Assessing the spatial and temporal variability of bacterial communities in two Bardenpho wastewater treatment systems via Illumina MiSeq sequencing

Xue, Jia; Schmitz, Bradley W.; Caton, Kevin; Zhang, Bowen; Zabaleta, Jovanny; Garai, Jone; Taylor, Christopher M.; Romanchishina, Tatiana; Gerba, Charles P.; Pepper, Ian L.; Sherchan, Samendra P.

doi:10.1016/j.scitotenv.2018.12.141

Cited by 56 publications

(19 citation statements)

References 52 publications

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“…The bacterial DNA extracts of wastewater samples were used for metagenomic sequencing via a MiSeq gene sequencer (Illumina, San Diego, CA, USA) as described previously [47]. Operational taxonomic units obtained were analyzed based on the bacterial domain, phylum, family, and genus.…”

Section: Ngs For Characterization Of Bacterial Communitiesmentioning

confidence: 99%

Reduction of Arcobacter at Two Conventional Wastewater Treatment Plants in Southern Arizona, USA

et al. 2019

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This study aimed to identify the bacterial community in two wastewater treatment plants (WWTPs) and to determine the occurrence and reduction of Arcobacter, along with virulence genes (ciaB and pldA). A total of 48 samples (24 influent and 24 effluent) were collected at two WWTPs in southern Arizona in the United States, monthly from August 2011 to July 2012. Bacterial DNA extract was utilized for 16S rRNA metagenomic sequencing. Quantification of Arcobacter 16S rRNA gene was conducted using a recently developed SYBR Green-based quantitative PCR assay. Among 847 genera identified, 113 (13%) were identified as potentially pathogenic bacteria. Arcobacter 16S rRNA gene was detected in all influent samples and ten (83%) and nine (75%) effluent samples at each plant, respectively. Log reduction ratios of Arcobacter 16S rRNA gene in Plant A and Plant B were 1.7 ± 0.9 (n = 10) and 2.3 ± 1.5 (n = 9), respectively. The ciaB gene was detected by quantitative PCR in eleven (92%) and twelve (100%) of 12 influent samples from Plant A and Plant B, respectively, while the pldA gene was detected in eight (67%) and six (50%) influent samples from Plant A and Plant B, respectively. The prevalence of potentially pathogenic bacteria in WWTP effluent indicated the need for disinfection before discharge into the environment.

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Section: Ngs For Characterization Of Bacterial Communitiesmentioning

confidence: 99%

Reduction of Arcobacter at Two Conventional Wastewater Treatment Plants in Southern Arizona, USA

et al. 2019

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“…Of the 18 samples collected, 13 samples, excluding five of six samples from Sundarijal in which bacterial DNA concentrations were not enough high, were subjected to metagenomics sequencing using a MiSeq gene sequencer (Illumina, San Diego, CA, USA) as previously described [18]. Briefly, the 16S rRNA library was prepared, and the sequence data were analyzed after purification, amplification, library quantification, normalization, and pooling.…”

Section: Ngs For the Characterization Of Bacterial Communitiesmentioning

confidence: 99%

Prevalence of Arcobacter and Other Pathogenic Bacteria in River Water in Nepal

Shrestha

Tandukar

Bhandari

et al. 2019

Water

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This study aims to determine the diversity of pathogenic bacteria in the Bagmati River, Nepal, during a one-year period. A total of 18 river water samples were collected from three sites (n = 6 per site) along the river. Bacterial DNA, which were extracted from the water samples, were analyzed for bacterial 16S rRNA genes by next-generation sequencing for 13 of 18 samples, and by quantitative PCR targeting Arcobacter for all 18 samples. The 16S rRNA sequencing identified an average of 97,412 ± 35,909 sequences/sample, which were then categorized into 28 phyla, 61 classes, and 709 bacterial genera. Eighteen (16%) genera of 111 potential pathogenic bacteria were detected with abundance ratios of >1%; Arcobacter, Acinetobacter, and Prevotella were the dominant genera. The Arcobacter abundance ratios were 28.6% (n = 1), 31.3 ± 15.8% (n = 6), and 31.8 ± 17.2% (n = 6) at the upstream, midstream, and downstream sites, respectively. Arcobacter was detected in 14 (78%) of 18 samples tested, with concentrations ranging from 6.7 to 10.7 log10 copies/100 mL, based on quantitative PCR. Our results demonstrate the poor bacterial quality of the Bagmati River water, suggesting a need for implementing more measures to reduce fecal contamination in the river water.

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“…A number of published data have illustrated spatial heterogeneity of bacterial communities in freshwater ecosystems 8 – 10 . Bacterial population’s seasonality in different water types and variant ecosystems, such as bacterioplankton communities 11 , 12 , bacterial communities in sediments 13 , wastewater treatment plants 14 , 15 , and drinking water works 16 , 17 , as well as in the estuarine ecosystems 18 , 19 , has repeatedly been observed. However, seasonal impacts on the lotic bacterial community structure remain sparsely addressed.…”

Section: Introductionmentioning

confidence: 96%

Seasonal dynamics of lotic bacterial communities assessed by 16S rRNA gene amplicon deep sequencing

Paruch

Eiken

et al. 2020

Sci Rep

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Aquatic microbial diversity, composition, and dynamics play vital roles in sustaining water ecosystem functionality. Yet, there is still limited knowledge on bacterial seasonal dynamics in lotic environments. This study explores a temporal pattern of bacterial community structures in lotic freshwater over a 2-year period. The aquatic bacterial communities were assessed using Illumina MiSeq sequencing of 16S rRNA genes. Overall, the communities were dominated by α-, β-, and γ-Proteobacteria, Bacteroidetes, Flavobacteriia, and Sphingobacteriia. The bacterial compositions varied substantially in response to seasonal changes (cold vs. warm), but they were rather stable within the same season. Furthermore, higher diversity was observed in cold seasons compared to warm periods. The combined seasonal-environmental impact of different physico-chemical parameters was assessed statistically, and temperature, suspended solids, and nitrogen were determined to be the primary abiotic factors shaping the temporal bacterial assemblages. This study enriches particular knowledge on the seasonal succession of the lotic freshwater bacteria.

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Assessing the spatial and temporal variability of bacterial communities in two Bardenpho wastewater treatment systems via Illumina MiSeq sequencing

Cited by 56 publications

References 52 publications

Reduction of Arcobacter at Two Conventional Wastewater Treatment Plants in Southern Arizona, USA

Reduction of Arcobacter at Two Conventional Wastewater Treatment Plants in Southern Arizona, USA

Prevalence of Arcobacter and Other Pathogenic Bacteria in River Water in Nepal

Seasonal dynamics of lotic bacterial communities assessed by 16S rRNA gene amplicon deep sequencing

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