Microbial community dynamics of surface water in British Columbia, Canada

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.

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Microbial community dynamics based on 16S rRNA gene profiles in a Pacific Northwest estuary and its tributaries

FEMS Microbiology Ecology ◽

10.1016/j.femsec.2004.10.016 ◽

2005 ◽

Vol 52 (1) ◽

pp. 115-128 ◽

Cited By ~ 72

Author(s):

Anne E. Bernhard ◽

Debbie Colbert ◽

James McManus ◽

Katharine G. Field

Keyword(s):

Microbial Community ◽

16S Rrna ◽

16S Rrna Gene ◽

Pacific Northwest ◽

Community Dynamics ◽

Rrna Gene ◽

Microbial Community Dynamics ◽

Gene Profiles

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Analysis of the Gull Fecal Microbial Community Reveals the Dominance of Catellicoccus marimammalium in Relation to Culturable Enterococci

Applied and Environmental Microbiology ◽

10.1128/aem.02414-13 ◽

2013 ◽

Vol 80 (2) ◽

pp. 757-765 ◽

Cited By ~ 15

Author(s):

Amber M. Koskey ◽

Jenny C. Fisher ◽

Mary F. Traudt ◽

Ryan J. Newton ◽

Sandra L. McLellan

Keyword(s):

Microbial Community ◽

16S Rrna ◽

16S Rrna Gene ◽

16S Rrna Gene Sequencing ◽

Illumina Miseq ◽

Rrna Gene ◽

Sequence Comparisons ◽

Fecal Indicator ◽

Fecal Samples ◽

Content Type

ABSTRACTGulls are prevalent in beach environments and can be a major source of fecal contamination. Gulls have been shown to harbor a high abundance of fecal indicator bacteria (FIB), such asEscherichia coliand enterococci, which can be readily detected as part of routine beach monitoring. Despite the ubiquitous presence of gull fecal material in beach environments, the associated microbial community is relatively poorly characterized. We generated comprehensive microbial community profiles of gull fecal samples using Roche 454 and Illumina MiSeq platforms to investigate the composition and variability of the gull fecal microbial community and to measure the proportion of FIB.EnterococcaceaeandEnterobacteriaceaewere the two most abundant families in our gull samples. Sequence comparisons between short-read data and nearly full-length 16S rRNA gene clones generated from the same samples revealedCatellicoccus marimammaliumas the most numerous taxon among all samples. The identification of bacteria from gull fecal pellets cultured on membrane-Enterococcusindoxyl-β-d-glucoside (mEI) plates showed that the dominant sequences recovered in our sequence libraries did not represent organisms culturable on mEI. Based on 16S rRNA gene sequencing of gull fecal isolates cultured on mEI plates, 98.8% were identified asEnterococcusspp., 1.2% were identified asStreptococcusspp., and none were identified asC. marimammalium. Illumina deep sequencing indicated that gull fecal samples harbor significantly higher proportions ofC. marimammalium16S rRNA gene sequences (>50-fold) relative to typical mEI culturableEnterococcusspp.C. marimammaliumtherefore can be confidently utilized as a genetic marker to identify gull fecal pollution in the beach environment.

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Longitudinal assessment of sputum microbiome by sequencing of the 16S rRNA gene in non-CF bronchiectasis patients

10.1101/050237 ◽

2016 ◽

Cited By ~ 2

Author(s):

Michael J Cox ◽

Elena M Turek ◽

Catherine Hennessy ◽

Ghazala K Mirza ◽

Phillip L James ◽

...

Keyword(s):

Microbial Community ◽

16S Rrna ◽

16S Rrna Gene ◽

Antibiotic Therapy ◽

Bacterial Overgrowth ◽

Microbial Community Analysis ◽

Rrna Gene ◽

Microbial Culture ◽

Study Objective ◽

Bronchial Infection

AbstractBackgroundBronchiectasis is accompanied by chronic bronchial infection that may drive disease progression. However, the evidence base for antibiotic therapy is limited. DNA based methods offer better identification and quantification of microbial constituents of sputum than standard clinical culture and may help inform patient management strategies. Our study objective was to determine the longitudinal variability of the non-CF bronchiectasis microbiome in sputum with respect to clinical variables.Eighty-five patients with non-cystic fibrosis (CF) bronchiectasis and daily sputum production were recruited from outpatient clinics and followed for six months. Monthly sputum samples and clinical measurements were taken, together with additional samples during exacerbations. 16S rRNA gene sequencing of the sputum microbiota was successful for 381 samples from 76 patients and analysed in conjunction with clinical data.ResultsMicrobial communities were highly individual in composition and stability, usually with limited diversity and often containing multiple pathogens. When compared to DNA sequencing, microbial culture had restricted sensitivity in identifying common pathogens. With some exceptions, community characteristics showed poor correlations with clinical features including underlying disease, antibiotic use and exacerbations, with the subject showing the strongest association with community structure. When present, certain pathogens may also shape the structure of the rest of the microbial community.ConclusionsThe use of microbial community analysis of sputum added to information from microbial culture. A simple model of exacerbations driven by bacterial overgrowth was not supported, suggesting a need for revision of principles for antibiotic therapy. In individual patients, the management of chronic bronchial infection may be improved by therapy specific to their microbiome, taking into account pathogen load, community stability, and acute and chronic community responses to antibiotics.

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Microbial Communities and Fecal Indicator Bacteria Associated with Cladophora Mats on Beach Sites along Lake Michigan Shores

Applied and Environmental Microbiology ◽

10.1128/aem.72.3.1932-1938.2006 ◽

2006 ◽

Vol 72 (3) ◽

pp. 1932-1938 ◽

Cited By ~ 69

Author(s):

Ola A. Olapade ◽

Morgan M. Depas ◽

Erika T. Jensen ◽

Sandra L. McLellan

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Environmental Protection Agency ◽

Lake Michigan ◽

Bacterial Community Composition ◽

Rrna Gene ◽

Fecal Indicator ◽

E Coli ◽

Sulfate Reducing ◽

Gram Positive Bacteria

ABSTRACT A high biomasses of Cladophora, a filamentous green alga, is found mainly during the summer along the shores of Lake Michigan. In this study, the abundance and persistence of the fecal indicator bacterium Escherichia coli and sulfate-reducing bacteria (SRB) on Cladophora mats collected at Lake Michigan beaches were evaluated using both culture-based and molecular analyses. Additionally, 16S rRNA gene cloning and sequencing were used to examine the bacterial community composition. Overall, E. coli was detected in all 63 samples obtained from 11 sites, and the average levels at most beaches ranged from 2,700 CFU/100 g (wet weight) of Cladophora to 7,500 CFU/100 g of Cladophora. However, three beaches were found to have site average E. coli densities of 12,800, 21,130, and 27,950 CFU/100 g of Cladophora. The E. coli levels in the lake water collected at the same time from these three sites were less than the recommended U.S. Environmental Protection Agency limit, 235 CFU/100 ml. E. coli also persisted on Cladophora mats in microcosms at room temperature for more than 7 days, and in some experiments it persisted for as long as 28 days. The SRB densities on Cladophora mats were relatively high, ranging from 4.4 × 106 cells/g (6.64 log CFU/g) to 5.73 × 106 cells/g (6.76 log CFU/g) and accounting for between 20% and 27% of the total bacterial counts. Partial sequences of the 16S rRNA gene clones revealed a phylogenetically diverse community, in which the Cytophaga-Flavobacterium-Bacteroides cluster and the low-G+C-content gram-positive bacteria were the dominant organisms, accounting for 40% and 12.8%, respectively, of the total clone library. These results further reveal the potential public health and ecological significance of Cladophora mats that are commonly found along the shoreline of Lake Michigan, especially with regard to the potential to harbor microorganisms associated with fecal pollution and odor-causing bacteria.

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Strengths and Limitations of 16S rRNA Gene Amplicon Sequencing in Revealing Temporal Microbial Community Dynamics

PLoS ONE ◽

10.1371/journal.pone.0093827 ◽

2014 ◽

Vol 9 (4) ◽

pp. e93827 ◽

Cited By ~ 246

Author(s):

Rachel Poretsky ◽

Luis M. Rodriguez-R ◽

Chengwei Luo ◽

Despina Tsementzi ◽

Konstantinos T. Konstantinidis

Keyword(s):

Microbial Community ◽

16S Rrna ◽

16S Rrna Gene ◽

Community Dynamics ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Microbial Community Dynamics

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Bacterial community dynamics during different stages of processing of smoked bacon using the 16S rRNA gene amplicon analysis

International Journal of Food Microbiology ◽

10.1016/j.ijfoodmicro.2021.109076 ◽

2021 ◽

pp. 109076

Author(s):

Xinfu Li ◽

Qiang Xiong ◽

Baocai Xu ◽

Haoxin Wang ◽

Hui Zhou ◽

...

Keyword(s):

Bacterial Community ◽

16S Rrna ◽

16S Rrna Gene ◽

Community Dynamics ◽

Rrna Gene ◽

Bacterial Community Dynamics ◽

The 16S Rrna Gene

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The diversity of active microbial groups in an activated sludge process treating painting process wastewater

E3S Web of Conferences ◽

10.1051/e3sconf/202014801002 ◽

2020 ◽

Vol 148 ◽

pp. 01002

Author(s):

Herto Dwi Ariesyady ◽

Mentari Rizki Mayanda ◽

Tsukasa Ito

Keyword(s):

Wastewater Treatment ◽

Microbial Community ◽

16S Rrna ◽

16S Rrna Gene ◽

Activated Sludge ◽

Biological Treatment ◽

Rrna Gene ◽

Activated Sludge Process ◽

Painting Process ◽

Process Wastewater

Activated sludge process is one of the wastewater treatment method that is applied for many wastewater types including painting process wastewater of automotive industry. This wastewater is well-known to have high heavy metals concentration which could deteriorate water environment if appropriate performance of the wastewater treatment could not be achieved. In this study, we monitored microbial community diversity in a Painting Biological Treatment (PBT) system. We applied a combination of cultivation and genotypic biological methods based on 16S rRNA gene sequence analysis to identify the diversity of active microbial community. The results showed that active microbes that could grow in this activated sludge system were dominated by Gram-negative bacteria. Based on 16S rRNA gene sequencing analysis, it was revealed that their microbial diversity has close association with Bacterium strain E286, Isosphaera pallida, Lycinibacillus fusiformis, Microbacterium sp., Orchobactrum sp., Pseudomonas guariconensis, Pseudomonas sp. strain MR84, Pseudomonas sp. MC 54, Serpens sp., Stenotrophomonas acidaminiphila, and Xylella fastidiosa with similarity of 86 – 99%. This findings reflects that microbial community in a Painting Biological Treatment (PBT) system using activated sludge process could adapt with xenobiotics in the wastewater and has a wide range of diversity indicating a complex metabolism mechanism in the treatment process.

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