Title of Oral/Poster Presentation

DNA STABLE ISOTOPE PROBING METHODS TO EXAMINE CARBON ASSIMILATION IN STREAM BIOFILMS

Class

Article

Graduation Year

2018

College

College of Science

Department

Biology Department

Faculty Mentor

Michelle Baker

Presentation Type

Poster Presentation

Abstract

DNA stable isotope probing (DNA-SIP) identifies microbial populations that assimilate a substrate of interest by tracking the movement of an isotopic label from a substrate into DNA. Although the technique has not been widely used in streams, DNA-SIP can be used to identify populations in stream biofilms that use different sources of carbon. We performed a DNA-SIP experiment to identify populations that assimilate mannitol and algal carbon. Stream biofilms grown on glass discs were incubated in a growth chamber in river water amended with 13C-mannitol or 13C-bicarbonate for 3 and 10 days. Biofilm DNA was extracted and separated by density using ultracentrifugation. To identify populations that assimilated our two carbon sources, we collected the heavier, isotopically-labeled DNA and sequenced the 16S rRNA gene. Sequences were analyzed using MOTHUR, operational taxonomic units identified using Megablast, and phylogenetic identities aligned against the Greengenes database. In addition to carbon assimilation, future studies can use DNA-SIP to identify populations contributing to nitrogen cycling and other stream biogeochemical processes, enhancing understanding of the link between microbial identity and ecosystem function.

Location

North Atrium

Start Date

4-13-2017 10:30 AM

End Date

4-13-2017 11:45 AM

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Apr 13th, 10:30 AM Apr 13th, 11:45 AM

DNA STABLE ISOTOPE PROBING METHODS TO EXAMINE CARBON ASSIMILATION IN STREAM BIOFILMS

North Atrium

DNA stable isotope probing (DNA-SIP) identifies microbial populations that assimilate a substrate of interest by tracking the movement of an isotopic label from a substrate into DNA. Although the technique has not been widely used in streams, DNA-SIP can be used to identify populations in stream biofilms that use different sources of carbon. We performed a DNA-SIP experiment to identify populations that assimilate mannitol and algal carbon. Stream biofilms grown on glass discs were incubated in a growth chamber in river water amended with 13C-mannitol or 13C-bicarbonate for 3 and 10 days. Biofilm DNA was extracted and separated by density using ultracentrifugation. To identify populations that assimilated our two carbon sources, we collected the heavier, isotopically-labeled DNA and sequenced the 16S rRNA gene. Sequences were analyzed using MOTHUR, operational taxonomic units identified using Megablast, and phylogenetic identities aligned against the Greengenes database. In addition to carbon assimilation, future studies can use DNA-SIP to identify populations contributing to nitrogen cycling and other stream biogeochemical processes, enhancing understanding of the link between microbial identity and ecosystem function.