Functional Potential of Soil Microbial Communities in the Maize Rhizosphere

Abstract

Microbial communities in the rhizosphere make significant contributions to crop health and nutrient cycling. However, their ability to perform important biogeochemical processes remains uncharacterized. Here, we identified important functional genes that characterize the rhizosphere microbial community to understand metabolic capabilities in the maize rhizosphere using the GeoChip-based functional gene array method. Significant differences in functional gene structure were apparent between rhizosphere and bulk soil microbial communities. Approximately half of the detected gene families were significantly (p<0.05) increased in the rhizosphere. Based on the detected gyrB genes, Gammaproteobacteria, Betaproteobacteria, Firmicutes, Bacteroidetes and Cyanobacteria were most enriched in the rhizosphere compared to those in the bulk soil. The rhizosphere niche also supported greater functional diversity in catabolic pathways. The maize rhizosphere had significantly enriched genes involved in carbon fixation and degradation (especially for hemicelluloses, aromatics and lignin), nitrogen fixation, ammonification, denitrification, polyphosphate biosynthesis and degradation, sulfur reduction and oxidation. This research demonstrates that the maize rhizosphere is a hotspot of genes, mostly originating from dominant soil microbial groups such as Proteobacteria, providing functional capacity for the transformation of labile and recalcitrant organic C, N, P and S compounds.

The effects of pig manure application on the spread of tetracycline resistance in bulk and cucumber rhizosphere soils: a greenhouse experiment

“…There were no significant differences between bulk and cucumber rhizosphere soils (Fig. 4), which was consistent with the result obtained by Li et al (2014). Unlike other ARGs such as major facilitator super gene family (MFS), small multidrug resistance gene family, and β-lactamase genes, accumulations of TRGs in rhizosphere are less than that in bulk soil.…”

“…Studies have demonstrated that plant roots influence the soil environment and its microbiota by exudation of growth substrates. It amplifies the effect of manure application on the abundance of ARB and ARGs in rhizosphere compared to those in bulk soil (Jechalke et al 2014;Jechalke et al 2013;Li et al 2014). However, it was found that sul1 and sul2 genes coding for dihydropteroate synthases were less abundant in the rhizosphere compared to bulk soil (Kopmann et al 2013).…”

A plant perspective on nitrogen cycling in the rhizosphere

“…We argue that, due to the higher C in the root vicinity, DNRA is likely favoured in the rhizosphere, allowing plants to conserve N in soil. This is supported by a recent study showing that bacteria possessing a key gene involved in DNRA were overrepresented in the rhizosphere compared to bulk soil (Li et al, ).…”

Wetland management strategies lead to tradeoffs in ecological structure and function

“…These phyla represent taxonomically and functionally diverse organisms typical in wetland sediments (Newton et al, 2011). For example, taxa in the phyla Acidobacteria have been shown to respond to nitrogen additions (Amend et al, 2016), and Acidobacteria and Proteobacteria are associated with higher potential for biogeochemical cycling of nitrogen, phosphorus, carbon, and sulfur (Li et al, 2014). Given that the restored wetland in this study is located on former agricultural land in an agriculturally dominated watershed (~62% land cover representing continuous corn, corn-soybean, and corn-hay) and thus receives non-point source nitrogen and phosphorus inputs due to fertilizer runoff (Kirsch, Kevin et al, 2002), our findings suggest that current or former local nutrient inputs drive bacterial community responses.…”