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.

Bacterial diversity and community structure in lettuce soil are shifted by cultivation time

“…The N application rate was significantly positively correlated with Firmicutes in summer samples (Li JG et al, 2016), in this study, fertilizers were not apply to soil; it may be the reason that proportion of Firmicutes decreased. It was consistent with the study of Susanne Schreiter et al (Schreiter S et al, 2014). The abundant presence of the phylum Chloroflexi was also found in non-fertilized control lettuce soils (Li JG et al, 2016), but not found in Susanne Schreiter's study (Schreiter S et al, 2014).…”

“…It was consistent with the study of Susanne Schreiter et al (Schreiter S et al, 2014). The abundant presence of the phylum Chloroflexi was also found in non-fertilized control lettuce soils (Li JG et al, 2016), but not found in Susanne Schreiter's study (Schreiter S et al, 2014). The major classes of Caldilineae and Anaerolineae within the Chloroflexi phylum can degrade and utilize cellular compounds derived from dead biomass and metabolites of anaerobic ammonium oxidation (Kindaichi T et al, 2012); they may increase the levels of nutrients in the lettuce soil.…”

“…Actinobacteria are known as decomposers of dead plant biomass (Warren RAJ, 1996;McCarthy AJ, 1987;Větrovský T et al, 2014), with the increase of lettuce growth time, dead plant biomass will increase, so members of the actinobacterial group will increase accordingly. This result was different from the notion of Susanne Schreiter et al (Schreiter S et al, 2014). The N application rate was significantly positively correlated with Firmicutes in summer samples (Li JG et al, 2016), in this study, fertilizers were not apply to soil; it may be the reason that proportion of Firmicutes decreased.…”

“…Soil processes are greatly influenced by bacterial community structure, activity, and stability (McCaig AE et (Schreiter S et al, 2014;Li JG et al, 2016). In this study, the ratio between Proteobacteria and Acidobacteria in early stage of lettuce soil samples (approximately<1.1) was lower than in late stage of lettuce soil (approximately>1.5).…”

Plant Growth Promoting Bacteria Isolated From a Mexican Natural Ecosystem Induce Water Stress Resistance in Maize and Sorghum Plants

“…However, few studies have been focused on biodiversity and growth rates of specific taxa in natural soil microbial communities. It has been known for some time that the soil hosts a large number of bacteria (often around 10 8 to 10 9 cells per gram of soil) but the number of culturable bacterial cells in soil is generally only about 1% out of the total number of cells present [13]. The most abundant bacterial genera in soil reported are, Azospirillum ssp., Alcaligenes ssp., Arthrobacte ssp., Acinetobacter ssp., Bacillus ssp., Burkholderia ssp., Erwinia ssp., Pseudomonas ssp., Rhizobium ssp., Rhodococcus ssp.…”