Characteristics of assembled scaffolds and the retrieved CAP IIC HKU-2 draft genome.

<p>Characteristics of assembled scaffolds and the retrieved CAP IIC HKU-2 draft genome.</p

Exploring the Shift in Structure and Function of Microbial Communities Performing Biological Phosphorus Removal

<div><p>A sequencing batch reactor fed mainly by acetate was operated to perform enhanced biological phosphorus removal (EBPR). A short-term pH shock from 7.0 to 6.0 led to a complete loss of phosphate-removing capability and a drastic change of microbial communities. 16S rRNA gene pyrosequencing showed that large proportions of glycogen accumulating organisms (GAOs) (accounted for 16% of bacteria) bloomed, including <i>Candidatus</i> Competibacter phosphatis and <i>Defluviicoccus</i>-related tetrad-forming organism, causing deteriorated EBPR performance. The EBPR performance recovered with time and the dominant <i>Candidatus</i> Accumulibacter (Accumulibacter) clades shifted from Clade IIC to IIA while GAOs populations shrank significantly. The Accumulibacter population variation provided a good opportunity for genome binning using a bi-dimensional coverage method, and a genome of Accumulibacter Clade IIC was well retrieved with over 90% completeness. Comparative genomic analysis demonstrated that Accumulibacter clades had different abilities in nitrogen metabolism and carbon fixation, which shed light on enriching different Accumulibacter populations selectively.</p></div

Maximum likelihood phylogenetic tree of Accumulibacter <i>ppk1</i> gene sequences.

<p>The <i>ppk1</i> genes of the reconstructed Accumulibacter genomes are indicated in green, while those from clone library of sludges A and C are colored in orange. Seven and nine partial <i>ppk1</i> gene sequences with 99% identity were obtained from sludge A and C respectively. Reference sequences attached with their accession numbers are extracted from NCBI database. Node labels refer to bootstrap support values and <i>Rhodocyclus tenuis ppk1</i> gene is employed as the outgroup sequence.</p

Phosphorus removal and sludge sampling for 16S rRNA gene pyrosequencing from the SBR performing EBPR.

<p>The pH of solution in the SBR was maintained at 7.2 ± 0.1 except at 60 d when accidentally overdosed acidic solution to decrease pH to 6.0 for around 20 h.</p

Venn diagram of conserved and unique genes for four Accumulibacter genomes of Clade IIC.

<p>Venn diagram of conserved and unique genes for four Accumulibacter genomes of Clade IIC.</p

The ANI and orthologous genes shared by each pair of Accumulibacter genomes.

<p>The ANI and orthologous genes shared by each pair of Accumulibacter genomes.</p

Relative abundances of <i>ppk1</i> genes of different clades in the microbial communities.

<p>The abundance of Accumulibacter was calculated according to the copy numbers of Accumulibacter and bacterial 16S rRNA genes by qPCR analysis. Meanwhile the 2 copies of <i>rrn</i> operon in CAP IIA UW-1 and 4 copies of <i>rrn</i> operon in the available bacterial finished genomes have been taken into account. The proportions of different <i>ppk1</i> genes in one sample was estimated by the copy numbers obtained from the qPCR assay using primer sets targeting <i>ppk1</i> genes of specific clades.</p

Extraction of the initial genome of Accumulibacter Clade IIC which dominated the PAOs in sludge samples A and C by using the coverage-defined method.

<p>Each circle represents an assembled scaffold, with the size proportional to its length and colored by phylum. Only scaffolds ≥ 10 kbp are shown. The box encloses scaffolds representing the initial CAP IIC HKU-2 genome bin.</p

Population dynamics of PAOs and GAOs involved in the SBR.

<p>The abundance was calculated based on bacterial pyro-tags which best hit the representative 16S rRNA gene sequences of specific PAO or GAO group with minimum identity of 97% and alignment length cutoff of 400 bp. Standard deviation was calculated from the triplicate pyrosequencing data sets for each sludge sample.</p