Using Stable Isotope Probing to Characterize Differences Between Free-Living and Sediment-Associated Microorganisms in the Subsurface

Abstract

Aquifers are subterranean reservoirs of freshwater with heterotrophic bacterial communities attached to the sediments and free-living in the groundwater. In the present study, mesocosms were used to assess factors controlling the diversity and activity of the subsurface bacterial community. The assimilation of ¹³C, derived from ¹³C-acetate, was monitored to determine whether the sediment-associated and free-living bacterial community would respond similarly to the presence of protozoan grazers. We observed a dynamic response in the sediment-associated bacterial community and none in the free-living community. The disparity in these observations highlights the importance of the sediment-associated bacterial community in the subsurface carbon cycle.

Keywords:

• microbial community structure
• stable-isotope probing
• subsurface microbiology
• top-down control

Acknowledgments

We thank Meagan Eagle Gonneea for help with installation of the groundwater well, Paul Henderson for obtaining the sediment, Ann Mulligan for discussions about the project and the research site, Mark Dennett for access to the flow cytometer, Ann Tarrant for access to Sequencher, Ben Van Mooy and Katie Barott for assistance with qPCR and T-RFLP analysis, Mar Nieto-Cid for help with the organic carbon measurements, Carl Johnson for guidance on sample preparation, and Marshall Otter at the Marine Biological Laboratory for the analysis of the carbon stable isotopes. We also thank the staff at the W. M. Keck Ecological and Evolutionary Genetics Facility at the Josephine Bay Paul Center at the Marine Biological Laboratory. We extend our special gratitude to the Waquoit Bay National Estuarine Research Reserve where this project was conducted. We appreciate the thoughtful and constructive comments of the reviewers. This research was supported by NSF grant EAR-0525166 to EBK.