Towards Unraveling Macroecological Patterns in Rhizosphere Microbiomes

Abstract

It is generally accepted that plants locally influence the composition and activity of their rhizosphere microbiome, and that rhizosphere community assembly further involves a hierarchy of constraints with varying strengths across spatial and temporal scales. However, our knowledge of rhizosphere microbiomes is largely based on single-location and time-point studies. Consequently, it remains difficult to predict patterns at large landscape scales, and we lack a clear understanding of how the rhizosphere microbiome forms and is maintained by drivers beyond the influence of the plant. By synthesizing recent literature and collating data on rhizosphere microbiomes, we point out the opportunities and challenges offered by advances in molecular biology, bioinformatics, and data availability. Specifically, we highlight the use of exact sequence variants, coupled with existing and newly generated data to decipher the rules of rhizosphere community assembly across large spatial and taxonomic scales. Unearthing the Macroecology of Rhizosphere Soil Microbes Recent advances in sequencing technologies have expanded our ability to study plantassociated microbial communities. This has transformed our perception of the interactions between the plant and its microbiome (see Glossary) [1], which are now increasingly regarded jointly as holobionts [2-5]. The rhizosphere (i.e., the interface of plant roots and soils [6]) hosts diverse communities of microorganisms that are crucial to the plants they associate with. The rhizosphere microbiome can supply plants with nutrients [7], and protect plants against pathogens [8]. Furthermore, microbiomes can stimulate plant growth by producing phytohormones [9,10], and improve plant resistance and tolerance to abiotic stressors. Recent research suggests that rhizosphere microbiomes can alter plant phenology (e.g., flowering time) [11], modify morphological and size-related traits (e.g., shoot and root length and biomass, and number of secondary roots and leaves) [12], have a major role in plant community dynamics [13-15], and mediate plant responses to global change [16,17]. While much progress has been made, we are still far from understanding the mechanisms that control rhizosphere microbiome assembly and maintain community structure and composition. It has long been hypothesized that the macroecological patterns (i.e., ecological patterns across large spatial scales) of the rhizosphere microbiome will relate to the macroecological patterns of plants [18]. However, few studies have found clear relationships between plant and rhizosphere diversity [19,20]. This is likely because there is a disconnect between the plant and the microbial scales (Box 1). For other (non-rhizosphere) microbiomes, large-scale sampling campaigns are leading the way by generating standardized raw data and metadata (e.g., the Earth Microbiome Project [21] or the Human Microbiome Project [22]). For macro-organisms, macroecological patterns are frequently identified by collating existing and newly generated data from ...

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