Key microbial taxa in the rhizosphere of sorghum and sunflower grown in crop rotation

Abstract

Microbes are key determinants of plant health and productivity. Previous studies have characterized the rhizosphere microbiomes of numerous plant species, but little information is available on how rhizosphere microbial communities change over time under crop rotation systems. Here, we document microbial communities in the rhizosphere of sorghum and sunflower (at seedling, flowering and senescence stages) grown in crop rotation in four different soils under field conditions. A comprehensive 16S rRNA-based amplicon sequencing survey revealed that the differences in alpha-diversity between rhizosphere and bulk soils changed over time. Sorghum rhizosphere soil microbial diversity at flowering and senescence were more diverse than bulk soils, whereas the microbial diversity of sunflower rhizosphere soils at flowering were less diverse with respect to bulk soils. Sampling time was also important in explaining the variation in microbial community composition in soils grown with both crops. Temporal changes observed in the rhizosphere microbiome were both plant-driven and due to seasonal changes in the bulk soil biota. Several individual taxa were relatively more abundant in the rhizosphere and/or found to be important in maintaining rhizosphere microbial networks. Interestingly, some of these taxa showed similar patterns at different sampling times, suggesting that the same organisms may play the same functional/structural role at different plant growth stages and in different crops. Overall, we have identified prominent microbial taxa that might be used to develop microbiome-based strategies for improving the yield and productivity of sorghum and sunflower.

Genome wide association study reveals plant loci controlling heritability of the rhizosphere microbiome

“…After removing rare OTUs with less than 3 reads in at least 20% of the samples and normalizing to an even read depth of 18,000 reads per sample, the data set included 1,189 high-abundance OTUs representing 29 bacterial phyla. Compositional analysis of the resulting microbiome dataset exhibited profiles consistent with recent microbiome studies involving the sorghum rhizosphere 4,22,23 from a variety of field sites, with Proteobacteria, Actinobacteria and Acidobacteria comprising the top three dominant phyla (Supplemental Figure 1).…”

Patterns of local, intercontinental and interseasonal variation of soil bacterial and eukaryotic microbial communities

“…Turnover and difference in variability in Bray-Curtis dissimilarity of each site for each group, with additional information on the amount of taxa during the 'high' and 'low' season, as well as the percentage of shared OTUs between the two time points. The lack of a correlation between interseasonal changes in community composition and edaphic parameters contradicts some of the earlier work on temporal changes in soil microbial communities (Bréchet et al 2018;Buscardo et al 2018;Lan et al 2018;Oberholster et al 2018;Ratcliffe, Bosman and Carnol 2018;Yang et al 2018;Zhang et al 2018). These studies found interseasonal changes in community composition or respiration, which were linked to temporal differences in precipitation, amount and quality of litter, and changes in the resident plant community.…”

Wheat dwarfing influences selection of the rhizosphere microbiome

“…On the other hand, members of Bacteroidetes accounted for less than 7% of module hubs and connectors and Verrucomicrobia members accounted for 16.67% in tall cultivars. Module hub and connector OTUs have been proposed as putative keystone taxa and ecological generalists, critical for maintaining community structure and function; peripherals on the other hand being considered isolated specialists 41,[69][70][71][72][73][74] . As such, Proteobacteria seem to be critical in maintaining the structure and functionality of bacterial communities in wheat rhizosphere for both tall and semi dwarf cultivars and these results are in accordance with data provided by Oberholster et al 71 , who also found Proteobacteria to be important keystone taxa for sorghum and sunflower rhizospheres.…”