Effects of Plant Biomass, Plant Diversity, and Water Content on Bacterial Communities in Soil Lysimeters: Implications for the Determinants of Bacterial Diversity

Abstract

Soils may comprise tens of thousands to millions of bacterial species. It is still unclear whether this high level of diversity is governed by functional redundancy or by a multitude of ecological niches. In order to address this question, we analyzed the reproducibility of bacterial community composition after different experimental manipulations. Soil lysimeters were planted with four different types of plant communities, and the water content was adjusted. Group-specific phylogenetic fingerprinting by PCR-denaturing gradient gel electrophoresis revealed clear differences in the composition of Alphaproteobacteria, Betaproteobacteria, Bacteroidetes, Chloroflexi, Planctomycetes, and Verrucomicrobia populations in soils without plants compared to that of populations in planted soils, whereas no influence of plant species composition on bacterial diversity could be discerned. These results indicate that the presence of higher plant species affects the species composition of bacterial groups in a reproducible manner and even outside of the rhizosphere. In contrast, the environmental factors tested did not affect the composition of Acidobacteria, Actinobacteria, Archaea, and Firmicutes populations. One-third (52 out of 160) of the sequence types were found to be specifically and reproducibly associated with the absence or presence of plants. Unexpectedly, this was also true for numerous minor constituents of the soil bacterial assemblage. Subsequently, one of the low-abundance phylotypes (beta10) was selected for studying the interdependence under particular experimental conditions and the underlying causes in more detail. This so-far-uncultured phylotype of the Betaproteobacteria species represented up to 0.18% of all bacterial cells in planted lysimeters compared to 0.017% in unplanted systems. A cultured representative of this phylotype exhibited high physiological flexibility and was capable of utilizing major constituents of root exudates. Our results suggest that the bacterial species composition in soil is determined to a significant extent by abiotic and biotic factors, rather than by mere chance, thereby reflecting a multitude of distinct ecological niches.

Soil amoebae rapidly change bacterial community composition in the rhizosphere of Arabidopsis thaliana

“…The DGGE profiles demonstrated that our inoculation procedure reestablished a diverse bacterial community, containing all major groups of rhizosphere bacteria (Zul et al, 2007) in our Magenta system. Cloning and matching of the sequences to excised bands proved not only the presence of a diverse range of different phylogenetic groups but even of uncultured bacteria, suggesting a successful establishment of natural microbial communities in our experimental systems.…”

Massilia brevitalea sp. nov., a novel betaproteobacterium isolated from lysimeter soil

“…Bacterial strains were isolated by streaking liquid cultures onto the medium described above, solidified with gellan gum (8 g l 21 ; Sigma-Aldrich Chemie). One of the cultured betaproteobacteria, strain byr23-80 T , was selected for further characterization since it occurred in association with higher plants (Zul et al, 2007). Subsequent physiological, biochemical and phylogenetic characterization revealed that the isolate represents a novel member of the genus Massilia within the family Oxalobacteraceae of the order Burkholderiales.…”

“…Strain byr23-80 T was isolated during the investigation of bacterial communities in soil lysimeters (Zul et al, 2007).…”

“…The high-throughput MicroDrop technique (Bruns et al, 2003) was employed to inoculate bacterial cells into microtitre plates containing soil solution equivalent (Angle et al, 1991), which was buffered at a pH of 7.0 using 10 mM HEPES and supplemented with artificial root exudates, yeast extract (0.01 %, w/v) and inducers, as described previously (Bruns et al, 2003;Zul et al, 2007). Cultures were incubated at 15 u C for 6 weeks.…”

Edaphobacter modestus gen. nov., sp. nov., and Edaphobacter aggregans sp. nov., acidobacteria isolated from alpine and forest soils

“…The medium was spiked with the inducer molecules cyclic AMP (cAMP), N-(oxohexanoyl)-DL-homoserine lactone (OHHL) and N-(butyryl)-DL-homoserine lactone (BHL), each at a final concentration of 10 mM (Bruns et al, 2003a). Each culture was inoculated with 50 bacterial cells and incubated at 15 u C. Enrichments were screened for the presence of acidobacteria by group-specific PCR after lysis of the cells by six consecutive freeze-thaw cycles, employing primers 31F and 341r and the conditions described previously (Zul et al, 2007). One of the positive enrichments was chosen to isolate strain Jbg-1 T on agarsolidified HD medium (1 : 10-diluted; 0.05 % casein peptone, 0.01 % glucose, 0.025 % yeast extract, w/v).…”