Abstract
In terrestrial ecosystems, plants interact with diverse taxonomic groups of bacteria and fungi in the phyllosphere and rhizosphere. Although recent studies based on high-throughput DNA sequencing have drastically increased our understanding of plant-associated microbiomes, we still have limited knowledge of how plant species in a species-rich community differ in their leaf and root microbiome compositions. In a cool-temperate semi-natural grassland in Japan, we compared leaf- and root-associated microbiomes across 137 plant species belonging to 33 plant orders. Based on the whole-microbiome inventory data, we analyzed how sampling season as well as the taxonomy, nativeness (native or alien), lifeform (herbaceous or woody), and mycorrhizal type of host plants could contribute to variation in microbiome compositions among co-occurring plant species. The data also allowed us to explore prokaryote and fungal lineages showing preferences for specific host characteristics. The list of microbial taxa showing significant host preferences involved those potentially having some impacts on survival, growth, or environmental resistance of host plants. Overall, this study provides a platform for understanding how plant and microbial communities are linked with each other at the ecosystem level.
Highlights
Plants interact with various taxonomic groups of microbes both in the phyllosphere and rhizosphere
Relationships between the number of sequencing reads and that of detected operational taxonomic units (OTUs) were examined for respective data matrices with the “rarecurve” function of the R vegan package
For each dataset, factors contributing to microbial community compositions were examined with the permutational analysis of variance [PERMANOVA; Anderson (2001)] using the vegan “adonis” function (10,000 permutations)
Summary
Plants interact with various taxonomic groups of microbes both in the phyllosphere and rhizosphere (van der Heijden et al, 1998; Berendsen et al, 2012; Bai et al, 2015; Peay et al, 2016). For example, are present on leaf surfaces, involved in underappreciated metabolic pathways (Mercier and Lindow, 2000; Delmotte et al, 2009; Hacquard et al, 2015). In addition to those epiphytes, a number of bacteria and filamentous fungi are known to inhabit leaf tissue (Ding and Melcher, 2016; Hamonts et al, 2018), playing pivotal roles in resistance of host plants against biotic and abiotic environmental stresses (Schardl and Phillips, 1997; Arnold et al, 2003; Hardoim et al, 2015; Santoyo et al, 2016). Understanding of the compositions of plant microbiomes is a prerequisite for understanding the physiology and ecology of plants in terrestrial ecosystems (van der Heijden et al, 2008; Schlaeppi and Bulgarelli, 2015; Toju et al, 2018a)
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