A Microbial Signature Approach to Identify Fecal Pollution in the Waters Off an Urbanized Coast of Lake Michigan
Reads0
Chats0
TLDR
Bacterial community sequencing of the V6 and V6V4 hypervariable regions of the bacterial 16S rRNA gene is exploited to identify bacterial distributions that signal the presence of sewer, fecal, and human fecal pollution.Abstract:
Urban coasts receive watershed drainage from ecosystems that include highly developed lands with sewer and stormwater infrastructure. In these complex ecosystems, coastal waters are often contaminated with fecal pollution, where multiple delivery mechanisms that often contain multiple fecal sources make it difficult to mitigate the pollution. Here, we exploit bacterial community sequencing of the V6 and V6V4 hypervariable regions of the bacterial 16S rRNA gene to identify bacterial distributions that signal the presence of sewer, fecal, and human fecal pollution. The sequences classified to three sewer infrastructure-associated bacterial genera, Acinetobacter, Arcobacter, and Trichococcus, and five fecal-associated bacterial families, Bacteroidaceae, Porphyromonadaceae, Clostridiaceae, Lachnospiraceae, and Ruminococcaceae, served as signatures of sewer and fecal contamination, respectively. The human fecal signature was determined with the Bayesian source estimation program SourceTracker, which we applied to a set of 40 sewage influent samples collected in Milwaukee, WI, USA to identify operational taxonomic units (≥97 % identity) that were most likely of human fecal origin. During periods of dry weather, the magnitudes of all three signatures were relatively low in Milwaukee’s urban rivers and harbor and nearly zero in Lake Michigan. However, the relative contribution of the sewer and fecal signature frequently increased to >2 % of the measured surface water communities following sewer overflows. Also during combined sewer overflows, the ratio of the human fecal pollution signature to the fecal pollution signature in surface waters was generally close to that of sewage, but this ratio decreased dramatically during dry weather and rain events, suggesting that nonhuman fecal pollution was the dominant source during these weather-driven scenarios. The qPCR detection of two human fecal indicators, human Bacteroides and Lachno2, confirmed the urban fecal footprint in this ecosystem extends to at least 8 km offshore.read more
Citations
More filters
Journal ArticleDOI
Microplastic in Surface Waters of Urban Rivers: Concentration, Sources, and Associated Bacterial Assemblages
Amanda R. McCormick,Timothy J. Hoellein,Maxwell G. London,Joshua Hittie,John W. Scott,John J. Kelly +5 more
TL;DR: Effluent from WWTPs in rivers is an important component of the global plastic “life cycle,” and microplastic serves as a novel substrate that selects and transports distinct bacterial assemblages in urban rivers.
Journal ArticleDOI
Marine microplastic-associated biofilms - a review
TL;DR: First insights and research gaps related to microplastic-associated microbial biofilm communities are summarized and the question about the potential of plastic particles to serve as vectors for harmful microorganisms is raised.
Journal ArticleDOI
Application of Illumina next-generation sequencing to characterize the bacterial community of the Upper Mississippi River
Christopher Staley,Tatsuya Unno,Trevor J. Gould,B. D. W. Jarvis,Jane Phillips,James B. Cotner,Michael J. Sadowsky +6 more
TL;DR: A next‐generation, Illumina‐based sequencing approach was used to characterize the bacterial community at ten sites along the Upper Mississippi River to evaluate shifts in the community potentially resulting from upstream inputs and land use changes.
Journal ArticleDOI
Next-generation sequencing (NGS) for assessment of microbial water quality: current progress, challenges, and future opportunities
BoonFei Tan,Charmaine Ng,Jean Pierre Nshimyimana,Jean Pierre Nshimyimana,Lay Leng Loh,Lay Leng Loh,Karina Yew-Hoong Gin,Janelle R. Thompson,Janelle R. Thompson +8 more
TL;DR: In this paper, the suitability and biases inherent in the application of NGS as a screening tool for assessment of biological risks and discuss the potential and limitations for direct quantitative interpretation of the NGS data.
Journal ArticleDOI
Catchment-scale biogeography of riverine bacterioplankton
Daniel S. Read,Hyun S. Gweon,Michael J. Bowes,Lindsay K. Newbold,Dawn Field,Mark J. Bailey,Robert I. Griffiths +6 more
TL;DR: It is shown that bacterial communities across the Thames basin exhibit an ecological succession along the river continuum, and that this is primarily driven by water residence time rather than the physico-chemical status of the river.
References
More filters
Journal Article
R: A language and environment for statistical computing.
TL;DR: Copyright (©) 1999–2012 R Foundation for Statistical Computing; permission is granted to make and distribute verbatim copies of this manual provided the copyright notice and permission notice are preserved on all copies.
vegan: Community Ecology Package
Jari Oksanen,F. Guillaume Blanchet,Roeland Kindt,Pierre Legendre,Peter R. Minchin,Robert B. O'Hara,Gavin Simpson,Péter Sólymos,M. Henry H. Stevens,Helene H. Wagner +9 more
Journal ArticleDOI
UCHIME improves sensitivity and speed of chimera detection
TL;DR: UCHIME has better sensitivity than ChimeraSlayer (previously the most sensitive database method), especially with short, noisy sequences, and in testing on artificial bacterial communities with known composition, UCHIME de novo sensitivity is shown to be comparable to Perseus.
Journal ArticleDOI
Diversity of the human intestinal microbial flora.
Paul B. Eckburg,Elisabeth M. Bik,Charles N. Bernstein,Elizabeth Purdom,Les Dethlefsen,Michael Sargent,Steven R. Gill,Karen E. Nelson,David A. Relman,David A. Relman,David A. Relman +10 more
TL;DR: A majority of the bacterial sequences corresponded to uncultivated species and novel microorganisms, and significant intersubject variability and differences between stool and mucosa community composition were discovered.
Journal ArticleDOI
A core gut microbiome in obese and lean twins
Peter J. Turnbaugh,Micah Hamady,Tanya Yatsunenko,Brandi L. Cantarel,Alexis E. Duncan,Ruth E. Ley,Mitchell L. Sogin,William J. Jones,Bruce A. Roe,Jason P. Affourtit,Michael Egholm,Bernard Henrissat,Andrew C. Heath,Rob Knight,Jeffrey I. Gordon +14 more
TL;DR: The faecal microbial communities of adult female monozygotic and dizygotic twin pairs concordant for leanness or obesity, and their mothers are characterized to address how host genotype, environmental exposure and host adiposity influence the gut microbiome.
Related Papers (5)
QIIME allows analysis of high-throughput community sequencing data.
J. Gregory Caporaso,Justin Kuczynski,Jesse Stombaugh,Kyle Bittinger,Frederic D. Bushman,Elizabeth K. Costello,Noah Fierer,Antonio Gonzalez Peña,Julia K. Goodrich,Jeffrey I. Gordon,Gavin A. Huttley,Scott T. Kelley,Dan Knights,Jeremy E. Koenig,Ruth E. Ley,Catherine A. Lozupone,Daniel McDonald,Brian D. Muegge,Meg Pirrung,Jens Reeder,Joel Sevinsky,Peter J. Turnbaugh,William A. Walters,Jeremy Widmann,Tanya Yatsunenko,Jesse R. Zaneveld,Rob Knight,Rob Knight +27 more