Effect of the soil type on the microbiome in the rhizosphere of field-grown lettuce

Abstract

The complex and enormous diversity of microorganisms associated with plant roots is important for plant health and growth and is shaped by numerous factors. This study aimed to unravel the effects of the soil type on bacterial communities in the rhizosphere of field-grown lettuce. We used an experimental plot system with three different soil types that were stored at the same site for 10 years under the same agricultural management to reveal differences directly linked to the soil type and not influenced by other factors such as climate or cropping history. Bulk soil and rhizosphere samples were collected 3 and 7 weeks after planting. The analysis of 16S rRNA gene fragments amplified from total community DNA by denaturing gradient gel electrophoresis and pyrosequencing revealed soil type dependent differences in the bacterial community structure of the bulk soils and the corresponding rhizospheres. The rhizosphere effect differed depending on the soil type and the plant growth developmental stage. Despite the soil type dependent differences in the bacterial community composition several genera such as Sphingomonas, Rhizobium, Pseudomonas, and Variovorax were significantly increased in the rhizosphere of lettuce grown in all three soils. The number of rhizosphere responders was highest 3 weeks after planting. Interestingly, in the soil with the highest numbers of responders the highest shoot dry weights were observed. Heatmap analysis revealed that many dominant operational taxonomic units were shared among rhizosphere samples of lettuce grown in diluvial sand, alluvial loam, and loess loam and that only a subset was increased in relative abundance in the rhizosphere compared to the corresponding bulk soil. The findings of the study provide insights into the effect of soil types on the rhizosphere microbiome of lettuce.

Keywords: 16S rRNA gene analysis; DGGE; Lactuca sativa; bacterial communities; pyrosequencing; rhizosphere responders.

Figure 1

Cluster analysis of bacterial communities from rhizosphere and bulk soil samples. Samples from rhizosphere of lettuce and the corresponding bulk soil of DS, AL, and LL soil were taken at 3 and 7 weeks after planting (3WAP, 7WAP). Similarities between samples were calculated as the Pearson correlation of the relative abundance of OTUs based on pyrosequencing data. Numbers in brackets indicate the number of sequences for the sample; r: rhizosphere samples; b: bulk soil samples; a–d: replicates.

Figure 2

Principal component analysis of the bacterial community composition according to pyrosequencing data. The relative abundance of OTUs (log transformed) in samples from rhizosphere (red circles) and bulk soil (blue circles) taken 3 and 7 weeks after planting (3WAP, 7WAP) of lettuce in soils DS, AL, and LL were compared. The first and second principal components are shown which explained 47 and 9% of the total variance, respectively. The data were analyzed together, but for clarity separated plots for each soil type and sampling are shown.

Figure 3

Relative abundance of the most dominant OTUs detected 3 weeks after planting. The heatmap indicates differences in the relative abundances of OTUs in the bulk soil and rhizosphere from lettuce, and between soil types DS, AL, and LL. The vertical columns represent one sample, horizontal rows depict OTUs. The color code grades from black (not detected) over yellow (low abundance), orange (medium abundance) to red (high abundance). Numbers in brackets indicate the number of the NCBI GenBank accession that was most similar to the OTU representative sequence. A strong increase in abundance was indicated by not detecting the OTU in the bulk soil (black) or only in one or two samples present (yellow), raising to a high abundance in the rhizosphere which was indicated by orange to red color. Asterisks indicate a significantly increased abundance of that OTU in the rhizosphere compared to bulk soil.

Figure 4

Relative abundance of the most dominant OTUs detected 7 weeks after planting. The heatmap indicates differences in the relative abundances of OTUs in the bulk soil and rhizosphere from lettuce, and between soil types DS, AL, and LL. The vertical columns represent one sample, horizontal rows depict OTU. The color code grades from black (not detected) over yellow (low abundance), orange (medium abundance) to red (high abundance). Numbers in brackets indicate the number of the NCBI GenBank accession that was most similar to the OTU representative sequence. A strong increase in abundance was indicated by not detecting the OTU in the bulk soil (black) or only in one or two samples present (yellow), raising to a high abundance in the rhizosphere which was indicated by orange to red color. Asterisks indicate a significantly increased abundance of that OTU in the rhizosphere compared to bulk soil.