Fecal contamination of storm sewers: Evaluating wastewater micropollutants, human-specific Bacteroides 16S rRNA, and mitochondrial DNA genetic markers as alternative indicators of sewer cross connections

Genetic markers derived from Bacteroidales spp. have been proposed as promising indicators for fecal contamination in the water environment. However, little is known about the persistency of Bacteroidales spp. 16S rRNA genetic markers in the natural environment, which hampers the precise identification of fecal contamination sources. In this study, the persistency of human-specific Bacteroidales spp. genetic markers in river water was investigated during a 3-week agitation. The copy number of Bacteroidales spp. genetic marker was decreased with agitation time, and was very sensitive to water temperature. After the 3-week agitation, three clones of 18S rRNA gene related to Glaucoma scintillans, Spumella-like flagellate, and Colpidium campylum were acquired. The presence of predators that can prey on target bacteria could also be a critical factor affecting the quantified value of genetic markers. It is very important to take these factors, water temperature and the presence of predator, into account for predicting the fate of genetic markers to accurately identify fecal pollution sources.

Download Full-text

Rediscovery of Rhacophorus yaoshanensis and Theloderma kwangsiensis at their type localities after five decades

Zootaxa ◽

10.11646/zootaxa.4379.4.2 ◽

2018 ◽

Vol 4379 (4) ◽

pp. 484 ◽

Cited By ~ 1

Author(s):

WEICAI CHEN ◽

XIAOWEN LIAO ◽

SHICHU ZHOU ◽

YUNMING MO ◽

YONG HUANG

Keyword(s):

Mitochondrial Dna ◽

16S Rrna ◽

Phylogenetic Relationships ◽

New Record ◽

Nature Reserve ◽

Guangxi Province ◽

Preliminary Assessment ◽

Phylogenetic Studies ◽

Pairwise Divergence ◽

High Support

Rhacophorus yaoshanensis Liu & Hu, 1962 and Theloderma kwangsiensis Liu & Hu, 1962 were described by Liu & Hu (1962) based on two specimens and one specimen, respectively, from the Dayaoshan Ranges, Guangxi, China. Since these two species were described, no additional specimens have been collected from their type localities, presenting an issue for phylogenetic studies of the genera. Five decades later, we have rediscovered R. yaoshanensis and T. kwangsiensis from their type localities. In this paper, we re-describe the two species and conduct a preliminary assessment of their phylogenetic relationships using two mitochondrial DNA genes (12S and 16S rRNA). The results indicate with high support that R. yaoshanensis is closely related to Rhacophorus pinglongensis. Theloderma kwangsiensis is nested within Theloderma corticale, with only 0.0–0.6% pairwise divergence, a level typical of intraspecific variation. Based on both molecular and morphological analyses, we further confirm that T. kwangsiensis is a synonym of T. corticale. Shiwandashan National Nature Reserve, Guangxi Province, China, is a new record for T. corticale.

Download Full-text

Microbial community dynamics of surface water in British Columbia, Canada

10.1101/719146 ◽

2019 ◽

Author(s):

Miguel I. Uyaguari-Diaz ◽

Matthew A. Croxen ◽

Kirby Cronin ◽

Zhiyao Luo ◽

Judith Isaac-Renton ◽

...

Keyword(s):

Microbial Community ◽

16S Rrna ◽

16S Rrna Gene ◽

Community Dynamics ◽

Fecal Contamination ◽

Rrna Gene ◽

Microbial Culture ◽

Sample Collection ◽

Fecal Indicator ◽

E Coli

AbstractTraditional methods for monitoring the microbiological quality of water focus on the detection of fecal indicator bacteria such as Escherichia coli, often tested as a weekly grab sample. To understand the stability of E.coli concentrations over time, we evaluated three approaches to measuring E. coli levels in water: microbial culture using Colilert, quantitative PCR for uidA and next-generation sequencing of the 16S rRNA gene. Two watersheds, one impacted by agricultural and the other by urban activities, were repeatedly sampled over a simultaneous ten-hour period during each of the four seasons. Based on 16S rRNA gene deep sequencing, each watershed showed different microbial community profiles. The bacterial microbiomes varied with season, but less so within each 10-hour sampling period. Enterobacteriaceae comprised only a small fraction (<1%) of the total community. The qPCR assay detected significantly higher quantities of E. coli compared to the Colilert assay and there was also variability in the Colilert measurements compared to Health Canada’s recommendations for recreational water quality. From the 16S data, other bacteria such as Prevotella and Bacteroides showed promise as alternative indicators of fecal contamination. A better understanding of temporal changes in watershed microbiomes will be important in assessing the utility of current biomarkers of fecal contamination, determining the best timing for sample collection, as well as searching for additional microbial indicators of the health of a watershed.

Download Full-text

RESTRICTED MITOCHONDRIAL DNA FRAGMENTS AS GENETIC MARKERS IN CYTOPLASMIC HYBRIDS

Extrachromosomal DNA ◽

10.1016/b978-0-12-198780-0.50036-2 ◽

1979 ◽

pp. 501-514 ◽

Cited By ~ 2

Author(s):

Ching Ho ◽

Hayden G. Coon

Keyword(s):

Mitochondrial Dna ◽

Genetic Markers ◽

Dna Fragments ◽

Cytoplasmic Hybrids

Download Full-text

Chicken- and duck-associated Bacteroides–Prevotella genetic markers for detecting fecal contamination in environmental water

Applied Microbiology and Biotechnology ◽

10.1007/s00253-012-4469-2 ◽

2012 ◽

Vol 97 (16) ◽

pp. 7427-7437 ◽

Cited By ~ 29

Author(s):

Ayano Kobayashi ◽

Daisuke Sano ◽

Jun Hatori ◽

Satoshi Ishii ◽

Satoshi Okabe

Keyword(s):

Genetic Markers ◽

Fecal Contamination ◽

Environmental Water

Download Full-text

Isolation of Bacteroides from fish and human fecal samples for identification of unique molecular markers

Canadian Journal of Microbiology ◽

10.1139/cjm-2013-0518 ◽

2013 ◽

Vol 59 (12) ◽

pp. 771-777 ◽

Cited By ~ 6

Author(s):

Leila Kabiri ◽

Absar Alum ◽

Channah Rock ◽

Jean E. McLain ◽

Morteza Abbaszadegan

Keyword(s):

Molecular Markers ◽

Natural Waters ◽

Fecal Contamination ◽

Rrna Gene ◽

Significant Similarity ◽

Fecal Samples ◽

Cultured Fish ◽

Unique Markers ◽

Current Sequence ◽

Human Specific

Bacteroides molecular markers have been used to identify human fecal contamination in natural waters, but recent work in our laboratory confirmed cross-amplification of several human-specific Bacteroides spp. assays with fecal DNA from fish. For identification of unique molecular markers, Bacteroides from human (n = 4) and fish (n = 7) fecal samples were cultured and their identities were further confirmed using Rapid ID 32A API strips. The 16S rDNA from multiple isolates from each sample was PCR amplified, cloned, and sequenced to identify unique markers for development of more stringent human-specific assays. In human feces, Bacteroides vulgatus was the dominant species (75% of isolates), whereas in tilapia feces, Bacteroides eggerthii was dominant (66%). Bacteroides from grass carp, channel catfish, and blue catfish may include Bacteroides uniformis, Bacteroides ovatus, or Bacteroides stercoris. Phylogenic analyses of the 16S rRNA gene sequences showed distinct Bacteroides groupings from each fish species, while human sequences clustered with known B. vulgatus. None of the fish isolates showed significant similarity to Bacteroides sequences currently deposited in NCBI (National Center for Biotechnology Information). This study expands the current sequence database of cultured fish Bacteroides. Such data are essential for identification of unique molecular markers in human Bacteroides that can be utilized in differentiating fish and human fecal contamination in water samples.

Download Full-text

Quantitative PCR for Genetic Markers of Human Fecal Pollution

Applied and Environmental Microbiology ◽

10.1128/aem.00305-09 ◽

2009 ◽

Vol 75 (17) ◽

pp. 5507-5513 ◽

Cited By ~ 105

Author(s):

Orin C. Shanks ◽

Catherine A. Kelty ◽

Mano Sivaganesan ◽

Manju Varma ◽

Richard A. Haugland

Keyword(s):

Quantitative Pcr ◽

Genetic Markers ◽

Quantitative Methods ◽

Animal Species ◽

Fecal Pollution ◽

Rrna Gene ◽

Target Dna ◽

Pcr Assays ◽

Wastewater Samples ◽

Human Specific

ABSTRACT Assessment of health risk and fecal bacterial loads associated with human fecal pollution requires reliable host-specific analytical methods and a rapid quantification approach. We report the development of quantitative PCR assays for quantification of two recently described human-specific genetic markers targeting Bacteroidales-like cell surface-associated genes. Each assay exhibited a range of quantification from 10 to 1 ï¿½ 106 copies of target DNA. For each assay, internal amplification controls were developed to detect the presence or absence of amplification inhibitors. The assays predominantly detected human fecal specimens and exhibited specificity levels greater than 97% when tested against 265 fecal DNA extracts from 22 different animal species. The abundance of each human-specific genetic marker in primary effluent wastewater samples collected from 20 geographically distinct locations was measured and compared to quantities estimated by real-time PCR assays specific for rRNA gene sequences from total Bacteroidales and enterococcal fecal microorganisms. Assay performances combined with the prevalence of DNA targets in sewage samples provide experimental evidence supporting the potential application of these quantitative methods for monitoring fecal pollution in ambient environmental waters.

Download Full-text

Identification of species-specific nuclear insertions of mitochondrial DNA (numts) in gorillas and their potential as population genetic markers

Molecular Phylogenetics and Evolution ◽

10.1016/j.ympev.2014.08.018 ◽

2014 ◽

Vol 81 ◽

pp. 61-70 ◽

Cited By ~ 10

Author(s):

Iván Darío Soto-Calderón ◽

Nicholas Jonathan Clark ◽

Julia Vera Halo Wildschutte ◽

Kelly DiMattio ◽

Michael Ignatius Jensen-Seaman ◽

...

Keyword(s):

Mitochondrial Dna ◽

Genetic Markers ◽

Population Genetic ◽

Identification Of Species ◽

Species Specific

Download Full-text

Phylogeny of Meloidogyne spp. based on 18S rDNA and the intergenic region of mitochondrial DNA sequences

Nematology ◽

10.1163/156854105776186325 ◽

2005 ◽

Vol 7 (6) ◽

pp. 851-862 ◽

Cited By ~ 58

Author(s):

Regina Carneiro ◽

Don Dickson ◽

Ayyamperumal Jeyaprakash ◽

Byron Adams ◽

Myrian Tigano

Keyword(s):

Mitochondrial Dna ◽

16S Rrna ◽

Dna Sequences ◽

18S Rdna ◽

Phylogenetic Trees ◽

Optimality Criteria ◽

Cytochrome Oxidase Subunit ◽

Meloidogyne Spp ◽

Rdna Analysis ◽

Cytochrome Oxidase Subunit Ii

AbstractThe 18S rDNA of 19 populations of Meloidogyne spp. was amplified and directly sequenced. The region of mitochondrial DNA, located in the 3′ portion of the gene that codes for cytochrome oxidase subunit II (COII) through a portion of the 16S rRNA (lRNA) gene, from 16 of these populations was cloned and sequenced. Heteroplasmic sequences were identified from both rDNA and mtDNA regions for several taxa. Several sequences sampled from nominal taxa differed from previously published accounts. Phylogenetic trees based on alignments of these sequences were constructed using distance, parsimony and likelihood optimality criteria. For 18S rDNA data, three main clades were identified. One well supported clade (86–91% bootstrap) included the most common and widely disseminated species, e.g.,M. arenaria, M. javanica and M. incognita, some recently described or redescribed species (M. floridensis, M. paranaensis, and M. ethiopica) plus numerous unidentified isolates. All mitotic parthenogenetic species, except for M. oryzae, were included in this clade. Other, less well supported clades included the amphimictic and facultative meiotic species M. hapla, M. microtyla, M. maritima and M. duytsi. One such clade comprised three meiotic parthenogens (M. exigua, M. graminicola and M. chitwoodi) and M. oryzae. This clade was moderately supported (77% bootstrap) but the relationships within this clade were poor. For mitochondrial DNA data, only the species in clade I from rDNA analysis, and M. hapla were analysed. These species formed a well supported clade (100% bootstrap) to the exclusion of M. mayaguensis and M. hapla. The addition of taxa and mtDNA data to publicly available records improved the discrimination sensitivity of species and atypical, non-identified, isolates.

Download Full-text