Bacterial communities in different sections of a municipal wastewater treatment plant revealed by 16S rDNA 454 pyrosequencing.
TL;DR: In this study, it is successfully demonstrated that 454 pyrosequencing was a powerful approach for investigating the bacterial communities in the activated sludge, digestionSludge, influent, and effluent samples of a full scale wastewater treatment plant treating saline sewage.
Abstract: In this study, we successfully demonstrated that 454 pyrosequencing was a powerful approach for investi- gating the bacterial communities in the activated sludge, digestion sludge, influent, and effluent samples of a full scale wastewater treatment plant treating saline sewage. For each sample, 18,808 effective sequences were selected and utilized to do the bacterial diversity and abundance analysis. In total, 2,455, 794, 1,667, and 1,932 operational taxonomic units were obtained at 3 % distance cutoff in the activated sludge, digestion sludge, influent, and effluent samples, respectively. The corresponding most dominant classes in the four samples are Alphaproteobacteria, Ther- motogae, Deltaproteobacteria, and Gammaproteobacteria. About 67 % sequences in the digestion sludge sample were found to be affiliated with the Thermotogales order. Also, these sequences were assigned into a recently proposed genus Kosmotoga by the Ribosomal Database Project clas- sifier. In the effluent sample, we found high abundance of Mycobacterium and Vibrio, which are genera containing pathogenic bacteria. Moreover, in this study, we proposed a method to differentiate the "gene percentage" and "cell per- centage" by using Ribosomal RNA Operon Copy Number
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TL;DR: This is the first study on the fate of ARGs in STP using metagenomic analysis with high-throughput sequencing and hopefully would enhance the knowledge on fate ofARGs inSTP.
410 citations
TL;DR: A critical summary of microbial characteristics was provided to obtain connects of microbial community structure with operational conditions at various states of AD, such as mesophilic and thermophilic, wet and dry, success and failure, pretreated or not, lab-scale and full-scale.
328 citations
TL;DR: This mini-review presents the types of microbial consortia in WWTP and discusses data on microbial groups including nitrifier, denitrifiers, Anammox bacteria, and phosphate- and glycogen-accumulating bacteria in full-scale aerobic systems to shed light on dependencies between the microbial ecology of biomass and the overall efficiency and functional stability of wastewater treatment systems.
Abstract: Bacterial metabolism determines the effectiveness of biological treatment of wastewater. Therefore, it is important to define the relations between the species structure and the performance of full-scale installations. Although there is much laboratory data on microbial consortia, our understanding of dependencies between the microbial structure and operational parameters of full-scale wastewater treatment plants (WWTP) is limited. This mini-review presents the types of microbial consortia in WWTP. Information is given on extracellular polymeric substances production as factor that is key for formation of spatial structures of microorganisms. Additionally, we discuss data on microbial groups including nitrifiers, denitrifiers, Anammox bacteria, and phosphate- and glycogen-accumulating bacteria in full-scale aerobic systems that was obtained with the use of molecular techniques, including high-throughput sequencing, to shed light on dependencies between the microbial ecology of biomass and the overall efficiency and functional stability of wastewater treatment systems. Sludge bulking in WWTPs is addressed, as well as the microbial composition of consortia involved in antibiotic and micropollutant removal.
295 citations
Cites background from "Bacterial communities in different ..."
...In the effluent from the WWTP treating salty wastewater, Mycobacterium sp. and Vibrio sp. were present; among these genera pathogenic microorganisms were numerous (Ye and Zhang 2013)....
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...were present; among these genera pathogenic microorganisms were numerous (Ye and Zhang 2013)....
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TL;DR: The results of this study demonstrate that a high throughput-based metagenomic approach combined with a structured database of ARGs provides a powerful tool for a comprehensive survey of the various ARGs not only in the activated sludge of a WWTP but in other environmental samples as well.
Abstract: In this study, the profiles of ARGs in activated sludge from the Shatin WWTP of Hong Kong were investigated using metagenomic analysis over a four-year period. Forty giga base pairs of metagenomic data were generated from eight activated sludge samples collected biannually at two seasons (winter and summer) from July 2007 to January 2011. A structured database of ARGs was proposed and constructed to facilitate the classification of ARGs in the collected samples from metagenomic data using a customized script. Analysis of the data showed the existence of a broad-spectrum of different ARGs, some of which have never been reported in activated sludge before. The most abundant ARGs were aminoglycoside and tetracycline resistance genes, followed by resistance genes of sulfonamide, multidrug, and chloramphenicol. Seasonal fluctuations were observed for 3 types of ARGs, that is, resistance genes of tetracycline, sulfonamide, and vancomycin. The abundances of these resistance genes were generally higher in the samples collected in the winters than the samples collected in the contiguous summer. Further analyses were carried out for the presence of subtypes of ARGs for aminoglycoside, tetracycline, and beta-lactam. The abundances of some ARGs subtypes were inconsistent with those reported in previous studies of activated sludge using the PCR approach. Statistical analyses showed that the activated sludge data sets from this study can be distinguished from other types of samples based on their ARGs profiles. Furthermore, the results of this study demonstrate that a high throughput-based metagenomic approach combined with a structured database of ARGs provides a powerful tool for a comprehensive survey of the various ARGs not only in the activated sludge of a WWTP but in other environmental samples as well. Thus, the profiling of ARGs in other ecologically important environmental matrixes may help elucidate those environmental factors contributing to the spread of ARGs.
290 citations
TL;DR: The hypothesis that some bacteria may share different water compartments and be also hosted by humans is discussed based on the comparison of the bacterial diversity in different types of water and with the human-associated microbiome.
Abstract: Water is one of the most important bacterial habitats on Earth. As such, water represents also a major way of dissemination of bacteria between different environmental compartments. Human activities led to the creation of the so-called urban water cycle, comprising different sectors (waste, surface, drinking water), among which bacteria can hypothetically be exchanged. Therefore, bacteria can be mobilized between unclean water habitats (e.g. wastewater) and clean or pristine water environments (e.g. disinfected and spring drinking water) and eventually reach humans. In addition, bacteria can also transfer mobile genetic elements between different water types, other environments (e.g. soil) and humans. These processes may involve antibiotic resistant bacteria and antibiotic resistance genes. In this review, the hypothesis that some bacteria may share different water compartments and be also hosted by humans is discussed based on the comparison of the bacterial diversity in different types of water and with the human-associated microbiome. The role of such bacteria as potential disseminators of antibiotic resistance and the inference that currently only a small fraction of the clinically relevant antibiotic resistome may be known is discussed.
288 citations
Cites background from "Bacterial communities in different ..."
...…as indicators of human fecal contamination, apparently these bacteria are not the most prevalent bacterial groups in sewage sludge or in wastewater (Sanapareddy et al., 2009; McLellan et al., 2010; Xia et al., 2010b; Yang et al., 2011; Wang et al., 2012; Ye & Zhang, 2012; Zhang et al., 2012) (Fig....
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References
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TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
88,255 citations
"Bacterial communities in different ..." refers methods in this paper
...2006) annotated with NCBI taxonomy using NCBI’s BLASTN tool (Altschul et al. 1990) and the default parameters except for the maximum hit number of 100 (Claesson et al....
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...…sequences obtained from pyrosequencing in this study were compared with Greengenes 16S rRNA gene database (DeSantis et al. 2006) annotated with NCBI taxonomy using NCBI’s BLASTN tool (Altschul et al. 1990) and the default parameters except for the maximum hit number of 100 (Claesson et al. 2009)....
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TL;DR: The RDP Classifier can rapidly and accurately classify bacterial 16S rRNA sequences into the new higher-order taxonomy proposed in Bergey's Taxonomic Outline of the Prokaryotes, and the majority of the classification errors appear to be due to anomalies in the current taxonomies.
Abstract: The Ribosomal Database Project (RDP) Classifier, a naive Bayesian classifier, can rapidly and accurately classify bacterial 16S rRNA sequences into the new higher-order taxonomy proposed in Bergey's Taxonomic Outline of the Prokaryotes (2nd ed., release 5.0, Springer-Verlag, New York, NY, 2004). It provides taxonomic assignments from domain to genus, with confidence estimates for each assignment. The majority of classifications (98%) were of high estimated confidence (≥95%) and high accuracy (98%). In addition to being tested with the corpus of 5,014 type strain sequences from Bergey's outline, the RDP Classifier was tested with a corpus of 23,095 rRNA sequences as assigned by the NCBI into their alternative higher-order taxonomy. The results from leave-one-out testing on both corpora show that the overall accuracies at all levels of confidence for near-full-length and 400-base segments were 89% or above down to the genus level, and the majority of the classification errors appear to be due to anomalies in the current taxonomies. For shorter rRNA segments, such as those that might be generated by pyrosequencing, the error rate varied greatly over the length of the 16S rRNA gene, with segments around the V2 and V4 variable regions giving the lowest error rates. The RDP Classifier is suitable both for the analysis of single rRNA sequences and for the analysis of libraries of thousands of sequences. Another related tool, RDP Library Compare, was developed to facilitate microbial-community comparison based on 16S rRNA gene sequence libraries. It combines the RDP Classifier with a statistical test to flag taxa differentially represented between samples. The RDP Classifier and RDP Library Compare are available online at http://rdp.cme.msu.edu/.
16,048 citations
"Bacterial communities in different ..." refers methods in this paper
...net/), so the reads flagged as chimeras were submitted to Ribosomal Database Project (RDP) classifier (Wang et al. 2007; Cole et al. 2009)....
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...Because all sequences flagged as chimeras are not recommended to be discarded blindly (http://microbiomeutil.sourceforge.net/), so the reads flagged as chimeras were submitted to Ribosomal Database Project (RDP) classifier (Wang et al. 2007; Cole et al. 2009)....
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TL;DR: Analysis of the genomic DNA from a bacterial biofilm grown under aerobic conditions suggests that sulfate-reducing bacteria, despite their anaerobicity, were present in this environment.
Abstract: We describe a new molecular approach to analyzing the genetic diversity of complex microbial populations. This technique is based on the separation of polymerase chain reaction-amplified fragments of genes coding for 16S rRNA, all the same length, by denaturing gradient gel electrophoresis (DGGE). DGGE analysis of different microbial communities demonstrated the presence of up to 10 distinguishable bands in the separation pattern, which were most likely derived from as many different species constituting these populations, and thereby generated a DGGE profile of the populations. We showed that it is possible to identify constituents which represent only 1% of the total population. With an oligonucleotide probe specific for the V3 region of 16S rRNA of sulfate-reducing bacteria, particular DNA fragments from some of the microbial populations could be identified by hybridization analysis. Analysis of the genomic DNA from a bacterial biofilm grown under aerobic conditions suggests that sulfate-reducing bacteria, despite their anaerobicity, were present in this environment. The results we obtained demonstrate that this technique will contribute to our understanding of the genetic diversity of uncharacterized microbial populations.
11,380 citations
"Bacterial communities in different ..." refers background or methods in this paper
...…decades by both isolation (Neilson 1978) and molecular methods, such as polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (Muyzer et al. 1993; Ye and Zhang 2010), terminal restriction fragment length polymorphism (Liu et al. 1997), cloning (Schuppler et al. 1995), and…...
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...2002), plays an essential role in the biological treatment reactors and has been studied for several decades by both isolation (Neilson 1978) and molecular methods, such as polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (Muyzer et al. 1993; Ye and Zhang 2010), terminal restriction fragment length polymorphism (Liu et al....
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TL;DR: A 16S rRNA gene database (http://greengenes.lbl.gov) was used to provide chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies as mentioned in this paper.
Abstract: A 16S rRNA gene database (http://greengenes.lbl.gov) addresses limitations of public repositories by providing chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. It was found that there is incongruent taxonomic nomenclature among curators even at the phylum level. Putative chimeras were identified in 3% of environmental sequences and in 0.2% of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages in the Archaea and Bacteria.
9,593 citations
TL;DR: An improved alignment strategy uses the Infernal secondary structure aware aligner to provide a more consistent higher quality alignment and faster processing of user sequences, and a new Pyrosequencing Pipeline that provides tools to support analysis of ultra high-throughput rRNA sequencing data.
Abstract: The Ribosomal Database Project (RDP) provides researchers with quality-controlled bacterial and archaeal small subunit rRNA alignments and analysis tools. An improved alignment strategy uses the Infernal secondary structure aware aligner to provide a more consistent higher quality alignment and faster processing of user sequences. Substantial new analysis features include a new Pyrosequencing Pipeline that provides tools to support analysis of ultra high-throughput rRNA sequencing data. This pipeline offers a collection of tools that automate the data processing and simplify the computationally intensive analysis of large sequencing libraries. In addition, a new Taxomatic visualization tool allows rapid visualization of taxonomic inconsistencies and suggests corrections, and a new class Assignment Generator provides instructors with a lesson plan and individualized teaching materials. Details about RDP data and analytical functions can be found at http://rdp.cme.msu.edu/.
4,616 citations
"Bacterial communities in different ..." refers methods in this paper
...net/), so the reads flagged as chimeras were submitted to Ribosomal Database Project (RDP) classifier (Wang et al. 2007; Cole et al. 2009)....
[...]
...Because all sequences flagged as chimeras are not recommended to be discarded blindly (http://microbiomeutil.sourceforge.net/), so the reads flagged as chimeras were submitted to Ribosomal Database Project (RDP) classifier (Wang et al. 2007; Cole et al. 2009)....
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