Original Research - Special Collection: Granite catena ecosystem

The rhizobiome of herbaceous plants in Clovelly and Sterkspruit soils of the Stevenson–Hamilton supersite

Marcele Vermeulen, Errol D. Cason, Wijnand J. Swart
Koedoe | Vol 62, No 2 | a1596 | DOI: https://doi.org/10.4102/koedoe.v62i2.1596 | © 2020 Marcele Vermeulen, Errol D. Cason, Wijnand J. Swart | This work is licensed under CC Attribution 4.0
Submitted: 26 September 2019 | Published: 29 October 2020

About the author(s)

Marcele Vermeulen, Microbial Biochemical and Food Biotechnology Department, Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein, South Africa
Errol D. Cason, Department of Animal, Wildlife and Grassland Sciences, Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein, South Africa
Wijnand J. Swart, Department of Plant Sciences, Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein, South Africa


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Abstract

By attracting microorganisms from the surrounding soil via root exudates, the composition of microbial populations in the rhizosphere of plants is regulated and maintained according to the genotype of the plant and its abiotic soil environment. This project investigated the bacterial diversity of the rhizosphere microbiome (i.e. rhizobiome) of the three most common herbaceous plants (Kyphocarpa angustifolia [Amaranthaceae, Caryophyllales], Melhania acuminata [Malvaceae, Malvales] and Sida cordifolia [Malvacae, Malvales]) growing mutually in two different soil types (Clovelly [top] and Sterkspruit [bottom]) with differing abiotic characteristics at a granite catenal supersite in the Kruger National Park, South Africa. Two plant species (K. angustifolia and S. cordifolia) occurred at both the top and bottom sites, whilst M. acuminata only occurred at the top site. Ten rhizosphere samples were collected per plant from both the top and bottom sites, comprising a total of 50 samples. Biolog EcoPlates™ were used to assess differences in carbon source utilisation patterns by bacteria in the rhizobiome. For next-generation sequencing analysis, the DNA from four randomly selected rhizosphere soil samples from each plant species, at both the top and bottom sites, was combined to yield two samples from each locality for each species. Targeted metagenomic sequencing of the 16S rRNA gene region (V3 and V4 regions) was used to characterise the rhizobiome. Actinobacteria and Proteobacteria were the most dominant phyla in all rhizobiomes, and unique and shared operational taxonomic units were identified in all the rhizobiomes. Principal component analysis of the Biolog data revealed no disparity between the five rhizobiomes.

Conservation implications: The results obtained in this study could play a role in micro-ecological scale conservation and management because microbial diversity in soils plays a vital role in shaping above-ground biodiversity and terrestrial ecosystem dynamics.


Keywords

Kruger National Park; Microbiome; Rhizobiome; 16S diversity; Stevenson–Hamilton Supersite; Granite catena

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Crossref Citations

1. Biotic and abiotic connections on a granitic catena: Framework for multidisciplinary research
Beanelri B. Janecke, Johan van Tol, Izak P.J. Smit, Andri C. van Aardt, Edward S. Riddell, Maitland T. Seaman, Wijnand J. Swart, Pieter J. du Preez, Pieter A.L. le Roux
KOEDOE - African Protected Area Conservation and Science  vol: 62  issue: 2  year: 2020  
doi: 10.4102/koedoe.v62i2.1600