title: Insights into the fate of a 13C labelled phenol pulse for stable isotope probing (SIP) experiments.
abstract: Stable isotope probing (SIP) using DNA or RNA as a biomarker has proven to be a useful method for attributing substrate utilisation to specific microbial taxa. In this study we followed the transfer of a (13)C(6)-phenol pulse in an activated sludge micro-reactor to examine the resulting distribution of labelled carbon in the context of SIP. Most of the added phenol was metabolically converted within the first 100 min after (13)C(6)-phenol addition, with 49% incorporated into microbial biomass and 6% respired as CO(2). Less than 1% of the total (13)C labelled carbon supplied was incorporated into microbial RNA and DNA, with RNA labelling 6.5 times faster than DNA. The remainder of the added (13)C was adsorbed and/or complexed to suspended solids within the sludge. The (13)C content of nucleic acids increased beyond the initial consumption of the (13)C-phenol pulse. This study confirms that RNA labels more efficiently than DNA and reveals that only a small proportion of a pulse is incorporated into nucleic acids. Evidence of continued (13)C incorporation into nucleic acids suggests that cross-feeding of the SIP substrate was rapid. This highlights both the benefits of using a biomarker that is rapidly labelled and the importance of sampling within appropriate timescales to avoid or capture the effects of cross-feeding, depending on the goal of the study.
authors.affiliation: Centre for Marine Biofouling and Bioinnovation, University of New South Wales, Sydney, 2052, Australia. manefield@unsw.edu.au
authors.forename: Mike
authors.initials: M
authors.lastname: Manefield
authors.forename: Rob
authors.initials: R
authors.lastname: Griffiths
authors.forename: Niall P
authors.initials: NP
authors.lastname: McNamara
authors.forename: Darren
authors.initials: D
authors.lastname: Sleep
authors.forename: Nick
authors.initials: N
authors.lastname: Ostle
authors.forename: Andrew
authors.initials: A
authors.lastname: Whiteley
mesh_terms: D018533:Biomass; D019149:Bioreactors; D002245:Carbon Dioxide / Q000378:metabolism; D002247:Carbon Isotopes / Q000378:metabolism*; D004269:DNA, Bacterial / Q000378:metabolism; D007553:Isotope Labeling / Q000379:methods*; D013058:Mass Spectrometry; D019800:Phenol / Q000378:metabolism*; D012329:RNA, Bacterial / Q000378:metabolism; D012722:Sewage / Q000382:microbiology*
chemical_list: D002247:Carbon Isotopes; D004269:DNA, Bacterial; D012329:RNA, Bacterial; D012722:Sewage; D002245:Carbon Dioxide; D019800:Phenol