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

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

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

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

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

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

Estimating the Transfer Range of Plasmids Encoding Antimicrobial Resistance in a Wastewater Treatment Plant Microbial Community

Wastewater treatment plants (WWTPs) have been suggested as reservoirs and sources of antibiotic resistance genes (ARGs) in the environment. In a WWTP ecosystem, human enteric and environmental bacteria are mixed and exposed to pharmaceutical residues, potentially favoring genetic exchange and thus ARG transmission. However, the contribution of microbial communities in WWTPs to ARG dissemination remains poorly understood. Here, we examined for the first time plasmid permissiveness of an activated sludge microbial community by utilizing an established fluorescent bioreporter system. The activated sludge microbial community was challenged in standardized filter matings with one of three multidrug resistance plasmids (pKJK5, pB10, and RP4) harbored by <i>Escherichia coli</i> or <i>Pseudomonas putida</i>. Different donor–plasmid combinations had distinct transfer frequencies, ranging from 3 to 50 conjugation events per 100000 cells of the WWTP microbial community. In addition, transfer was observed to a broad phylogenetic range of 13 bacterial phyla with several taxa containing potentially pathogenic species. Preferential transfer to taxa belonging to the predicted evolutionary host range of the plasmids was not observed. Overall, the ARG dissemination potential uncovered in WWTP communities calls for a thorough risk assessment of ARG transmission across the wastewater system, before identification of possible mitigation strategies