Determinants of the Bacterial Diversity in Manipulated and Natural Soils

Soils harbor highly diverse bacterial communities. It is still
poorly understood whether functional redundancy or a multitude of
ecological niche modify the abundance and community composition of
bacteria in soil. Understanding why soil microorganisms are so
diverse and which factors control their community composition is of
importance because they are essential for maintaining ecosystem
processes and functions. Alterations of biotic or abiotic factors
as results of natural or anthropogenic disturbances are known to
influence soil bacterial diversity. However, the relation of those
factors on microbial diversity is not well understood. This work
examined effects of several environmental factors, specifically the
presence of higher plant species, water content, land use, and soil
properties, on bacterial diversity by employing two different soil
sources. The reproducibility of bacterial community composition in
manipulated soil was analyzed by use of group-specific phylogenetic
PCR-DGGE fingerprinting. Soils were taken from lysimeters that had
been planted with four different types of plant communities and the
water content was adjusted. The composition of Alphaproteobacteria,
Betaproteobacteria, Bacteroidetes, Chloroflexi, Plancto-mycetes,
and Verrucomicrobia populations were clearly different from soils
without plants compared to that of populations in planted soils. In
contrast, the composition of Acidobacteria, Actinobacteria,
Archaea, and Firmicutes populations did not influenced by the
environmental factors tested. No clear influence of plant diversity
and water content could be observed. The reproducibility of
bacterial composition associated with the absence or presence of
plants was true, even for the low-abundance phylotypes as shown by
phylotype beta10 representing up to 0.18% of all bacterial cells in
planted soils compared to 0.017% in those unplanted. A high
throughput cultivation approach was performed by employing the
MicroDrop and the soil slurry dilution techniques.
Soil-solution-equivalent medium (pH 7.0) supplemented with
artificial root exudates, yeast extract, and inducers was utilized.
From 217 cultures obtained, isolate byr23-80 showing the same
sequence with phylotype beta10 was recovered and studied in detail
as this phylotype displayed a distinct response towards the
presence of higher plant species and its sequence affiliated with
uncultured bacteria, so far. The strain exhibited high
physiological flexibility and was capable of utilizing major
constituents of root exudates. A polyphasic taxonomic analysis and
DNA-DNA hybridization data supported an assignment of strain
byr23-80 as a novel species to the genus Massilia within the family
Oxalobacteraceae of the subphylum Betaproteobacteria, for which the
name Massilia brevitalea is proposed. Effects of land use and soil
properties on the bacterial diversity and activity were determined
by employing natural soil from the Kavango region, Namibia. Soil
properties in fact controlled the soil respiration rates rather
than land use as pristine dark loam soil had remarkably higher
respiration rate than pristine sand soil. Exoenzyme activities
greatly varied among sites, but did not show a clear correlation to
one of the two factors. The quantitative PCR identified
Acidobacteria and Actinobacteria as the most abundant phyla about
of 30 and 20% of all Bacteria, respectively. Alphaproteobacteria,
Bacteroidetes, and Planctomycetes accounted for below 10%, whereas
Betaproteobacteria, Chloroflexi, and Firmicutes represented less
than 1%. Clone library of 16S rRNA genes from pristine dark loam
soil revealed a high bacterial diversity with an estimated number
of about 5600 phylotypes. The PCR-DGGE fingerprinting of
Acidobacteria and Actinobacteria did only show minor differences in
composition of the bacterial communities among sampling sites. This
study suggests that the bacterial species compositions in soil are
determined to a significant extent by abiotic and biotic factors,
rather than by mere chance, thereby reflecting a multitude of
distinct ecological niches.