Compositional and temporal stability of fecal taxon libraries for use with SourceTracker in sub-tropical catchments

O'Dea, Christian; Zhang, Qian; Staley, Christopher; Masters, Nicole; Kuballa, Anna; Fisher, Paul; Veal, Cameron; Stratton, Helen; Sadowsky, Michael J.; Ahmed, Warish; Katouli, Mohammad

doi:10.1016/j.watres.2019.114967

Cited by 13 publications

(11 citation statements)

References 58 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…fast expectation–maximization microbial source tracking predicted that the largest fecal input in sites R1 to R6 was from human source under dry weather conditions, whereas a bovine or swine source was dominant during the wet season, in agreement with the analysis results using host-associated molecular markers. FEAST is a promising tool to detect low-level bacterial signatures of freshwater, which were similar to those obtained using SourceTracker ( O’Dea et al, 2019 ). FEAST analyses assigned the contamination of the river water samples collected during dry weather to human fecal signatures, comprising 0.34%–3.15% of the total bacterial community ( Figure 6 and Table 2 ).…”

Section: Discussionsupporting

confidence: 58%

“…For example, only a very small sample size was analyzed by the FEAST program and only fecal samples were included to build the “source” library. In this study, most microbial taxa in the sink did not match the fecal signature in the “source” library, thus being classified as unknown, as in the case of published studies using SourceTracker ( Newton et al, 2013 ; Staley et al, 2018 ; O’Dea et al, 2019 ). Therefore, more samples, especially potential sources near the sampling sites (e.g., soil and rainwater samples), need to be included in the “source” library if the composition of the unknown source is to be clarified.…”

Section: Discussionmentioning

confidence: 98%

See 1 more Smart Citation

Synergistic Application of Molecular Markers and Community-Based Microbial Source Tracking Methods for Identification of Fecal Pollution in River Water During Dry and Wet Seasons

Liang

Wang

et al. 2021

Front. Microbiol.

View full text Add to dashboard Cite

It is important to track fecal sources from humans and animals that negatively influence the water quality of rural rivers and human health. In this study, microbial source tracking (MST) methods using molecular markers and the community-based FEAST (fast expectation–maximization microbial source tracking) program were synergistically applied to distinguish the fecal contributions of multiple sources in a rural river located in Beijing, China. The performance of eight markers were evaluated using 133 fecal samples based on real-time quantitative (qPCR) technique. Among them, six markers, including universal (BacUni), human-associated (HF183-1 and BacH), swine-associated (Pig-2-Bac), ruminant-associated (Rum-2-Bac), and avian-associated (AV4143) markers, performed well in the study. A total of 96 water samples from the river and outfalls showed a coordinated composition of fecal pollution, which revealed that outfall water might be a potential input of the Fsq River. In the FEAST program, bacterial 16S rRNA genes of 58 fecal and 12 water samples were sequenced to build the “source” library and “sink,” respectively. The relative contribution (<4.01% of sequence reads) of each source (i.e., human, swine, bovine, or sheep) was calculated based on simultaneous screening of the operational taxonomic units (OTUs) of sources and sinks, which indicated that community-based MST methods could be promising tools for identifying fecal sources from a more comprehensive perspective. Results of the qPCR assays indicated that fecal contamination from human was dominant during dry weather and that fecal sources from swine and ruminant were more prevalent in samples during the wet season than in those during the dry season, which were consistent with the findings predicted by the FEAST program using a very small sample size. Information from the study could be valuable for the development of improved regulation policies to reduce the levels of fecal contamination in rural rivers.

show abstract

Section: Discussionsupporting

confidence: 58%

Section: Discussionmentioning

confidence: 98%

Synergistic Application of Molecular Markers and Community-Based Microbial Source Tracking Methods for Identification of Fecal Pollution in River Water During Dry and Wet Seasons

Liang

Wang

et al. 2021

Front. Microbiol.

View full text Add to dashboard Cite

show abstract

“…The identification of new markers is increasingly supported by advances in sequencing technology and bioinformatics [84,[94][95][96], and next-generation sequencing (NGS)-based MST approaches continue to be refined [97]. Although highly dependent on fecal library composition (the collection of metagenomic sequences from known fecal sources that informs source identification algorithms) [97][98][99][100][101], NGS-MST has the potential to identify finer distinctions between sources, as demonstrated by a study in Kenya that distinguished between fecal contamination from young children and adults [102•]. The recent introduction of more affordable and portable long-read sequencing platforms, while currently error prone, promises to accelerate the use of sequencing to characterize fecal contamination [103,104].…”

Section: Microbial Source Trackingmentioning

confidence: 99%

Microbial Indicators of Fecal Pollution: Recent Progress and Challenges in Assessing Water Quality

Holcomb

Stewart

2020

Curr Envir Health Rpt

102

View full text Add to dashboard Cite

Purpose of Review Fecal contamination of water is a major public health concern. This review summarizes recent developments and advancements in water quality indicators of fecal contamination. Recent Findings This review highlights a number of trends. First, fecal indicators continue to be a valuable tool to assess water quality and have expanded to include indicators able to detect sources of fecal contamination in water. Second, molecular methods, particularly PCR-based methods, have advanced considerably in their selected targets and rigor, but have added complexity that may prohibit adoption for routine monitoring activities at this time. Third, risk modeling is beginning to better connect indicators and human health risks, with the accuracy of assessments currently tied to the timing and conditions where risk is measured. Summary Research has advanced although challenges remain for the effective use of both traditional and alternative fecal indicators for risk characterization, source attribution and apportionment, and impact evaluation.

show abstract

“…The diatom OTUs in our study were used as reference sequences to perform highthroughput sequence similarity searches using VSEARCH v.2.14.1 (Rognes et al, 2016) with minimum nucleotide identity cut-off of 97% (-usearch_global -id 0.97). This reference (Kaestli et al, 2019;O'Dea et al, 2019;Trevathan-Tackett et al, 2020 sequence based method streamlined the bioinformatics process and focused on the spatial distribution of the diatoms detected in our biofilm samples.…”

Section: Detection Of Selected Diatom Otus In Other Australian 16s Rrna Datasetsmentioning

confidence: 99%

“…3A, 3B). The lowest number of diatoms ( 24) and lowest similarity was shared with the freshwater samples from Queensland (O'Dea et al, 2019).…”

Section: Occurrence Of Selected Diatom Otus In Other Australian 16s Rrna Datasetsmentioning

confidence: 99%

Dumpster diving for diatom plastid 16S rRNA genes

Bonfantine

Trevathan‐Tackett

Matthews

et al. 2021

PeerJ

View full text Add to dashboard Cite

High throughput sequencing is improving the efficiency of monitoring diatoms, which inhabit and support aquatic ecosystems across the globe. In this study, we explored the potential of a standard V4 515F-806RB primer pair in recovering diatom plastid 16S rRNA sequences. We used PhytoREF to classify the 16S reads from our freshwater biofilm field sampling from three stream segments across two streams in south-eastern Australia and retrieved diatom community data from other, publicly deposited, Australian 16S amplicon datasets. When these diatom operational taxonomic units (OTUs) were traced using the default RDPII and NCBI databases, 68% were characterized as uncultured cyanobacteria. We analysed the 16S rRNA sequences from 72 stream biofilm samples, separated the chloroplast OTUs, and classified them using the PhytoREF database. After filtering the reads attributed to Bacillariophyta (relative abundance >1%), 71 diatom OTUs comprising more than 90% of the diatom reads in each stream biofilm sample were identified. Beta-diversity analyses demonstrated significantly different diatom assemblages and discrimination among river segments. To further test the approach, the diatom OTUs from our biofilm sampling were used as reference sequences to identify diatom reads from other Australian 16S rRNA datasets in the NCBI-SRA database. Across the three selected public datasets, 67 of our 71 diatom OTUs were detected in other Australian ecosystems. Our results show that diatom plastid 16S rRNA genes are readily amplified with existing 515F-806RB primer sets. Therefore, the volume of existing 16S rRNA amplicon datasets initially generated for microbial community profiling can also be used to detect, characterize, and map diatom distribution to inform phylogeny and ecological health assessments, and can be extended into a range of ecological and industrial applications. To our knowledge, this study represents the first attempt to classify freshwater samples using this approach and the first application of PhytoREF in Australia.

show abstract

Compositional and temporal stability of fecal taxon libraries for use with SourceTracker in sub-tropical catchments

Cited by 13 publications

References 58 publications

Synergistic Application of Molecular Markers and Community-Based Microbial Source Tracking Methods for Identification of Fecal Pollution in River Water During Dry and Wet Seasons

Synergistic Application of Molecular Markers and Community-Based Microbial Source Tracking Methods for Identification of Fecal Pollution in River Water During Dry and Wet Seasons

Microbial Indicators of Fecal Pollution: Recent Progress and Challenges in Assessing Water Quality

Dumpster diving for diatom plastid 16S rRNA genes

Contact Info

Product

Resources

About