Spatiotemporal organization of bacteria/archaea in maize rhizosphere

Plants interact with the rhizosphere microbiome via root exudates that consist of numerous metabolites serving as energy or carbon sources for microbial growth and as modulators of the uncountable rhizosphere interactions. The rhizosphere microbiome plays also an important role in plant health, growth, and productivity. Different drivers are known to shape the rhizosphere microbiome, but limited investigation exists whether there is a spatial variability in the microbiome along the root system (depth). The present study aimed to assess effects of potentially different drivers such as soil substrates, soil compartments (rhizosphere, and bulk soil), depths, and plant genotypes on bacterial/archaeal communities associated with two maize genotypes, root hair defective mutant (rth3), and the corresponding wild-type (WT). Experiments using maize genotypes rth3 and WT, grown on soil substrates loam, and sand under growth chamber, and field conditions were performed. Under growth camber conditions, the rhizosphere samples were harvested at twenty-two days after sowing the maize seeds from three different soil depths at 4.5 – 6.1 (GD1), 9.0 – 10.6 (GD2), and 13.5 – 15.1 (GD3) cm from soil surface. Under field conditions, analyses were carried out using both rhizosphere, and bulk soil samples taken at three developmental growth stages BBCH14, -19, and -59 of the maize plants; each from two depths at (0 – 20) FD1, and FD2 (20 - 40) cm from soil surface, except the BBCH14 (only samples from D1 were available). Bacterial/archaeal communities were analyzed by MiSeq Illumina sequencing of 16S rRNA gene fragments amplified from total community DNAs.

Under growth chamber conditions, we observed shifts in bacterial/archaeal diversity of maize rhizosphere at different depths as plant genotype- and soil substrate-dependent effects. Depth-dependent effects of maize rhizosphere (rth3/WT) on bacterial/archaeal compositions displayed high differences between GD1, and the GD3 on both soil substrates. The relative abundances of the bacterial phylum Proteobacteria were significantly higher at GD3 than GD1 for both plant genotypes on sand, but not on loam. Overall, the factor soil substrate was the strongest driver of bacterial/archaeal maize rhizosphere, followed by depth, and maize genotype.

Under field conditions, depths affected the rhizosphere bacterial/archaeal diversity only at the BBCH59 for WT grown on sand. Lower bacterial/archaeal diversity in soil substrates sand than loam was observed at both FD1 and FD2 in the rhizosphere, but not in bulk soil at all developmental growth stages of maize. The bacterial/archaeal diversity of both maize genotypes was not affected by developmental growth stages of maize on both soil substrates, and soil compartments. Depth gradients of bacterial/archaeal community composition in rhizosphere, and bulk soil displayed at BBCH59 on both soil substrates, and they were relatively higher on sand than loam (rhizosphere). Differences in relative abundances of the bacterial phyla Proteobacteria, and Actinobacteria between soil compartments, developmental growth stages of maize were observed mainly at FD1. Overall, factor soil compartment is the strongest driver of bacterial/archaeal communities followed by soil substrates, developmental growth stages and sampling depths for maize grown under field conditions.