Community-based
microbial source tracking (MST) utilizes high-throughput
DNA sequencing to profile and compare the microbial communities in
different fecal sources and environmental samples. SourceTracker,
a program that compares a library of OTUs from fecal sources (i.e.,
sources) to those in environmental samples (i.e., sinks) in order
to determine sources of fecal contamination, is an emerging tool for
community-based MST studies. In this study, we investigated the ability
of SourceTracker to determine sources of known fecal contamination
in spiked, in situ mesocosms containing different
source contributors. We also evaluated how SourceTracker results were
impacted by accounting for autochthonous taxa present in the sink
environment. While SourceTracker was able to predict most sources
present in the in situ mesocosms, fecal source library
composition substantially influenced the program’s ability
to predict source contributions. Moreover, prediction results were
most reliable when the library contained only known sources, autochthonous
taxa were accounted for and when source profiles had low intragroup
variability. Although SourceTracker struggled to differentiate between
sources with similar bacterial community structures, it was able to
consistently identify abundant and expected sources, suggesting that
the SourceTracker program can be a useful tool for community-based
MST studies.
In methanogenic habitats, volatile fatty acids (VFA), such as propionate and butyrate, are major intermediates in organic matter degradation. VFA are further metabolized to H 2 , acetate and CO 2 by syntrophic fatty acid-degrading bacteria (SFAB) in association with methanogenic archaea. Despite their indispensable role in VFA degradation, little is known about SFAB abundance and their environmental distribution. To facilitate ecological studies, we developed four novel genus-specific quantitative PCR (qPCR) assays, with primer sets targeting known SFAB: Syntrophobacter, Smithella, Pelotomaculum and Syntrophomonas. Primer set specificity was confirmed using in silico and experimental (target controls, clone libraries and melt-curve analysis) approaches. These qPCR assays were applied to quantify SFAB in a variety of mesophilic methanogenic habitats, including a laboratory propionate enrichment culture, pilotand full-scale anaerobic reactors, cow rumen, horse faeces, an experimental rice paddy soil, a bog stream and swamp sediments. The highest SFAB 16S rRNA gene copy numbers were found in the propionate enrichment culture and anaerobic reactors, followed by the bog stream and swamp sediment samples. In addition, it was observed that SFAB and methanogen abundance varied with reactor configuration and substrate identity. To our knowledge, this research represents the first comprehensive study to quantify SFAB in methanogenic habitats using qPCR-based methods. These molecular tools will help investigators better understand syntrophic microbial communities in engineered and natural environments.
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