Resilience of microbial communities in a simulated drinking water distribution system subjected to disturbances: role of conditionally rare taxa and potential implications for antibiotic-resistant bacteria

Gomez-Alvarez, Vicente; Pfaller, Stacy; Pressman, Jonathan G.; Wahman, David G.; Revetta, Randy P.

doi:10.1039/c6ew00053c

Cited by 34 publications

(43 citation statements)

References 67 publications

(92 reference statements)

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“…For instance, Boutin et al (2015) showed that the structure between different samples from lung disease patients was visible with the Bray Curtis (quantitative) distance and absent with the qualitative Jaccard distance, highlighting the role of the abundances of certain pathogenic microbes in the disease. In other studies, the response of bacterial communities to stress or environmental changes was shown to be driven by the increase in abundance of some rare taxa (Shade et al, 2014;Genitsaris et al, 2015;Coveley, Elshahed & Youssef, 2015;Gomez-Alvarez et al, 2016).…”

Section: Discussionmentioning

confidence: 91%

Multiple comparative metagenomics using multisetk-mer counting

Benoit

Peterlongo

Mariadassou

et al. 2016

PeerJ Computer Science

114

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Background. Large scale metagenomic projects aim to extract biodiversity knowledge between different environmental conditions. Current methods for comparing microbial communities face important limitations. Those based on taxonomical or functional assignation rely on a small subset of the sequences that can be associated to known organisms. On the other hand, de novo methods, that compare the whole sets of sequences, either do not scale up on ambitious metagenomic projects or do not provide precise and exhaustive results. Methods. These limitations motivated the development of a new de novo metagenomic comparative method, called Simka. This method computes a large collection of standard ecological distances by replacing species counts by k-mer counts. Simka scales-up today's metagenomic projects thanks to a new parallel k-mer counting strategy on multiple datasets. Results. Experiments on public Human Microbiome Project datasets demonstrate that Simka captures the essential underlying biological structure. Simka was able to compute in a few hours both qualitative and quantitative ecological distances on hundreds of metagenomic samples (690 samples, 32 billions of reads). We also demonstrate that analyzing metagenomes at the k-mer level is highly correlated with extremely precise de novo comparison techniques which rely on all-versus-all sequences alignment strategy or which are based on taxonomic profiling.

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Section: Discussionmentioning

confidence: 91%

Multiple comparative metagenomics using multisetk-mer counting

Benoit

Peterlongo

Mariadassou

et al. 2016

PeerJ Computer Science

114

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“…In DWDS samples, the high abundance of a Methylobacterium -like ASV is consistent with other studies as Methylobacterium has been found to be ubiquitous in cloraminated DWDS as planktonic cells or forming part of biofilms (Gallego et al ., 2005; Gomez-Alvarez et al ., 2012 and 2016; Wang et al ., 2013). Furthermore, as observed by Potgieter et al .…”

Section: Discussionmentioning

confidence: 99%

Reproducible microbial community dynamics of two drinking water systems treating similar source waters

Potgieter

Pinto²,

Havenga

et al. 2019

Preprint

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26In addition to containing higher concentrations of organics and bacterial cells, 27 surface waters are often more vulnerable to pollution and microbial contamination 28 with intensive industrial and agricultural activities frequently occurring in areas 29 surrounding the water source. Therefore, surface waters typically require additional 30 treatment, where the choice of treatment strategy is critical for water quality. Using 31 16S rRNA gene profiling, this study provides a unique opportunity to simultaneously 32 investigate and compare two drinking water treatment plants and their 33 corresponding distribution systems. The two treatment plants treat similar surface 34 waters, from the same river system, with the same sequential treatment strategies. 35 Here, the impact of treatment and distribution on the microbial community within and 36 between each system was compared over an eight-month sampling campaign. 37 Overall, reproducible spatial and temporal dynamics within both DWTPs and their 38 corresponding DWDSs were observed. Although source waters showed some 39 dissimilarity in microbial community structure and composition, pre-disinfection 40 treatments (i.e. coagulation, flocculation, sedimentation and filtration) resulted in 41 highly similar microbial communities between the filter effluent samples. This 42 indicated that the same treatments resulted in the development of similar microbial 43 communities. Conversely, post-disinfection (i.e. chlorination and chloramination) 44 resulted in increased dissimilarity between disinfected samples from the two 45 systems, showing alternative responses of the microbial community to disinfection. 46 Lastly, it was observed that within the distribution system the same dominant taxa 47 were selected where samples increased in similarity with increased residence time. 48 Although, differences were found between the two systems, overall treatment and 49 distribution had a similar impact on the microbial community in each system. This 50 study therefore provides valuable information on the impact of treatment and 51 distribution on the drinking water microbiome. 52 53 Keywords: drinking water treatment; drinking water distribution; disinfection; 54 microbial community dynamics; Illumina MiSeq. 55 56 Highlights 57  Source waters show some dissimilarity in microbial community. 58  Treatment processes increases similarity and selects for the same dominant 59 taxa. 60  Differential response to chlorination causing increased dissimilarity and 61 variation. 62  Stabilisation of DWDS microbial community through selection of same 63 dominant taxa. 64  Microbial community dynamics are reproducible between the two systems. 65 66 Abbreviations 67 DWDS, drinking water distribution system; DWTP, drinking water treatment plant; 68 DADA2, Divisive Amplicon Denoising Algorithm; ASV, amplicon sequence variant; 69 AMOVA, analysis of molecular variance; MRA, mean relative abundance; PCoA, 70 Principal coordinate analysis; ANOVA, One-way analysis of varianc...

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“…A library of V4 region of 16S rRNA was constructed using modified F515 and R806 primers (Caporaso et al, 2012) as described previously (Derakhshani et al, 2016). PCR reaction for each sample was performed in duplicate and contained 1.0 µL of pre-normalized DNA, 1.0 µL of each forward and reverse primers (10 µM), 12 µL HPLC grade water (Fisher Scientific, Ottawa, ON, Canada) and 10 µL 5 Prime Hot MasterMix® (5 Prime, Inc., Gaithersburg, MD, USA).…”

Section: S Rrna Illumina Sequencingmentioning

confidence: 99%

Bacteria in drinking water sources of a First Nation reserve in Canada

Farenhorst

Jahan

et al. 2017

Science of The Total Environment

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Approximately 20% of the 600 First Nations reserves across Canada are under a drinking water advisory, often due to unacceptable levels of bacteria. In this study, we detected fecal bacteria at an alarmingly high frequency in drinking water sources in a fly-in First Nations community, most notably in buckets/drums of homes without running water where Escherichia coli levels ranged from 20 to 62,000 CFU/100mL. The water leaving the water treatment plant was free of E. coli and its free residual chlorine concentration (0.67 mg/L) was within the range typically observed for treated water in Canada. Water samples from taps in homes served by cisterns, and those sampled from the water truck and community standpipe, always showed unacceptable levels of E. coli (1 to 2,100 CFU/100mL) and free residual chlorine concentrations below the 0.2 mg/L required to prevent bacterial regrowth. Samples from taps in homes served by piped water had lower levels of E. coli (0 to 2 CFU/100mL). DNA-and RNA-based 16S rRNA Illumina sequencing demonstrated that piped and cisterns water distribution systems showed an abundance of viable cells of Alphaproteobacteria indicative of biofilm formation in pipes and cisterns. The alpha diversity, based on observed OTUs and three other indices, was lowest in water truck samples that supplied water to the cistern and the low free residual chlorine concentration (0.07 mg/L) and predominance of Betaproteobacteria (63% of viable cells) that were immediately detected after the truck had filled up at the water treatment plant was indicative of contamination by particulate matter. Given these findings, First Nation residents living without running water and relying on inadequate water distribution systems are at higher risk of contracting water-born illnesses. We urge all governments in Canada to expand their investments in supporting and sustaining water as a human right in Canada's First Nations communities. 3 GRAPHICAL ABSTRACT

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Resilience of microbial communities in a simulated drinking water distribution system subjected to disturbances: role of conditionally rare taxa and potential implications for antibiotic-resistant bacteria

Abstract: CIRCOS plots representing the pan-genome and resistome of waterborne resistant bacteria.

Cited by 34 publications

References 67 publications

Multiple comparative metagenomics using multisetk-mer counting

Multiple comparative metagenomics using multisetk-mer counting

Reproducible microbial community dynamics of two drinking water systems treating similar source waters

Bacteria in drinking water sources of a First Nation reserve in Canada

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