Characterization of coastal urban watershed bacterial communities leads to alternative community-based indicators Page: 4 of 35
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With the advent of high throughput culture-independent characterization of microbial
communities, such as microarray and sequencing approaches [12,13,14,15,16], detailed
studies of bacterial community fluctuations due to physical, chemical and biological influences
are now feasible. One such phylogenetic microarray, the PhyloChip, targets much of the
known diversity within Bacteria and Archaea, and has been employed in a number of complex
environments and conditions [17,18,19,20,21,22,23,24,25]. The current version (G2) of the
PhyloChip provides the capability of identifying up to 8,741 Bacterial and Archaeal OTUs
simultaneously [17], and allows for relative quantification of individual OTUs over a wide
dynamic range [18,26]. The highly parallel and reproducible nature of this array allows
tracking community dynamics over time and treatment.
Bacterial communities in urban watersheds are sensitive to environmental perturbations and
could provide information on impacts of fecal influence and overall ecosystem health. It is
important to monitor the conditions of these watersheds because they are intricately tied in
with downstream waterways, which could have public health risk and economic implications.
Previous studies monitoring FIB most probable numbers (MPN) in urban creeks have found
high temporal variability even during dry weather [27,28,29]. In Santa Barbara, California,
exfiltration from sewer lines into the storm drain systems has been suspected to cause the
observed high densities of FIB and human-specific Bacteroides markers (HBM) in urban
watersheds that discharge into a recreational beach [29]. Here we analyze whole bacterial
communities from the same Sercu et al. [29] samples in order to gain insights regarding the
temporal and spatial dynamics of urban watershed bacterial community composition relevant
to fecal pollution. Amplified 16S rRNA gene sequences from creek (including storm drains),
lagoon and ocean sites in the Lower Mission Creek and Laguna watersheds in Santa Barbara,
CA, along with 3 samples of fecal origin, were hybridized onto the PhyloChip for a complete
microbial community analysis. Characterization of the whole bacterial community is crucial for4
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Wu, C. H.; Sercu, B.; Van De Werhorst, L. C.; Wong, J.; DeSantis, T. Z.; Brodie, E. L. et al. Characterization of coastal urban watershed bacterial communities leads to alternative community-based indicators, article, March 1, 2010; Berkeley, California. (https://digital.library.unt.edu/ark:/67531/metadc1014111/m1/4/: accessed April 23, 2024), University of North Texas Libraries, UNT Digital Library, https://digital.library.unt.edu; crediting UNT Libraries Government Documents Department.