Prokaryotic Diversity Changes and their Functional Interrelation to Land Use

 

 

Scientific investigators:

Prof. Dr. Jörg Overmann

Vanessa Baumgartner

(DSMZ & TU Braunschweig)

Prof. Dr. Michael Friedrich

(University Bremen)

Hypotheses:

1. Acidobacteria are a major group of prokaryotes in soil and relevant for ecosystem functions.
2. Diversity and activity of Acidobacteria correlate with plant diversity.
3. The functional diversity of Acidobacteria is affected by land use.

The Acidobacteria represent a ubiquitous and abundant, but poorly studied phylum of the domain Bacteria. Based on 16S rRNA gene surveys, Acidobacteria are observed in a wide variety of environments, including soils and sediments, hot springs, peat bogs, acidic mining lakes, deep Mediterranean plankton and caves.

It is assumed that their phylogenetic diversity and abundance in soils is nearly as great as in the phylum Proteobacteria. Thus, Acidobacteria can account for half or even 80% of all soil bacteria and are physiologically active in situ. The phylogenetic diversity, ubiquity and abundance of this group, particularly in soil habitats, suggest an important role in biogeochemical processes and extensive metabolic versatility. Yet, the functional implications of the diversity of this major bacterial group and its coupling to land use so far have remained unknown.

Using a land use gradient as the major variable, we investigate the composition, physiological key traits, and the functional implications of Acidobacteria diversity.

 

Methods

Diversity changes and physiologically active types of Acidobacteria are monitored using the fingerprinting methods DGGE and T-RFLP analysis of 16S rRNA and 16S rRNA genes. To identify the dominant populations, 16S rRNA gene clone libraries will be constructed and clones sequenced. Novel information on the metabolic traits of dominant soil Acidobacteria will be obtained by analyses of existing metagenomic libraries and by retrieving representative strains with improved cultivation methods. By adding different 13C-labeled carbon substrates and following their incorporation by stable isotope probing of 16S rRNA the functional role of the different phylotypes of Acidobacteria will be resolved. To assess the seasonal variation of the Acidobacteria community, all VIP-plots will be sampled in April, June, August and October 2009 and the bacterial composition will be analyzed by cell counts and DGGE and T-RFLP analysis of 16S rRNA and 16S rRNA genes.

Bild ProFIL
soil sampling at very intensive research plot in grassland (VIP)
Grassland VIP in the Exploratory Schwäbische Alb.
Bacteria cell count
Micro titer plate with sampling material of the Exploratory Schwäbische Alb.

 

Results

So far, cell counts revealed that the soils of the Exploratory Schwäbische Alb harbor most cells/g soil, followed by the Exploratory Hainich-Dün and the Exploratory Schorfheide-Chorin. Cluster analysis of the acidobacterial diversity changes of DGGE and T-RFLP analyses revealed that soil samples from one Exploratory cluster generally close together but are separated by the type of land use (forest/grassland). The composition and abundance differs in forest and grassland soil samples, resulting in separated clusters. Especially, the Schorfheide-Chorin forest soil samples differ significantly from all other soils resulting in an only distantly related cluster. As the occurrence of Acidobacteria is highly pH-dependent, these findings could be explained by the fact that forest soils showed lower pH values (~ pH 5.0) than grassland soils (~ pH 6.5). Furthermore, the Schorfheide-Chorin forest soil showed the lowest pH values (~ pH 3.5) of all exploratory soil samples.

T-RF-Abundanzen Acidobacteria
Fig.1: Comparison of Bacteria abundances of four samples taken from each exploratory (Schwäbische Alb: AEG2, AEG9, AEW1, AEW6; Hainich-Dün: HEG1, HEG8, HEW4, HEW10 and Schorfheide-Chorin: SEG2, SEG8, SEW2, SEW8.)