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.
Highlights
The rhizosphere is characterised by high microbial activity and an array of complex and dynamic physical, chemical and biological interactions termed the ‘rhizosphere effect’ (Helliwell et al 2019; Hiltner 1904)
Microbes associated with the rhizosphere represent a vast reservoir of microbial diversity that includes fungi, bacteria, nematodes, protozoa, algae, viruses and arthropods (Berg & Smalla 2009; Bonkowski et al 2000; Bonkowski, Villenave & Griffiths 2009; Bulgarelli et al 2013)
Plant species actively determine the composition of their rhizobiome by secreting root exudates that attract or repel specific bacteria from the surrounding bulk soil (Berg & Smalla 2009; Doornbos, Van Loon & Bakker 2012)
Summary
The rhizosphere is characterised by high microbial activity and an array of complex and dynamic physical, chemical and biological interactions termed the ‘rhizosphere effect’ (Helliwell et al 2019; Hiltner 1904). These interactions play a crucial role in plant nutrition (Raaijmakers et al 2009; Sørensen 1997) and ecosystem functioning in terrestrial ecosystems (Singh et al 2004). Plant species actively determine the composition of their rhizobiome by secreting root exudates that attract or repel specific bacteria from the surrounding bulk soil (Berg & Smalla 2009; Doornbos, Van Loon & Bakker 2012). Comparative studies on the effect of specific edaphic variables on the composition of the rhizobiome are rare because of a lack of suitable study sites where the influence of different soil types on the same plant species in close proximity can be compared effectively
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