Abstract
Microbes form close associations with host plants including rice as both surface (epiphytes) and internal (endophytes) inhabitants. Yet despite rice being one of the most important cereal crops agriculturally and economically, knowledge of its microbiome, particularly core inhabitants and any functional properties bestowed is limited. In this study, the microbiome in rice seedlings derived directly from seeds was identified, characterized and compared to the microbiome of the seed. Rice seeds were sourced from two different locations in Arkansas, USA of two different rice genotypes (Katy, M202) from two different harvest years (2013, 2014). Seeds were planted in sterile media and bacterial as well as fungal communities were identified through 16S and ITS sequencing, respectively, for four seedling compartments (root surface, root endosphere, shoot surface, shoot endosphere). Overall, 966 bacterial and 280 fungal ASVs were found in seedlings. Greater abundance and diversity were detected for the microbiome associated with roots compared to shoots and with more epiphytes than endophytes. The seedling compartments were the driving factor for microbial community composition rather than other factors such as rice genotype, location and harvest year. Comparison with datasets from seeds revealed that 91 (out of 296) bacterial and 11 (out of 341) fungal ASVs were shared with seedlings with the majority being retained within root tissues. Core bacterial and fungal microbiome shared across seedling samples were identified. Core bacteria genera identified in this study such as Rhizobium, Pantoea, Sphingomonas, and Paenibacillus have been reported as plant growth promoting bacteria while core fungi such as Pleosporales, Alternaria and Occultifur have potential as biocontrol agents.
Highlights
Macro-organisms such as plants form close interactions with microbes, which together can be considered as meta-organisms or holobionts (Berg et al, 2014)
The number of reads before and after quality control and the number of amplicon sequence variants (ASVs) per sample as well as per tissue compartment are shown in Supplementary Tables 1, 2
With the exception of the root surface sample from fungi, the number of high-quality reads per tissue compartment after quality control ranged between 955,602–2,496,917
Summary
Macro-organisms such as plants form close interactions with microbes, which together can be considered as meta-organisms or holobionts (Berg et al, 2014). Bacteria, viruses, archaea and protista that are closely associated with plants are often referred to as the “second genome” (Berendsen et al, 2012). Different plant compartments such as roots, leaves, stems, flowers, fruits as. Various rhizobia and mycorrhizal fungi have been demonstrated to improve the acquisition of nutrients by plants (Hawkins et al, 2000; Zehr et al, 2003; Richardson et al, 2009; Miransari, 2011) Fungal endophytes such as Neotyphodium lolii can influence host plant CO2 fixation (Spiering et al, 2006). Unlike pathogenic microbes that cause disease on plants, microbes from Proteobacteria, Firmicutes, and Actinobacteria are known to suppress plant disease (Mendes et al, 2011)
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