Impact of root system architecture on rhizosphere and root microbiome

Saleem, Muhammad; Law, Audrey D.; Sahib, Mohammad Radhi; Pervaiz, Zahida Hassan; Zhang, Qingming

doi:10.1016/j.rhisph.2018.02.003

Cited by 232 publications

(155 citation statements)

References 33 publications

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“…It also plays important roles in biogeochemical processes of the Earth such as carbon sequestration, water cycling, as well as emission of greenhouse gases [2,45]. In agroecosystems, it is important to characterize the spatial distribution of soil microbiota along soil profiles as the vertical distribution of crop roots system has a significant effect on soil microbial communities [46]. Emerging evidence has indicated that “digging deeper” to assess the impact of deep roots on soil microbial communities is essential to enhance our understandings of community ecology and ecosystem functioning [24].…”

Section: Discussionmentioning

confidence: 99%

The effects of soil depth on the structure of microbial communities in agricultural soils in Iowa, USA

Hao

Chai

Ordóñez

et al. 2020

Preprint

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17 The determination of how microbial community structure changes within the soil profile, 18 will be beneficial to understanding the long-term health of agricultural soil ecosystems 19 and will provide a first step towards elucidating how deep soil microbial communities 20 contribute to carbon sequestration. This study aimed to investigate the differences in the 21 microbial community abundance, composition and diversity throughout from the surface 22 layers down to deep soils in corn and soybean fields in Iowa, USA. We used 16S rRNA 23 amplicon sequencing of soil samples to characterize the change in microbial community 24 structure. Our results revealed decreased richness and diversity in bacterial community 25 structure with increasing soil depth. We also observed distinct distribution patterns of 26 bacterial community composition along soil profiles. Soil and root data at different 27 depths enabled us to demonstrate that the soil organic matter, soil bulk density and 28 plant water availability were all significant factors in explaining the variation in soil 29 microbial community composition. Our findings provide valuable insights in the changes 30 in microbial community structure to depths of 180 cm in one of the most productive 31 agricultural regions in the world. This knowledge will be important for future 32 management and productivity of agroecosystems in the face of increasing demand for 33 food and climate change. 34 35 36

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Section: Discussionmentioning

confidence: 99%

The effects of soil depth on the structure of microbial communities in agricultural soils in Iowa, USA

Hao

Chai

Ordóñez

et al. 2020

Preprint

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“…However, these studies are limited to a small fraction of plant genes predicted to function in microbiome-related processes. Additionally, many plant traits expected to impact microbiome composition and activity, such as root exudation 8 and root system architecture 9 , are inherently complex and potentially governed by a very large number of genes. For these reasons, there is a need for alternative, large-scale and unbiased methods for identifying the genes that regulate host-mediated selection of the microbiome.…”

Section: Introductionmentioning

confidence: 99%

Genome wide association study reveals plant loci controlling heritability of the rhizosphere microbiome

Deng

Caddell

Yang

et al. 2020

Preprint

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45Host genetics has recently been shown to be a driver of plant microbiome composition. However, 46 identifying the underlying genetic loci controlling microbial selection remains challenging. 47 Genome wide association studies (GWAS) represent a potentially powerful, unbiased method to 48 identify microbes sensitive to host genotype, and to connect them with the genetic loci that 49 influence their colonization. Here, we conducted a population-level microbiome analysis of the 50 rhizospheres of 200 sorghum genotypes. Using 16S rRNA amplicon sequencing, we identify 51 rhizosphere-associated bacteria exhibiting heritable associations with plant genotype, and identify 52 significant overlap between these lineages and heritable taxa recently identified in maize. 53Furthermore, we demonstrate that GWAS can identify host loci that correlate with the abundance 54 of specific subsets of the rhizosphere microbiome. Finally, we demonstrate that these results can 55 be used to predict rhizosphere microbiome structure for an independent panel of sorghum 56 genotypes based solely on knowledge of host genotypic information. 57 58 sorghum 60 61Recent work has shown that root-associated microbial communities are in part shaped by host 63 genetics 1-4 . A study comparing the root microbiomes of a broad range of cereal crops has 64 demonstrated a strong correlation between host genetic differences and microbiome composition 4 , 65 suggesting that a subset of the plant microbiome may be influenced by host genotype across a 66 range of plant hosts. In maize, these genotype-sensitive, or "heritable", microbes are 67 phylogenetically clustered within specific taxonomic groups 5 ; however, it is unclear whether the 68 increased genotype sensitivity in these lineages is unique to the maize microbiome or is common 69 to other plant hosts as well. 71Despite consistent evidence of the interaction between host genetics and plant microbiome 72 composition, identifying specific genetic elements driving host-genotype dependent microbiome 73 acquisition and assembly in plants remains a challenge. Recent efforts guided by a priori 74 hypotheses of gene involvement have begun to dissect the impact of individual genes on 75 microbiome composition 6,7 . However, these studies are limited to a small fraction of plant genes 76 predicted to function in microbiome-related processes. Additionally, many plant traits expected to 77 impact microbiome composition and activity, such as root exudation 8 and root system architecture 9 , 78 are inherently complex and potentially governed by a very large number of genes. For these 79 reasons, there is a need for alternative, large-scale and unbiased methods for identifying the genes 80 that regulate host-mediated selection of the microbiome. 82Genome-wide association studies (GWAS) represent a powerful approach to map loci that are 83 associated with complex traits in a genetically diverse population. Though pioneered for use in 84 human genetics, to date the majority of GWAS have been conducted in pla...

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“…This observation is in line with our second hypothesis, and with the last part of our third hypothesis. A few studies have also found that root phenotypic traits or architecture potentially influence rhizosphere and root microbial communities in Phaseolus vulgaris and Nicotiana species [23,24]. Similar observations have been shown in wild and domesticated Phaseolus vulgaris, where the divergence in rhizobacterial community composition between wild and modern bean accessions is associated with differences in specific root length [22].…”

Section: Plant Shade Tolerance Is Related To Bacterial Community Compmentioning

confidence: 53%

“…Studies have indicated that root phenotypic traits can potentially influence the root and the rhizospheric soil microbiome [22,23]. Saleem et al [24] also showed that the root system architecture filters and recruits different microbial communities. However, there is little understanding of how shade influences root morphology and root-associated bacterial communities in turfgrasses.…”

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confidence: 99%

Effects of shade stress on turfgrasses morphophysiology and rhizosphere soil bacterial communities

Luo

Sun

et al. 2019

Preprint

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Background: The shade represents one of the major environmental limitations for turfgrass growth. Shade influences plant growth and alters plant metabolism, yet little is known about how shade affects the structure of rhizosphere soil microbial communities and the role of soil microorganisms in plant shade responses. In this study, a glasshouse experiment was conducted to examine the impact of shade on the growth and photosynthetic capacity of two contrasting shadetolerant turfgrasses, shade-tolerant dwarf lilyturf (Ophiopogon japonicus, OJ) and shade-intolerant perennial turf-type ryegrass (Lolium perenne, LP). We also examined soil-plant feedback effects on shade tolerance in the two turfgrass genotypes. The composition of the soil bacterial community was assayed using high-throughput sequencing. Results: OJ maintained higher photosynthetic capacity and root growth than LP under shade stress, thus OJ was found to be more shade-tolerant than LP. Shade-intolerant LP responded better to both shade and soil microbes than shade-tolerant OJ. The shade and live soil decreased LP growth, but increased biomass allocation to shoots in the live soil. The plant shade response index of LP is higher in live soil than sterile soil, driven by weakened soilplant feedback under shade stress. In contrast, there was no difference in these values for OJ under similar shade and soil treatments. Shade stress had little impact on the diversity of the OJ and the LP bacterial communities, but instead impacted their composition. The OJ soil bacterial communities were mostly composed of Proteobacteria and Acidobacteria. Further pairwise fitting analysis showed that a positive correlation of shade-tolerance in two turfgrasses and their bacterial community compositions. Several soil properties (NO3--N, NH4+-N, AK) showed a tight coupling with several major bacterial communities under shade stress. Moreover, OJ shared core bacterial taxa known to promote plant growth and confer tolerance to shade stress, which suggests common principles underpinning OJ-microbe interactions. Conclusion: Soil microorganisms mediate plant responses to shade stress via plant-soil feedback and shade-induced change in the rhizosphere soil bacterial community structure for OJ and LP plants. These findings emphasize the importance of understanding plant-soil interactions and their role in the mechanisms underlying shade tolerance in shade-tolerant turfgrasses.3 Background Light provides energy for photosynthesis, modulating plant growth, development, and morphogenesis [1]. Shade stress adversely impacts chlorophyll content, chloroplast ultrastructure, photosynthetic processes, and plant morphology [2][3][4][5]. Urban greening currently employs a combination of trees, shrubs and grass, resulting in an increase in shaded lawn area. As a result, shade stress presents a major challenge to turf grass growth in urban environments. It has been estimated that 20-25% of all turf grass in the USA [6], and 50% of turf grass in China, are subjected to varying degrees of shade [...

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Impact of root system architecture on rhizosphere and root microbiome

Cited by 232 publications

References 33 publications

The effects of soil depth on the structure of microbial communities in agricultural soils in Iowa, USA

The effects of soil depth on the structure of microbial communities in agricultural soils in Iowa, USA

Genome wide association study reveals plant loci controlling heritability of the rhizosphere microbiome

Effects of shade stress on turfgrasses morphophysiology and rhizosphere soil bacterial communities

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