@article{he_so_de los reyes_2016, title={Shifts in microbial communities in bioaugmented grease interceptors removing fat, oil, and grease (FOG)}, volume={100}, ISSN={0175-7598 1432-0614}, url={http://dx.doi.org/10.1007/s00253-016-7398-7}, DOI={10.1007/s00253-016-7398-7}, abstractNote={To understand the effect of daily bioaugmentation in full-scale grease interceptors (GIs), we compared the microbial communities occurring in two full-scale GIs during bioaugmented and non-bioaugmented cycles. The changes in microbial communities were determined using terminal restriction fragment length polymorphism (T-RFLP) and 16S rRNA gene clone library construction. Differences in the microbial community structure between control and bioaugmented cycles were observed in all cases, although the dominant terminal restriction fragments in the biological product were not detected. The addition of bioaugmentation products and changes in the GI microbial ecology were related to differences in GI performance. Understanding the shifts due to bioaugmentation will result in more informed assessments of the benefits of bioadditives on FOG removal in GIs as well as the effects on downstream sewer lines.}, number={16}, journal={Applied Microbiology and Biotechnology}, publisher={Springer Science and Business Media LLC}, author={He, Xia and So, Mark Jason and de los Reyes, Francis L.}, year={2016}, month={Feb}, pages={7025–7035} }
 @article{mota_so_reyes_2012, title={Identification of Nitrite-Reducing Bacteria Using Sequential mRNA Fluorescence In Situ Hybridization and Fluorescence-Assisted Cell Sorting}, volume={64}, ISSN={["1432-184X"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84862493741&partnerID=MN8TOARS}, DOI={10.1007/s00248-012-0018-x}, abstractNote={Sequential mRNA fluorescence in situ hybridization (mRNA FISH) and fluorescence-assisted cell sorting (SmRFF) was used for the identification of nitrite-reducing bacteria in mixed microbial communities. An oligonucleotide probe labeled with horseradish peroxidase (HRP) was used to target mRNA of nirS, the gene that encodes nitrite reductase, the enzyme responsible for the dissimilatory reduction of nitrite to nitric oxide. Clones for nirS expression were constructed and used to provide proof of concept for the SmRFF method. In addition, cells from pure cultures of Pseudomonas stutzeri and denitrifying activated sludge were hybridized with the HRP probe, and tyramide signal amplification was performed, conferring a strongly fluorescent signal to cells containing nirS mRNA. Flow cytometry-assisted cell sorting was used to detect and physically separate two subgroups from a mixed microbial community: non-fluorescent cells and an enrichment of fluorescent, nitrite-reducing cells. Denaturing gradient gel electrophoresis (DGGE) and subsequent sequencing of 16S ribosomal RNA (rRNA) genes were used to compare the fragments amplified from the two sorted subgroups. Sequences from bands isolated from DGGE profiles suggested that the dominant, active nitrite reducers were closely related to Acidovorax BSB421. Furthermore, following mRNA FISH detection of nitrite-reducing bacteria, 16S rRNA FISH was used to detect ammonia-oxidizing and nitrite-oxidizing bacteria on the same activated sludge sample. We believe that the molecular approach described can be useful as a tool to help address the longstanding challenge of linking function to identity in natural and engineered habitats.}, number={1}, journal={MICROBIAL ECOLOGY}, publisher={Springer Science \mathplus Business Media}, author={Mota, Cesar R. and So, Mark Jason and Reyes, Francis L., III}, year={2012}, month={Jul}, pages={256–267} }