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Traditionally, fine roots were grouped using arbitrary size categories, rarely capturing the heterogeneity in physiology, morphology and functionality among different fine root orders. Fine roots with different functional roles are rarely separated in microbiome‐focused studies and may result in confounding microbial signals and host‐filtering across different root microbiome compartments. Using a 26‐year‐old common garden, we sampled fine roots from four temperate tree species that varied in root morphology and sorted them into absorptive and transportive fine roots. The rhizoplane and rhizosphere were characterized using 16S rRNA gene and internal transcribed spacer region amplicon sequencing and shotgun metagenomics for the rhizoplane to identify potential microbial functions. Fine roots were subject to metabolomics to spatially characterize resource availability. Both fungi and bacteria differed according to root functional type. We observed additional differences between the bacterial rhizoplane and rhizosphere compartments for absorptive but not transportive fine roots. Rhizoplane bacteria, as well as the root metabolome and potential microbial functions, differed between absorptive and transportive fine roots, but not the rhizosphere bacteria. Functional differences were driven by sugar transport, peptidases and urea transport. Our data highlights the importance of root function when examining root‐microbial relationships, emphasizing different host selective pressures imparted on different root microbiome compartments. Summary Statement: Functionally discrete fine roots are often homogenized in microbiome studies. Here, we show that the microbial composition, potential microbial functions and the root metabolome differ with root functional type for four temperate tree species: Liriodendron tulipifera, Pinus strobus, Acer saccharum and Quercus rubra. [ABSTRACT FROM AUTHOR]

Google Scholar Google Preview OpenURL Placeholder Text WorldCat COPAC 10 Hendriks M, Ravenek JM, Smit-Tiekstra AE, van der Paauw JW, de Caluwe H, van der Putten WH, de Kroon H, Mommer L. 2015. Google Scholar Crossref Search ADS PubMed WorldCat 12 Keel SG, Campbell CD, Högberg MN, Richter A, Wild B, Zhou X, Hurry V, Linder S, Näsholm T, Högberg P. 2012. Keywords: In situ; microbiome; rhizosphere; root traits; scale; spatial analysis; variation partitioning analysis EN In situ microbiome rhizosphere root traits scale spatial analysis variation partitioning analysis 1751 1757 7 04/12/23 20230328 NES 230328 Box 1. Google Scholar Crossref Search ADS PubMed WorldCat 14 Lavely EK, Chen W, Peterson KA, Klodd AE, Volder A, Marini RP, Eissenstat DM. 2020. [Extracted from the article]

Microbial relationships with roots influence many ecosystem functions and nutrient fluxes, including their sometimes-profound effects on plant health and productivity. Fine roots were often classified with a diameter less than 2 mm, but fine roots under that size perform distinct functional roles in the environment. Importantly, two broad functional categories of fine roots are absorptive and transportive , with absorptive fine roots acting as metabolic hotspots for root activity. In two of our recent studies, we have shown that several microbial community characteristics differ between absorptive and transportive fine roots, including composition, abundance, and function, as well as the root metabolome. This highlights a growing recognition within microbial ecology that we must consider fine-scale environmental variability, such as root physiology and morphology, when interpreting microbial patterns. In this commentary, we summarize the findings of our latest article, further speculate on some of these patterns, and suggest future studies for examining decomposition and applying cutting-edge single-cell sequencing techniques., Competing Interests: Declaration of conflicting interestsThe authors declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.