Rapid decay of host-specific fecal Bacteroidales cells in seawater as measured by quantitative PCR with propidium monoazide

Bae, Sung Woo; Wuertz, Stefan

doi:10.1016/j.watres.2009.06.053

Cited by 136 publications

(132 citation statements)

References 32 publications

Supporting

Mentioning

120

Contrasting

Order By: Relevance

“…The results indicated a 90%-99% reduction of B. fragilis cells within the first two days. Similarly, Bae and Wuertz [108] also reported the short survival (T 90 < 2 days) of Bacteroidales cells in seawater and freshwater exposed to sunlight and dark conditions. In contrast, T 90 decay of Bacteroidales DNA and RNA range from three to 12 days [44,106].…”

Section: Decay Of Human-specific Bacteroides Markers In Environmentalmentioning

confidence: 73%

“…Several studies also reported faster decay rates for Bacteroides markers exposed to dark compared to sunlight [103,[109][110][111]. In contrast, slower decay rates of Bacteroidales markers exposed to sunlight have been observed by others [105,108,110]. Studies also reported that the decay rates of the several Bacteroides markers including human-specific Bacteroides (BsteriF1, BuniF2, GenBac3, HF183, HF134, and HumM2) in freshwater were somewhat greater than the corresponding decay rate in seawater [106,112].…”

Section: Decay Of Human-specific Bacteroides Markers In Environmentalmentioning

confidence: 83%

“…Bacteroidales culturable cells tend to persist a relatively short time in environmental waters compared to DNA signal [107,108]. For example, Okabe and Shizuma [107] monitored the decay of Bacteroides fragilis cells in filtered and non-filtered river and seawater.…”

Section: Decay Of Human-specific Bacteroides Markers In Environmentalmentioning

confidence: 99%

“…Studies also reported that the decay rates of the several Bacteroides markers including human-specific Bacteroides (BsteriF1, BuniF2, GenBac3, HF183, HF134, and HumM2) in freshwater were somewhat greater than the corresponding decay rate in seawater [106,112]. Bae and Wuertz [108] used propidium monoazide (PMA)-qPCR to differentiate between live and dead cells or extracellular DNA. The authors concluded that this approach might be explored to estimate the age (recent vs. old) of fecal pollution in water.…”

Section: Decay Of Human-specific Bacteroides Markers In Environmentalmentioning

confidence: 99%

See 3 more Smart Citations

Current Status of Marker Genes of Bacteroides and Related Taxa for Identifying Sewage Pollution in Environmental Waters

Ahmed

Hughes

Harwood

2016

Water

112

View full text Add to dashboard Cite

Abstract:Microbial source tracking (MST) endeavors to determine sources of fecal pollution in environmental waters by capitalizing on the association of certain microorganisms with the gastrointestinal tract and feces of specific animal groups. Several decades of research have shown that bacteria belonging to the gut-associated order Bacteroidales, and particularly the genus Bacteroides, tend to co-evolve with the host, and are, therefore, particularly suitable candidates for MST applications. This review summarizes the current research on MST methods that employ genes belonging to Bacteroidales/Bacteroides as tracers or "markers" of sewage pollution, including known advantages and deficiencies of the many polymerase chain reaction (PCR)-based methods that have been published since 2000. Host specificity is a paramount criterion for confidence that detection of a marker is a true indicator of the target host. Host sensitivity, or the prevalence of the marker in feces/waste from the target host, is necessary for confidence that absence of the marker is indicative of the absence of the pollution source. Each of these parameters can vary widely depending on the type of waste assessed and the geographic location. Differential decay characteristics of bacterial targets and their associated DNA contribute to challenges in interpreting MST results in the context of human health risks. The HF183 marker, derived from the 16S rRNA gene of Bacteroides dorei and closely related taxa, has been used for almost two decades in MST studies, and is well characterized regarding host sensitivity and specificity, and in prevalence and concentration in sewage in many countries. Other markers such as HumM2 and HumM3 show promise, but require further performance testing to demonstrate their widespread utility. An important limitation of the one-marker-one-assay approach commonly used for MST is that given the complexities of microbial persistence in environmental waters, and the methodological challenges of quantitative PCR (qPCR) in such samples, the absence of a given marker does not ensure the absence of fecal pollution in the source water. Approaches under development, such as microarray and community analysis, have the potential to improve MST practices, thereby increasing our ability to protect human and ecosystem health.

show abstract

Section: Decay Of Human-specific Bacteroides Markers In Environmentalmentioning

confidence: 73%

Section: Decay Of Human-specific Bacteroides Markers In Environmentalmentioning

confidence: 83%

Section: Decay Of Human-specific Bacteroides Markers In Environmentalmentioning

confidence: 99%

Section: Decay Of Human-specific Bacteroides Markers In Environmentalmentioning

confidence: 99%

See 2 more Smart Citations

Current Status of Marker Genes of Bacteroides and Related Taxa for Identifying Sewage Pollution in Environmental Waters

Ahmed

Hughes

Harwood

2016

Water

112

View full text Add to dashboard Cite

show abstract

“…Recently, DNA‐intercalating dyes such as ethidium monoazide (EMA) and propidium monoazide (PMA) have been proposed as useful molecular methods to quantify intact bacterial cells in environments (Nogva et al ., 2003; Rudi et al ., 2005; Nocker et al ., 2006). PMA or EMA with PCR technique has been widely used to assess cell viability in water, soil, air and food (Rogers et al ., 2008; Bae and Wuertz, 2009; Miotto et al ., 2012; Kaushik and Balasubramanian, 2013; Li and Chen, 2013). …”

Section: Introductionmentioning

confidence: 99%

Molecular viability testing of viable but non‐culturable bacteria induced by antibiotic exposure

Lee

Bae

2017

Microbial Biotechnology

Self Cite

View full text Add to dashboard Cite

SummaryNucleic acid amplification‐based methods are limited by their inability to discriminate between viable and dead cells. To overcome this drawback, propidium monoazide (PMA) combined with qPCR has been used to differentiate viable from nonviable cells in environmental samples. However, assessing bacterial physiology using PMA‐qPCR remains a challenge due to its incapability of detecting metabolic activities, leading to overestimation of the viable bacteria population under an inactivation condition (e.g. antibiotic treatments). A recent advanced technique to amplify ribosomal RNA precursors (pre‐rRNA) has been shown to detect viable cells because pre‐rRNAs are intermediates in rRNA synthesis. This study investigated the effect of different types of antibiotics on the bacterial viability or viable but non‐culturable (VBNC) state using both PMA‐qPCR and pre‐rRNA analyses with Pseudomonas aeruginosa. This study demonstrated that P. aeruginosa was more sensitive to colistin than it was to carbenicillin, gentamicin and levofloxacin. We could discriminate VBNC P. aeruginosa cells using PMA‐qPCR when antibiotic pressure induced the VBNC state. Also, pre‐rRNA was able to distinguish viable cells from colistin‐inactivated bacteria cells, and it could detect the presence of VBNC and persister cells. Our results showed that these two molecular methods could successfully eliminate false‐positive signals derived from antibiotics‐inactivated cells.

show abstract

Detection of vertebrates from natural and artificial inland water bodies in a semi‐arid habitat using eDNA from filtered, swept, and sediment samples

McDonald

Bateman

Cooper

et al. 2023

Ecology and Evolution

View full text Add to dashboard Cite

Biomonitoring is vital for establishing baseline data that is needed to identify and quantify ecological change and to inform management and conservation activities. However, biomonitoring and biodiversity assessment in arid environments, which are predicted to cover 56% of the Earth's land surface by 2100, can be prohibitively time consuming, expensive, and logistically challenging due to their often remote and inhospitable nature. Sampling of environmental DNA (eDNA) coupled with high‐throughput sequencing is an emerging biodiversity assessment method. Here we explore the application of eDNA metabarcoding and various sampling approaches to estimate vertebrate richness and assemblage at human‐constructed and natural water sources in a semi‐arid region of Western Australia. Three sampling methods: sediment samples, filtering through a membrane with a pump, and membrane sweeping in the water body, were compared using two eDNA metabarcoding assays, 12S‐V5 and 16smam, for 120 eDNA samples collected from four gnammas (gnamma: Australian Indigenous Noongar language term–granite rock pools) and four cattle troughs in the Great Western Woodlands, Western Australia. We detected higher vertebrate richness in samples from cattle troughs and found differences between assemblages detected in gnammas (more birds and amphibians) and cattle troughs (more mammals, including feral taxa). Total vertebrate richness was not different between swept and filtered samples, but all sampling methods yielded different assemblages. Our findings indicate that eDNA surveys in arid lands will benefit from collecting multiple samples at multiple water sources to avoid underestimating vertebrate richness. The high concentration of eDNA in small, isolated water bodies permits the use of sweep sampling that simplifies sample collection, processing, and storage, particularly when assessing vertebrate biodiversity across large spatial scales.

show abstract

Rapid decay of host-specific fecal Bacteroidales cells in seawater as measured by quantitative PCR with propidium monoazide

Cited by 136 publications

References 32 publications

Current Status of Marker Genes of Bacteroides and Related Taxa for Identifying Sewage Pollution in Environmental Waters

Current Status of Marker Genes of Bacteroides and Related Taxa for Identifying Sewage Pollution in Environmental Waters

Molecular viability testing of viable but non‐culturable bacteria induced by antibiotic exposure

Detection of vertebrates from natural and artificial inland water bodies in a semi‐arid habitat using eDNA from filtered, swept, and sediment samples

Contact Info

Product

Resources

About