Enrichment of specific bacterial and eukaryotic microbes in the rhizosphere of switchgrass (Panicum virgatum L.) through root exudates

Abstract

Identification of microbes that actively utilize root exudates is essential to understand plant-microbe interactions. To identify active root exudate-utilizing microorganisms associated with switchgrass - a potential bioenergy crop - plants were labelled in situ with (13) CO2 , and 16S and 18S rRNA genes in the (13) C-labelled rhizosphere DNA were pyrosequenced. Multi-pulse labelling for 5 days produced detectable (13) C-DNA, which was well separated from unlabelled DNA. Methylibium from the order Burkholderiales were the most heavily labelled bacteria. Pythium, Auricularia and Galerina were the most heavily labelled eukaryotic microbes. We also identified a Glomus intraradices-like species; Glomus members are arbuscular mycorrhizal fungi that are able to colonize the switchgrass root. All of these heavily labelled microorganisms were also among the most abundant species in the rhizosphere. Species belonging to Methylibium and Pythium were the most heavily labelled and the most abundant bacteria and eukaryotes in the rhizosphere of switchgrass. Our results revealed that nearly all of the dominant rhizosphere bacterial and eukaryotic microbes were able to utilize root exudates. The enrichment of microbial species in the rhizosphere is selective and mostly due to root exudation, which functions as a nutrition source, promoting the growth of these microbes.

Ecological diversity and co-occurrence patterns of bacterial community through soil profile in response to long-term switchgrass cultivation

“…The rhizodeposits from plant roots appear to be a major driving force in the regulation of microbial diversity and activity 29–31 . Previous study revealed that switchgrass could enrich specific microbial species in the rhizosphere, which were able to utilize root exudates 5 . However, we did not observe significant difference in bacterial communities between switchgrass cultivation and fallow soils.…”

“…It has received considerable attentions during the last several decades since it is recognized as a promising crop for biofuel production by the US Department of Energy (DOE) Herbaceous Energy Crops Program (HECP) 2–4 . The widespread of this perennial biofuel crops could shift the land use towards the renewable, biomass-based energy systems, and influence the soil ecosystems subsequently 5 . Particularly, soil microbes can respond rapidly to the environmental changes caused by plant 6, 7 .…”

Microbial communities and diazotrophic activity differ in the root‐zone of Alamo and Dacotah switchgrass feedstocks

“…1), root-zone exudates (e.g., amino acids, Fig. 2), KEGG analysis (Figs 4, 5, S6, and S7), and plant-microbial interactions (B€ urgmann et al, 2005;Mao et al, 2014). Different plant cultivars and growth stages have previously been shown to impact microbial community structure in plant root-zones (Berg & Smalla, 2009;Mao et al, 2011;Chaudhary et al, 2012;Chaparro et al, 2014).…”

“…Switchgrass is useful in the prevention of soil erosion and provides wildlife habitat and carbon sequestration (Ma, 1999;Skinner, 2009;Follett et al, 2012). Due to the various environmental and monetary benefits of switchgrass, identifying microbes for its sustainable production has been an active area of research (Jesus et al, 2010(Jesus et al, , 2016Mao et al, 2011Mao et al, , 2013Mao et al, , 2014Chaudhary et al, 2012;Hargreaves et al, 2015). These studies have shown presence of bacteria that are capable of nitrogen fixation; however, studies rarely confirm the occurrence and extent of nitrogen fixation associated with switchgrass.…”

Acidobacteria strains from subdivision 1 act as plant growth-promoting bacteria

“…Nevertheless, a number of studies have compared distribution and diversity of Acidobacteria in relation to plant root proximity (Chow et al 2002; Filion et al 2004; da Rocha et al 2010; Chaparro et al 2014) and/or plant exudates (Shi et al 2011; Mao et al 2014). For example, acidobacterial strains have been obtained from internal plant tissues hinting to an endophytic lifestyle (Idris et al 2004; Nissinen et al 2012; Poosakkannu et al 2015).…”