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The Ecology of Acidobacteria: Moving beyond Genes and Genomes

Kielak, Anna M., Barreto, Cristine C., Kowalchuk, George A., van Veen, Johannes A., Kuramae, Eiko E.·2016·Frontiers in Microbiology
DOI 10.3389/fmicb.2016.00744PMC PMC4885859
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FIGURE 1 Dendrogram showing the general characteristics of Acidobacteria type species, only. The dendrogram was obtained using nearly-full 16S rRNA gene sequences obtained and aligned using the Ribosomal Database Project. Dendrogram were obtained with MEGA7 (Tamura et al., 2011) using the Neighbor-joining method (Saitou and Nei, 1987); bootstrapping values were based on 1000 repetitions and are shown next to the branches (Felsenstein, 1985). There were a total of 1343 positions in the final dataset. 1. Acidobacterium capsulatum was originally described as an aerobic bacteria, but later it was demonstrated a weak anaerobic growth by fermentation (Pankratov et al., 2012). 2. H. foetida is homoacetogen and G. fermentans is fermentative. ND, not determined. Quote marks (‘) indicate that this species is deposited in a culture collection, but its name does not retain its validity and standing in nomenclature.
FIGURE 1 Dendrogram showing the general characteristics of Acidobacteria type species, only. The dendrogram was obtained using nearly-full 16S rRNA gene sequences obtained and aligned using the Ribosomal Database Project. Dendrogram were obtained with MEGA7 (Tamura et al., 2011) using the Neighbor-joining method (Saitou and Nei, 1987); bootstrapping values were based on 1000 repetitions and are shown next to the branches (Felsenstein, 1985). There were a total of 1343 positions in the final dataset. 1. Acidobacterium capsulatum was originally described as an aerobic bacteria, but later it was demonstrated a weak anaerobic growth by fermentation (Pankratov et al., 2012). 2. H. foetida is homoacetogen and G. fermentans is fermentative. ND, not determined. Quote marks (‘) indicate that this species is deposited in a culture collection, but its name does not retain its validity and standing in nomenclature.CC BY · PubMed Central
FIGURE 2 Usage of carbon sources by Acidobacteria in culture-based experiments with type strain species. A positive score was recorded if at least one species within a genus is able to use a respective sugar. (A) Acidobacteria subdivision 1. (B) Acidobacteria subdivisions 3 and 4. Usage of carbon source obtained from original references that described each of the type species, in order of publication: Kishimoto et al., 1991; Liesack et al., 1994; Coates et al., 1999; Eichorst et al., 2007; Fukunaga et al., 2008; Koch et al., 2008; Kulichevskaya et al., 2010, 2012, 2014; Pankratov and Dedysh, 2010; Männistö et al., 2011, 2012; Okamura et al., 2011; Dedysh et al., 2012; Izumi et al., 2012; Pankratov et al., 2012; Baik et al., 2013; Foesel et al., 2013, 2016; Losey et al., 2013; Crowe et al., 2014; Huber et al., 2014; Whang et al., 2014; Yamada et al., 2014; Pascual et al., 2015; Tank and Bryant, 2015; Garcia-Fraile et al., 2016; Jiang et al., 2016; Llado et al., 2016).
FIGURE 2 Usage of carbon sources by Acidobacteria in culture-based experiments with type strain species. A positive score was recorded if at least one species within a genus is able to use a respective sugar. (A) Acidobacteria subdivision 1. (B) Acidobacteria subdivisions 3 and 4. Usage of carbon source obtained from original references that described each of the type species, in order of publication: Kishimoto et al., 1991; Liesack et al., 1994; Coates et al., 1999; Eichorst et al., 2007; Fukunaga et al., 2008; Koch et al., 2008; Kulichevskaya et al., 2010, 2012, 2014; Pankratov and Dedysh, 2010; Männistö et al., 2011, 2012; Okamura et al., 2011; Dedysh et al., 2012; Izumi et al., 2012; Pankratov et al., 2012; Baik et al., 2013; Foesel et al., 2013, 2016; Losey et al., 2013; Crowe et al., 2014; Huber et al., 2014; Whang et al., 2014; Yamada et al., 2014; Pascual et al., 2015; Tank and Bryant, 2015; Garcia-Fraile et al., 2016; Jiang et al., 2016; Llado et al., 2016).CC BY · PubMed Central
FIGURE 3 Enzymes encoding genes of polysaccharide degradation (EC.3.2-) in different Acidobacteria subdivisions (GP) genomes. The comparisons were done using IMG: the integrated microbial genomes database and comparative analysis system.
FIGURE 3 Enzymes encoding genes of polysaccharide degradation (EC.3.2-) in different Acidobacteria subdivisions (GP) genomes. The comparisons were done using IMG: the integrated microbial genomes database and comparative analysis system.CC BY · PubMed Central
FIGURE 4 Families of transporters (TC:3.A) in different Acidobacteria subdivisions (GP) genomes. The comparisons were done using IMG: the integrated microbial genomes database and comparative analysis system.
FIGURE 4 Families of transporters (TC:3.A) in different Acidobacteria subdivisions (GP) genomes. The comparisons were done using IMG: the integrated microbial genomes database and comparative analysis system.CC BY · PubMed Central
FIGURE 5 The Acidobacteria subdivisions phylogenetic tree. The phylogenetic tree is based on 220 sequences of 26 different subdivisions (GPs) of Acidobacteria from Silva database (http://www.arb-silva.de/) classified by RDP classifier. The sequences were aligned in Clustal X12 and the selection of conserved blocks from multiple alignment was carried out by Gblocks (Talavera and Castresana, 2007) for phylogenetic analysis. The phylogenetic tree was based on Neighbor-Joining clustering algorithm with 1000 bootstrap. Circles in the branches of the tree represent bootstrap support more than 75%. Outgroup is Castenholzii roseiflexus.
FIGURE 5 The Acidobacteria subdivisions phylogenetic tree. The phylogenetic tree is based on 220 sequences of 26 different subdivisions (GPs) of Acidobacteria from Silva database (http://www.arb-silva.de/) classified by RDP classifier. The sequences were aligned in Clustal X12 and the selection of conserved blocks from multiple alignment was carried out by Gblocks (Talavera and Castresana, 2007) for phylogenetic analysis. The phylogenetic tree was based on Neighbor-Joining clustering algorithm with 1000 bootstrap. Circles in the branches of the tree represent bootstrap support more than 75%. Outgroup is Castenholzii roseiflexus.CC BY · PubMed Central

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Cited by

Sorted by citations

Metadata

Authors
Kielak, A. M., Barreto, C. C., Kowalchuk, G. A., van Veen, J. A., & Kuramae, E. E.
Venue
Frontiers in Microbiology
Publisher
Frontiers Media SA
Published
2016-05-31
Volume
7
ISSN
1664-302X
DOI
10.3389/fmicb.2016.00744
PMC
PMC4885859
Cited by
1,033
References
3

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