A metagenome of a full-scale microbial community carrying out enhanced biological phosphorus removal

Abstract

Enhanced biological phosphorus removal (EBPR) is widely used for removal of phosphorus from wastewater. In this study, a metagenome (18.2 Gb) was generated using Illumina sequencing from a full-scale EBPR plant to study the community structure and genetic potential. Quantitative fluorescence in situ hybridization (qFISH) was applied as an independent method to evaluate the community structure. The results were in qualitative agreement, but a DNA extraction bias against gram positive bacteria using standard extraction protocols was identified, which would not have been identified without the use of qFISH. The genetic potential for community function showed enrichment of genes involved in phosphate metabolism and biofilm formation, reflecting the selective pressure of the EBPR process. Most contigs in the assembled metagenome had low similarity to genes from currently sequenced genomes, underlining the need for more reference genomes of key EBPR species. Only the genome of 'Candidatus Accumulibacter', a genus of phosphorus-removing organisms, was closely enough related to the species present in the metagenome to allow for detailed investigations. Accumulibacter accounted for only 4.8% of all bacteria by qFISH, but the depth of sequencing enabled detailed insight into their microdiversity in the full-scale plant. Only 15% of the reads matching Accumulibacter had a high similarity (495%) to the sequenced Accumulibacter clade IIA strain UW-1 genome, indicating the presence of some microdiversity. The differences in gene complement between the Accumulibacter clades were limited to genes for extracellular polymeric substances and phage-related genes, suggesting a selective pressure from phages on the Accumulibacter diversity.

Comparative genomics analyses on EPS biosynthesis genes required for floc formation of Zoogloea resiniphila and other activated sludge bacteria

“…We also conducted comparative genomics analyses among the closely related AS proteobacteria Zoogloea, Azoarcus, Thauera, Dechloromonas, Candidatus Accumulibacter and Nitrosospira strains. Our results indicate that those AS bacteria, including the yet-uncultured polyphosphate-accumulating Candidatus Accumulibacter phosphatis (CAP) strains (Hesselmann et al, 1999;Albertsen et al, 2012;Flowers et al, 2013), harbor the EPS biosynthesis gene cluster(s) required for formation of flocs, thereby facilitating their enrichment in the AS process.…”

A metabolic model for members of the genus Tetrasphaera involved in enhanced biological phosphorus removal

“…The model displayed the mechanisms thought to account for phosphate accumulation, and has since provided a basis for analysis of the transcription of key genes (He et al, 2010). A metagenomic study of a full-scale EBPR plant has also confirmed the presence of Accumulibacter populations although their genomes show substantial differences to that of the reference genome (Albertsen et al, 2011).…”

Overall functional gene diversity of microbial communities in three full-scale activated sludge bioreactors

“…Despite the microbiological methods used, plenty of the studies on microbial communities of activated sludge bioreactors have been conducted to profile taxonomic information based on 16S rRNA genes, using technical approaches of clone library (Wells et al 2011;Yang et al 2011), denaturing gradient gel electrophoresis (DGGE) (Yang et al 2011), terminal restriction fragment length polymorphism (T-RELP) (Wells et al 2011;Yang et al 2011), fluorescence in situ hybridization (FISH) (Mielczarek et al 2012(Mielczarek et al , 2013, Illumina (Albertsen et al 2012), 454-pyrosequencing (Hu et al 2012;Wang et al 2012a), and PhyloChips (Xia et al 2010). However, 16S rRNA gene-based ways may not be efficient in distinguishing some closely related but ecologically distinct groups of microorganisms as a consequence of the low evolutionary rate of 16S rRNA genes (Palys et al 1997).…”