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

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

Análisis de diversidad genética mediante microsatélites (SSR) en cultivares del germoplasma cubano de yuca

A study was carried out in order to make a deep analysis of the current knowledges cassava (Manihot esculenta Crantz) genetic diversity, and to evaluate its phylogenetic relationship with relatives cultivated in Africa, and South and Central America in order to facilitate a sustainable management of the genetic resources available in Cuba. A number of 94 cultivars from the Cuban cassava germplasm were studied according to their genetic or economic importance; besides, 54 clones from Africa and America, and 13 genotypes of genetic interest were incorporated. Diversity and genetic differentiation analysis were developed from data of 34 microsatellite markers (SSR). Genetic diversity indexes evidenced the high polymorphism observed for the tested microsatellites. The plant material, coming from Cuba, showed the highest allele average number per locus with 5.8 and as Guatemala, it illustrated 100% polymorphic loci. The highest mean heterozygosity indexes (Ho) are presented by Cuba and Tanzania. The mean rate of heterozygous individuals observed (Ho) was high (0.5918 ±0.0351). These results reported in Cuba for the first time in cassava, offer an important contribution to the genetic breeding program and to the sustainable management of the cassava genetic diversity in Cuba and in the Caribbean area.Key words: genetic differentiation, Manihot, markers, polymorphism, phylogenetic relationshipSe realizó un estudio con el objetivo de profundizar en el conocimiento de la diversidad genética de la yuca (Manihot esculenta Crantz), y para evaluar sus relaciones filogenéticas con parientes cultivados de África, Sur y Centroamérica, con vistas a garantizar un manejo sostenible de los recursos genéticos de que dispone Cuba. Se estudiaron 94 cultivares pertenecientes a la Colección Cubana de Yuca de acuerdo con su importancia económica y genética, además, se incorporaron 54 clones procedentes de África y América y otros 13 genotipos de interés genético. Los análisis de diversidad y diferenciación genética fueron desarrollados a partir de los datos de 34 marcadores microsatélites (SSR). Los índices de diversidad genética evidenciaron el alto polimorfismo observado para los microsatélites ensayados, el material vegetal procedente de Cuba mostró el mayor número promedio de alelos por loci con 5.8 y al igual que Guatemala presentó el 100% de los loci polimórficos; Cuba y Tanzania presentan los mayores índices de heterocigocidad media observada (Ho). La proporción promedio de individuos heterocigotos observados (Ho) fue alta (0.5918 ± 0.0351). Estos resultados, alcanzados por primera vez en Cuba en yuca, son importantes para su programa de mejoramiento genético y para el manejo sostenible de la diversidad genética en Cuba y en la región del Caribe.Palabras clave: diferenciación genética, Manihot, marcadores, polimorfismo, relaciones filogenético

Stochastic Inoculum, Biotic Filtering and Species-Specific Seed Transmission Shape the Rare Microbiome of Plants

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

Analysis by microsatellites (SSR) of genetic diversity in cultivars of Cuban cassava germplasm

A study was carried out in order to make a deep analysis of the current knowledges cassava (Manihot esculenta Crantz) genetic diversity, and to evaluate its phylogenetic relationship with relatives cultivated in Africa, and South and Central America in order to facilitate a sustainable management of the genetic resources available in Cuba. A number of 94 cultivars from the Cuban cassava germplasm were studied according to their genetic or economic importance; besides, 54 clones from Africa and America, and 13 genotypes of genetic interest were incorporated. Diversity and genetic differentiation analysis were developed from data of 34 microsatellite markers (SSR). Genetic diversity indexes evidenced the high polymorphism observed for the tested microsatellites. The plant material, coming from Cuba, showed the highest allele average number per locus with 5.8 and as Guatemala, it illustrated 100% polymorphic loci. The highest mean heterozygosity indexes (Ho) are presented by Cuba and Tanzania. The mean rate of heterozygous individuals observed (Ho) was high (0.5918 ±0.0351). These results reported in Cuba for the first time in cassava, offer an important contribution to the genetic breeding program and to the sustainable management of the cassava genetic diversity in Cuba and in the Caribbean area. Key words: genetic differentiation, Manihot, markers, polymorphism, phylogenetic relationshi