species. We applied this protocol to quantify the 16S rRNA V4 and ITS2 amplicon composition and variability for individual seeds harvested from replicate common bean plants grown under standard, controlled conditions to maintain health. Using metagenomic DNA extractions from individual seeds, we compared seed-to-seed, pod-to-pod, and plant-to-plant microbiomes, and found highest microbiome variability at the plant level. This suggests that several seeds from the same plant could be pooled for microbiome assessment, given experimental designs that apply treatments at the maternal plant level. This study adds protocols and insights to the growing toolkit of approaches to understand the plant-microbiome engagements that support the health of agricultural and environmental ecosystems.

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“…Recent scientific inquiries have unveiled the seed microbiome's profound role in controlling fundamental aspects of plant life, including germination, growth, flowering, and fruiting. Studies on wheat seed microbiota have illuminated higher microbial diversity in the seed endosperm than in the embryo [110]. This microbial consortium does not merely passively coexist with seeds; it actively releases phytohormones, enzymes, and biocontrol agents, thereby propelling the degradation of pesticides and enhancing seedling germination even under stressful conditions [111][112][113].…”

Section: Seed Microbiomementioning

confidence: 99%

Phytomicrobiomes: A Potential Approach for Sustainable Pesticide Biodegradation

Salam,

Mahmood,

Asghar

et al. 2024

Applied Sciences

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Globally, pest-induced crop losses ranging from 20% to 40% have spurred the extensive use of pesticides, presenting a double-edged sword that threatens not only human health but also our environment. Amidst various remediation techniques, bioremediation stands out as a compelling and eco-friendly solution. Recently, the phytomicrobiome has garnered increasing attention as endophytic microbes, colonizing plants from their roots, not only foster plant growth but also enhance the host plant’s resilience to adverse conditions. Given the persistent demand for high crop yields, agricultural soils often bear the burden of pesticide applications. Biodegradation, the transformation of complex pesticide compounds into simpler forms through the activation of microbial processes and plant-based enzymatic systems, emerges as a pivotal strategy for restoring soil health. Manipulating the phytomicrobiome may emerge as a viable solution for this purpose, offering a native metabolic pathway that catalyzes pollutant degradation through enzymatic reactions. This review delves into the pivotal role of phytomicrobiomes in the degradation of diverse pesticides in soil. It explores contemporary innovations and paves the way for discussions on future research directions in this promising field.

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Studying Seed Microbiomes

Cited by 11 publications

References 37 publications

Soil legacies of tree species richness in a young plantation do not modulate tree seedling response to watering regime

Soil legacies of tree species richness in a young plantation do not modulate tree seedling response to watering regime

Endophytic microbiome variation at the level of a single plant seed

Phytomicrobiomes: A Potential Approach for Sustainable Pesticide Biodegradation

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