Microbial Structures, Functions, and Metabolic Pathways in Wastewater Treatment Bioreactors Revealed Using High-Throughput Sequencing

Abstract

The objective of this study was to explore microbial community structures, functional profiles, and metabolic pathways in a lab-scale and a full-scale wastewater treatment bioreactors. In order to do this, over 12 gigabases of metagenomic sequence data and 600,000 paired-end sequences of bacterial 16S rRNA gene were generated with the Illumina HiSeq 2000 platform, using DNA extracted from activated sludge in the two bioreactors. Three kinds of sequences (16S rRNA gene amplicons, 16S rRNA gene sequences obtained from metagenomic sequencing, and predicted proteins) were used to conduct taxonomic assignments. Specially, relative abundances of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were analyzed. Compared with quantitative real-time PCR (qPCR), metagenomic sequencing was demonstrated to be a better approach to quantify AOA and AOB in activated sludge samples. It was found that AOB were more abundant than AOA in both reactors. Furthermore, the analysis of the metabolic profiles indicated that the overall patterns of metabolic pathways in the two reactors were quite similar (73.3% of functions shared). However, for some pathways (such as carbohydrate metabolism and membrane transport), the two reactors differed in the number of pathway-specific genes.

Using high-throughput sequencing to assess the impacts of treated and untreated wastewater discharge on prokaryotic communities in an urban river

“…So discharging untreated wastewater to the river may be serious harmful to human health. In this study we did not identify any nitrification genes in the samples from metagenomic analysis due to the nonspecific amplification and/or the formation of a primer dimer (Ye et al 2012), in particular for ammonia oxidation genes (amo). For a supplement study, we detected bacterial and archaeal amoA genes using real-time PCR (Fig.…”

Abundance and Diversity of Bacterial Nitrifiers and Denitrifiers and Their Functional Genes in Tannery Wastewater Treatment Plants Revealed by High-Throughput Sequencing

“…After removing redundancies, the local database contained 17,483 sequences of AOA amoA gene, 12,211 sequences of AOB amoA gene, 5,716 sequences of nirK gene, 7,615 sequences of nirS gene and 5,436 sequences of nosZ gene. BLASTn was used to align all the sequencing reads against the local database, and a read was identified as amoA, nirK, nirS or nosZ if the BLAST hit (E-value cutoff at 10 25 ) had a nucleotide sequence identity of above 90% over an alignment of at least 50 bp [10].…”

“…The BLASTX results were visualized with MEGAN (http://ab.inf.uni-tuebingen.de/software/megan/) at a threshold of bitscore.50 [10].…”

“…Recently, high-throughput sequencing techniques, such as 454 pyrosequencing and Illumina sequencing methods, have shown great advantages on microbial community analysis due to their unprecedented sequencing depth, which have been used to deeply explore microbial communities in drinking water [7], soil [8] and WWTPs [9][10][11]. However, the metagenomic methods have not been used for comprehensive insights into the communities of nitrifies and denitrifies in tannery WWTPs.…”

- Assessing Bacterial Diversity in a Seawater-Processing Wastewater Treatment Plant by 454-Pyrosequencing of the 16S rRNA and amoA Genes

“…Knowledge is still lacking in regard to microbial community functional structures and their linkages to environmental variables. To date, there have been only a limited number of studies that characterized the overall functional profiles and metabolic pathways in the activated sludge of WWTPs using highthroughput sequencing [12,13].…”