The majority of studies presented in this thesis focused on investigating bacterial communities and their functions in soils. In the studies from Chapter II and III, more than 4,75 million partial 16S rRNA gene and gene transcript sequences were analyzed. The dominant phyla in the bacterial community of a grassland soil were Proteobacteria (DNA 31.1%, RNA 45.7%), Firmicutes (DNA 27.4%, RNA 35.7%), Chloroflexi (DNA 17%, RNA 9.1%), Acidobacteria (DNA 13.3%, RNA 3.4%), and Actinobacteria (DNA 6%, RNA 3.4%) (Figure 1A and B). The five phyla accounted for up to 96% of all analyzed
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sequences. Similar results were obtained in soil communities of two aspen demes. Here, the dominant phyla were Proteobacteria (DNA 32.4%, RNA 44.2%), Firmicutes (DNA 27.2%, RNA 36.5%), Chloroflexi (DNA 16%, RNA 9.1%), Acidobacteria (DNA 13.3%, RNA 3.5%), and Actinobacteria (DNA 6.1%, RNA 3.8%) (Figure 1A and B).
Figure 1. Most abundant phyla and proteobacterial classes of the total (A) and the active (B) bacterial community identified from soil samples of aspen deme Geismar 2 (G2) and aspen deme Geismar 8 (G8) as well as from fertilized (fe) and non-fertilized (nf) grassland soil samples.
These findings were generally in accordance with previous studies of bacterial communities in forest and grassland soils (e.g. Will et al., 2010; Nacke et al., 2011;
Baldrian et al., 2012; Pan et al., 2014). Janssen (2006) identified the dominant bacterial
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phyla from 31 libraries of 16S rRNA and 16S rRNA genes in different soils, e.g. grassland and forest soils. In this study, Proteobacteria, Acidobacteria, Actinobacteria, Verrucomicrobia, Bacteroidetes, Chloroflexi, Planctomycetes, and Firmicutes were the dominant phyla in the libraries and accounted for 92% of all analyzed bacterial sequences.
Nacke et al. (2011) found that Proteobacteria were the most abundant bacterial phylum in forest (45%) and grassland soils (35%). Will et al. (2010) observed similar high abundances of Proteobacteria in grassland soils (42%). This is in line with the results of Uroz et al. (2010) who analyzed the bacterial diversity in the rhizosphere and in the bulk soil of an oak forest. They found the highest abundance of Proteobacteria with up to 38%
in the bulk soil and 41% in the rhizosphere soil. Thus, Proteobacteria is one of most dominant and ubiquitous taxonomic groups in soils. Members of this phylum play a key role as plant growth-promoting bacteria (Mendes et al., 2011, Brown et al., 2012), e.g.
Burkholderiales (Estrada-De los Santos et al., 2001, Suarez-Moreno, 2012).
The second most abundant phylum was Firmicutes (DNA 27.3% and RNA 36.1%). This result is in contrast to other studies (e.g. Janssen, 2006; Will et al., 2010; Nacke et al., 2011; Rampelotto et al., 2013). Firmicutes form a large group of Gram-positive bacteria and are divided into three main classes, Bacilli, Erysipelotrichi, and Clostridia (Ludwig et al., 2009). In this study, sequences affiliated to the Firmicutes were mostly assigned to the genus Bacillus. Members of the Bacillus are aerobic bacteria with the ability to form UV-resistant endospores that also endure drought and oxidizing agents (Popham et al., 1995).
Members of the genus Bacillus are common in soil, well accommodated to this habitat, and known as beneficial for plant growth and health (Berg, 2009). The high number of Firmicutes in this study may result from the former land-use history of the study site, which was for hay-making or for grazing.
In this thesis, the phylum Chloroflexi represents 16.5% of all analyzed sequences in the total and 9.1% in the active bacterial community. Janssen (2006) found that the abundance of this phylum varied between 0 % and 16% in the entire soil bacterial community. We found several subphyla of Chloroflexi with Ktedonobacteria as most abundant class (5.39% of all analyzed 16S rRNA gene and gene transcript sequences). Davis et al. (2005 and 2011) isolated some members of the Chloroflexi subphyla such as Ktedonobacteria and Thermomicrobia from paddock soil by inoculation experiments. They characterized these groups as slow-growing and mini-colony-forming bacteria. Yamada et al. (2005) investigated the community of Chloroflexi subphylum I in mesophilic and thermophilic sludge granules. They isolated and analyzed 3 strains belonging to this subphylum and
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suggested that Chloroflexi might contribute to the degradation of carbohydrates and other cellular components such as amino acids. Thus, this observation may give us a hint about the role of Chloroflexi in soil.
Another abundant phylum in the total community was Acidobacteria. Members of this phylum form a highly abundant and diverse group (Quaiser et al., 2003) and their abundance is often linked to soil pH (Lauber et al., 2009) and an oligotrophic lifestyle (Fierer et al., 2007; Naether et al., 2012). Oligotrophic bacteria show a high substrate affinity and low growth rate but are well adapted to poor soil conditions. As consequence, they have an advantage compared to bacteria with a copiotrophic lifestyle. Copiotrophic bacteria such as Betaproteobacteria exhibit high growth rates at high-nutrient conditions (Naether et al., 2012). In this thesis, Acidobacteria represents 13.3% and 3.5% of all analyzed sequences at DNA and RNA level, respectively. Correlation studies with soil parameters such as pH, C/N, and water content had shown that the abundance of this phylum is significantly correlated with pH. In a study by Jones et al. (2009), the relative abundance of Acidobacteria within 87 different soil samples varied from 2.4 to 78.5%.
The abundance of this phylum correlated strongly with pH, with higher abundances at low pH values. Within the Acidobacteria, the distinct subclasses correlated differently with pH.
While the acidobacterial subclasses 1, 2, 3, 12, 13, and 15 decreased, the acidobacterial subclasses 4, 6, 7, 10, 11, 16, 17, 18, 22, and 25 increased with rising pH. The abundance of the active members of subgroup 1 correlated significantly negatively with pH, while that of subgroup 7 is significantly positively correlated with pH.
The phylum Actinobacteria (DNA 6% and RNA 3.6%) forms a large group of mainly Gram-positive bacteria. Actinobacteria are divided into six classes and are characterized as an extremely diverse group with high GC-content (Stackebrandt and Schumann, 2006; Lu and Zhang, 2012). In a study by Lauber et al. (2009), the relative abundances of Actinobacteria varied between 5 and 24% with an average of 13%. They found approximately 7% abundance of Actinobacteria within a pH range of 4 to 6 and this is in line with the result from our study of the total soil bacterial community.
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5.2. Active and total bacterial communities differs with respect to their diversity