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Application of compost and clay under water-stressed conditions influences functional diversity of rhizosphere bacteria

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Abstract

Applications of compost and clay to ameliorate soil constraints such as water stress are potential management strategies for sandy agricultural soils. Water repellent sandy soils in rain-fed agricultural systems limit production and have negative environmental effects associated with leaching and soil erosion. The aim was to determine whether compost and clay amendments in a sandy agricultural soil influenced the rhizosphere microbiome of Trifolium subterraneum under differing water regimes. Soil was amended with compost (2% w/w), clay (5% w/w) and a combination of both, in a glasshouse experiment with well-watered and water-stressed (70 and 35% field capacity) treatments. Ion Torrent 16S rRNA sequencing and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis of functional gene prediction were used to characterise the rhizosphere bacterial community and its functional component involved in nitrogen (N) cycling and soil carbon (C) degradation. Compost soil treatments increased the relative abundance of copiotrophic bacteria, decreased labile C and increased the abundance of recalcitrant C degrading genes. Predicted N cycling genes increased with the addition of clay (N2 fixation, nitrification, denitrification) and compost + clay (N2 fixation, denitrification) and decreased with compost (for denitrification) amendment. Water stress did not alter the relative abundance of phylum level taxa in the presence of compost, although copiotrophic Actinobacteria increased in relative abundance with addition of clay and with compost + clay. A significant role of compost and clay under water stress in influencing the composition of rhizosphere bacteria and their implications for N cycling and C degradation was demonstrated.

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Authors and Affiliations

  1. UWA School of Agriculture and Environment (M079), The University of Western Australia, Perth, WA, 6009, Australia

    Bede S. Mickan, Lynette K. Abbott, Kadambot H. M. Siddique, Zakaria M. Solaiman & Sasha N. Jenkins

  2. The UWA Institute of Agriculture (M082), The University of Western Australia, Perth, WA, 6009, Australia

    Bede S. Mickan, Lynette K. Abbott, Kadambot H. M. Siddique, Zakaria M. Solaiman & Sasha N. Jenkins

  3. Richgro Garden Products, 203 Acourt Rd, Jandakot, WA, 6164, Australia

    Bede S. Mickan

  4. State Key Laboratory of Grassland Agro-ecosystems, Institute of Arid Agroecology, School of Life Sciences, Lanzhou University, Lanzhou, Gansu Province, 730000, China

    Jingwei Fan

  5. Biology, University of British Columbia Okanagan, Kelowna, BC, V1V 1V7, Canada

    Miranda M. Hart

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  1. Bede S. Mickan
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Correspondence to Bede S. Mickan.

Electronic supplementary material

ESM 1

(DOC 34 kb)

Supplementary Fig. S1

Rarefaction curve for (a) well-watered treatment (35% FC), (b) water-stressed treatment (70% FC). Soil treatments are the addition of compost (2% w/w), clay (5% w/w) and the combination of compost and clay (2% w/w, 5% w/w) respectively. Error bars are the standard error of the mean (n = 4). (PNG 100 kb)

Supplementary Fig. S2

Relative abundance of the rhizosphere bacteria (phylum) community for (top) water-stressed (35% FC) and (b) well-watered conditions (70% FC) from the addition of compost (2% w/w), clay (5% w/w) and the combination of compost and clay (2% w/w, 5% w/w) respectively. Error bars are the standard error of the mean (n = 4). (PNG 72 kb)

Supplementary Fig. S3

Gene count of detected Nitrogen cycling genes under different soil treatments. Soil treatments are the addition of compost (2% w/w), clay (5% w/w) and the combination of compost and clay (2% w/w, 5% w/w) respectively (control is no addition of compost or clay). The bars represent the mean for each treatment and the error bars are the standard error of the mean (n = 4). (PNG 39 kb)

Supplementary Fig. S4

Gene count of detected C degrading genes under different soil treatments. Soil treatments are the addition of compost (2% w/w), clay (5% w/w) and the combination of compost and clay (2% w/w, 5% w/w) respectively (control is no addition of compost or clay). The complexity of the C substrates is presented in order from labile (starch) to recalcitrant (lignin). The bars represent the mean for each treatment and the error bars are the standard error of the mean (n = 4). (PNG 44 kb)

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Mickan, B.S., Abbott, L.K., Fan, J. et al. Application of compost and clay under water-stressed conditions influences functional diversity of rhizosphere bacteria. Biol Fertil Soils 54, 55–70 (2018). https://doi.org/10.1007/s00374-017-1238-5

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  • DOI: https://doi.org/10.1007/s00374-017-1238-5

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