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Stochastic inoculum, biotic filtering and species-specific seed transmission shape the rare imcrobiome of plants

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Title Stochastic inoculum, biotic filtering and species-specific seed transmission shape the rare imcrobiome of plants
 
Creator Johnston-Monje, David
Gutiérrez Artunduaga, Janneth Patricia
Becerra López Lavelle, Luis Augusto
 
Subject rhizosphere
phyllosphere
endophytes
vertical transmission
microbiomes
soil microorganisms
 
Description A plant’s health and productivity is influenced by its associated microbes. Although the common/core microbiome is often thought to be the most influential, significant numbers of rare or uncommon microbes (e.g., specialized endosymbionts) may also play an important role in the health and productivity of certain plants in certain environments. To help identify rare/specialized bacteria and fungi in the most important angiosperm plants, we contrasted microbiomes of the seeds, spermospheres, shoots, roots and rhizospheres of Arabidopsis, Brachypodium, maize, wheat, sugarcane, rice, tomato, coffee, common bean, cassava, soybean, switchgrass, sunflower, Brachiaria, barley, sorghum and pea. Plants were grown inside sealed jars on sterile sand or farm soil. Seeds and spermospheres contained some uncommon bacteria and many fungi, suggesting at least some of the rare microbiome is vertically transmitted. About 95% and 86% of fungal and bacterial diversity inside plants was uncommon; however, judging by read abundance, uncommon fungal cells are about half of the mycobiome, while uncommon bacterial cells make up less than 11% of the microbiome. Uncommon-seed-transmitted microbiomes consisted mostly of Proteobacteria, Firmicutes, Bacteriodetes, Ascomycetes and Basidiomycetes, which most heavily colonized shoots, to a lesser extent roots, and least of all, rhizospheres. Soil served as a more diverse source of rare microbes than seeds, replacing or excluding the majority of the uncommon-seed-transmitted microbiome. With the rarest microbes, their colonization pattern could either be the result of stringent biotic filtering by most plants, or uneven/stochastic inoculum distribution in seeds or soil. Several strong plant–microbe associations were observed, such as seed transmission to shoots, roots and/or rhizospheres of Sarocladium zeae (maize), Penicillium (pea and Phaseolus), and Curvularia (sugarcane), while robust bacterial colonization from cassava field soil occurred with the cyanobacteria Leptolyngbya into Arabidopsis and Panicum roots, and Streptomyces into cassava roots. Some abundant microbes such as Sakaguchia in rice shoots or Vermispora in Arabidopsis roots appeared in no other samples, suggesting that they were infrequent, stochastically deposited propagules from either soil or seed (impossible to know based on the available data). Future experiments with culturing and cross-inoculation of these microbes between plants may help us better understand host preferences and their role in plant productivity, perhaps leading to their use in crop microbiome engineering and enhancement of agricultural production.
 
Date 2022-09-02
2023-01-24T15:31:25Z
2023-01-24T15:31:25Z
 
Type Journal Article
 
Identifier Johnston-Monje, D.; Gutiérrez, J.P.; Becerra Lopez-Lavalle, L.A. (2022) Stochastic inoculum, biotic filtering and species-specific seed transmission shape the rare imcrobiome of plants. Life (Basel) 12(9):1372. ISSN: 2075-1729
2075-1729
https://hdl.handle.net/10568/128070
https://doi.org/10.3390/life12091372
 
Language en
 
Rights CC-BY-4.0
Open Access
 
Format application/pdf
 
Publisher MDPI AG
 
Source Life (Basel)