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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]

The rhizosphere is a nexus for plant–microbe interactions and, as a host-structured environment, a location of high activity for distinct microbes and plant species. Although our insights into this habitat have exploded in recent years, we are still limited in our ability to answer key questions about the specificity of these root-microbial relationships. In particular, it can be difficult to confirm or reject microbiome heritability in many plant systems and to pinpoint which microbial taxa are key to plant functioning. Like other host-structured environments, the rhizosphere is structurally, chemically, and biologically complex, driven largely by differences in root anatomy, location, and function. In this Correspondence, we describe a review of 377 "rhizosphere microbiome" research papers and demonstrate how matching a sampling method to the biological question can advance our understanding of host-microbe interactions in a functionally heterogeneous environment. We found that the vast majority of studies (92%) pool all roots from a root system during sampling, ignoring variation in microbial composition between roots of different function and limiting insight into key root-microbial relationships. Furthermore, approaches for removing root-associated microbes are highly variable and non-standard, complicating multi-study analyses. Our understanding of the strength and nature of host-microbe relationships in heterogenous host-microbiome environments can be clarified by targeting sampling to locations of high interaction. While the high complexity of the rhizosphere creates logistical challenges, we suggest that unambiguous language and refined approaches will improve our ability to match methods to research questions and advance our understanding of the specificity of plant-microbial interactions. [ABSTRACT FROM AUTHOR]

Aims: Vegetative groundcover and rootstock selection are popular growth control practices for fruit and nut crops. Theoretically, plant potential growth rate should influence competitive effectiveness; however, it is unclear if rootstock vigor alters crop productivity when groundcover is present. Methods: In a humid-climate vineyard we grew young grapevines on low- and medium-vigor rootstocks with and without groundcover. Vegetative growth was determined on dormant stems; yield was determined at harvest. Roots were extracted with soil cores and distribution, morphology, and mycorrhizal colonization were determined. Resource competition was assessed by water and nutrient depletion in vines and soil. Results: Compared to vines on low-vigor rootstocks, vines on medium-vigor rootstocks exhibited greater reductions in vegetative (40% vs 19%) and reproductive (22% vs 0%) growth by presence of groundcover. Irrespective of rootstock vigor, grapevine root systems coped with competition by increasing specific root length, decreasing absorptive root diameter, and redistributing roots deeper. Competition for nutrients was the apparent main cause of growth reductions with groundcover; however, mechanisms for differential rootstock responses remain unclear. Conclusions: This study suggests that in a wet year, young grapevines grafted on low-vigor rootstocks may be more tolerant of groundcover competition than those on medium-vigor rootstocks; however, both rootstocks cope with a similar root response. [ABSTRACT FROM AUTHOR]

In vineyards, cover crops typically grow concurrently with grapevines and can impart a multitude of agroecosystem services; yet concerns over potential disservices might limit adoption. Reductions in yield and vegetative growth are key disservices of concern, but at sites with high soil resources, reducing excessive vegetative growth is often considered beneficial, if the yield is not strongly penalized. To optimize agroecosystem services provided by cover crops, it is crucial to examine above- and belowground plant responses over multiple years. Documentation of the responses of fruit crop root systems to cover crops may clarify potential benefits for long-term agroecosystem services associated with aboveground growth and soil resources. In 2016, we established a perennial grass under young vines (full floor cover) to examine if agroecosystem services imparted by an under-vine cover crop change in the first five years of vineyard production and depend on rootstock vigor. Overall, cover crop reduced grapevine vegetative growth between 13% and 30% across all years and with a trend of more substantial reductions in the first two years. In contrast, yield was reduced in only three of the five years, between 9% and 25%, depending on the rootstock. Furthermore, neither cover crop nor differences in rootstock vigor resulted in relevant or consistent changes in fruit chemistry during the study. Overall, we found that in a relatively fertile, young vineyard, combining a lower vigor rootstock with a perennial, under-vine cover crop imparts substantial agroecosystem services in comparison to the more common practices of using a medium vigor rootstock and spraying herbicide under the vines. These services included improved crop load (ratio of fruit to vegetative mass), increased soil phosphorus availability, increased deep soil water content, and presumably lower labor and other costs associated with vineyard maintenance. Studies on a decadal timescale are needed to further clarify whether these services persist, accumulate with time, or if competition from the cover crop eventually leads to unacceptable decreases in vine nutrient status, growth, and production. • Cover crops (CC) impart agroecosystem services, but can reduce grapevine growth. • In high-soil resource vineyards, vegetative growth reductions can be beneficial. • Grapevine root responses to CC clarify plant growth and soil agroecosystem services. • Combining CC and a low vigor rootstock imparted substantial agroecosystem services. [ABSTRACT FROM AUTHOR]

• In fruit agroecosystems, groundcovers directly increase shallow root density and can induce deeper crop rooting. • After three years, groundcover root production substantially increased shallow (<40 cm) soil carbon (C) but grapevine roots negligibly affected deep C. • Results suggest a need for long term measurements of soil C beyond the 0–20 cm depth often measured in fruit agroecosystems. Soil carbon may be enhanced in agroecosystems by increasing root density throughout the soil profile. In vineyards and orchards, groundcovers that grow concurrently with the grapevines directly increase shallow root biomass and may induce deeper rooting of the fruit crop. We examined root distributions and soil properties associated with soil carbon in a vineyard that varies in groundcover and rootstock management practices. In comparison to an herbicide control, the grass groundcover substantially increased root biomass inputs in shallow soil zones (<40 cm) and appreciably influenced grapevine root mass distribution throughout the soil profile. Groundcover root growth enhanced soil carbon and nitrogen by nearly 50 % between 0−40 cm depths, but there was no significant influence of groundcover or rootstock on soil parameters at deeper depths (> 40 cm). Collectively, our results suggest that undervine groundcovers can substantially increase shallow soil carbon, but the potential for increases beyond the groundcover root zone remains unclear. [ABSTRACT FROM AUTHOR]

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]

Fine roots vary dramatically in their functions, which range from resource absorption to within-plant resource transport. These differences should alter resource availability to root-associated microorganisms, yet most root microbiome studies involve fine root homogenization. We hypothesized that microbial filtering would be greatest in the most distal roots. To test this, we sampled roots of six temperate tree species from a 23-year-old common garden planting, separating by branching order. Rhizoplane bacterial composition was characterized with 16S rRNA gene sequencing, while bacterial abundance was determined on a subset of trees through flow cytometry. Root order strongly impacted composition across tree species, with absorptive lower order roots exerting the greatest selective pressure. Microbial carrying capacity was higher in absorptive roots in two of three tested tree species. This study indicates lower order roots as the main point of microbial interaction with fine roots, suggesting that root homogenization could mask microbial recruitment signatures. William King, Caylon Yates, and colleagues utilize a 23-year-old common garden experiment to investigate how microbial filtering acts across root branching order. Their results demonstrate that roots of different orders have different microbial assemblages, and point to lower order roots as the main point of microbial interaction with fine roots. [ABSTRACT FROM AUTHOR]

Aims: Key functional root traits, including mycorrhizal association and root diameter, can help project ecosystem processes like root turnover and soil carbon sequestration. It is less clear, however, how such traits relate to variations in soil biology and chemistry. Here, we examined the impact of tree species with varied root traits on soil properties and rhizoplane bacterial composition, focusing specifically on mycorrhizal association type and root diameter. Methods: Within a long-term common garden in central Pennsylvania, USA, we selected three arbuscular mycorrhizal (AM) and three ectomycorrhizal (EM) tree species and assessed changes in (1) soil and leaf chemistry and (2) bacterial composition along fine absorptive roots, through 16S rRNA gene sequencing. Results: AM trees increased soil pH and soil available nitrogen relative to EM trees, and mycorrhizal association type was significantly associated with rhizoplane-associated bacterial composition. Absorptive root diameter did not clearly explain soil variability but was associated with changes in the composition of rhizoplane-associated bacteria. Conclusions: Tree-mediated shifts to soil properties were linked to mycorrhizal association type, whereas rhizoplane recruitment of bacteria was linked to both mycorrhizal type and root diameter. This has implications for predicting changes in biogeochemical processes following shifts in tree species composition. [ABSTRACT FROM AUTHOR]