Bulk and Rhizosphere Soil Bacterial Communities Studied by Denaturing Gradient Gel Electrophoresis: Plant-Dependent Enrichment and Seasonal Shifts Revealed

Abstract

The bacterial rhizosphere communities of three host plants of the pathogenic fungus Verticillium dahliae, field-grown strawberry (Fragaria ananassa Duch.), oilseed rape (Brassica napus L.), and potato (Solanum tuberosum L.), were analyzed. We aimed to determine the degree to which the rhizosphere effect is plant dependent and whether this effect would be increased by growing the same crops in two consecutive years. Rhizosphere or soil samples were taken five times over the vegetation periods. To allow a cultivationindependent analysis, total community DNA was extracted from the microbial pellet recovered from root or soil samples. 16S rDNA fragments amplified by PCR from soil or rhizosphere bacterium DNA were analyzed by denaturing gradient gel electrophoresis (DGGE). The DGGE fingerprints showed plant-dependent shifts in the relative abundance of bacterial populations in the rhizosphere which became more pronounced in the second year. DGGE patterns of oilseed rape and potato rhizosphere communities were more similar to each other than to the strawberry patterns. In both years seasonal shifts in the abundance and composition of the bacterial rhizosphere populations were observed. Independent of the plant species, the patterns of the first sampling times for both years were characterized by the absence of some of the bands which became dominant at the following sampling times. Bacillus megaterium and Arthrobacter sp. were found as predominant populations in bulk soils. Sequencing of dominant bands excised from the rhizosphere patterns revealed that 6 out of 10 bands resembled gram-positive bacteria. Nocardia populations were identified as strawberry-specific bands.

In-field rates of decomposition and microbial communities colonizing residues vary by depth of residue placement and plant part, but not by crop genotype for residues from two Cry1Ab Bt corn hybrids and their non-transgenic isolines

“…Our results show that neither the decomposition rate nor the composition of corn residue surface-colonizing decomposer communities was affected by the presence of Cry1Ab Bt protein in these residues. Instead, our results re-confirm the strong influence that residue quality has on its decomposition rate, and how strongly microbial community composition is affected by environmental conditions (Smalla et al, 2001), particularly variations in moisture and temperature related to litterbag field placement (Briar et al, 2012).…”

Dynamics of the bacterial community structure in the rhizosphere of a maize cultivar

“…1). Because DGGE showed similar dynamic patterns as those revealed by pyrosequencing, it is a useful technique to give a snapshot of the diversity of the most abundant rhizosphere bacteria (Gomes et al, 2001;Smalla et al, 2001). However, pyrosequencing results provided more specific insight into shifts in bacteria community composition at the levels of family, genus and OTU (Fig.…”

“…Some studies suggested that seasonal variations in the activity and relative abundance of rhizosphere bacterial communities are plant-dependent (Dunfield and Germida, 2003;Houlden et al, 2008;Mougel et al, 2006;Smalla et al, 2001). Although some research showed dynamic changes of maize rhizosphere bacterial community at different growth stages using culture-dependent (Cavaglieri et al, 2009;Nacamulli et al, 1997) and fingerprinting methods (Di Cello et al, 1997), detail phylogenetic compositions cannot be monitored due to low resolution of these approaches.…”

Horizontal gene transfer between bacteria

“…Soil treatments with manure, decomposing plant material or plant-derived root exudates are considered to stimulate HGT in soil (Götz and Smalla, 1997;Heuer and Smalla, 2007). The plant species-dependent bacterial diversity in the rhizosphere (Costa et al, 2006a;2006b;Smalla et al, 2001), which is believed to be caused by different root exudation patterns and differences of root shape, has recently been shown to also influence plasmid transfer frequencies (Mølbak et al, 2007). Key abiotic and biotic factors that affect the extent of HGT in hot spots in the phytosphere or in soil have been reviewed recently (Van Elsas et al, 2003;.…”