Strategies to Map the Microbiome of Freshwater Lakes: Sampling and Context
Freshwater lakes are indispensible resources for humankind and as such also exposed to significant pressure from anthropogenic activities and environmental change. Organic matter holds a central role in these ecosystems, both in providing energy for the food web and in modifying water quality. The transformation, degradation, and internal production of organic matter is largely mediated by microorganisms and there is hence great interest in learning more about the ecology and function of these microscopic but abundant key players in lake ecosystems. The focus of this chapter is thus on strategies to study the spatial and temporal organization of the freshwater lake microbiome, with special attention to representative and rational sampling of freshwater lakes for subsequent analyses of microbial process or community features. Within-system heterogeneity across spatial and temporal scales will be presented and linkages between the physical structure, chemical gradients, and microbial distribution patterns will be discussed. Useful practical considerations to sample water for experiments or cells for biomolecular analyses will be presented along with recommendations regarding how to collect and compile basic but critically important contextual information. It is evident that the long-standing myth of freshwater lakes as homogenous systems delimited by defined shoreline boundaries is incorrect and that heterogeneity should be considered already in designing sampling strategies.
Keywords:Community composition Freshwater lakes Metabolism Microorganisms Particles Sampling Sediments Stratification
I thank Andrea Garcia-Bravo for valuable comments on an early draft of the manuscript. I owe countless colleagues gratitude for training and inspiration in limnological field work, but I particularly want to mention the late Peter Blomqvist, Anders Broberg, Wilhelm Granéli, Jan Johansson, Lars Tranvik, Lena Lundman, Trina McMahon, and her UW-Madison team for great ideas on how to sample lakes.
- 4.Kalff J (2002) Limnology: inland water ecosystems. Prentice Hall, New Jersey, p 592Google Scholar
- 5.Wetzel RG (2001) Limnology - lake and river ecosystems, 3rd edn. Elsevier Academic Press, San DiegoGoogle Scholar
- 8.ISO 5667-4 (1987) Water quality - sampling - guidance on sampling from lakes, natural and manmade. International Organization for StandardizationGoogle Scholar
- 12.Stevenson LH, Wyman B (1991) Hypoxia. In: Dictionary of environmental science. Facts on File, Inc., New York, p 125Google Scholar
- 27.Aitkenhead-Peterson JA, McDowell WH, Neff JC (2003) Production and regulation of allochthonous dissolved organic matter inputs to surface waters. In: Findlay SEG, Sinsabaugh RL (eds) Aquatic ecosystems: interactivity of dissolved organic matter. Academic, New York, pp 26–70Google Scholar
- 29.Schwarzenbach RP, Gschwend PM, Imboden DM (2003) Environmental organic geochemistry. Wiley, HobokenGoogle Scholar
- 31.Cornelissen G, Gusafsson Ö, Bucheli TD, JOnker MTO, Koelmans AA, van Noort PCM (2005) Extensive sorption of organic compounds to black carbon, coal and kerogen in sediments and soils: mechanisms and consequences for distribution, bioaccumulation and biodegradation. Environ Sci Technol 39:6881–6895CrossRefPubMedGoogle Scholar
- 36.Bertilsson S (2008) The environmental context for metagenomic data. In: Moran MA, Amann R (eds) EC-US Workshop report on Cyberinfrastructure resources for genome-enabled research on microbial life and the marine environment. Arlington, VA, USA, Sept 2007Google Scholar
- 43.Palmer FE, Methot RD Jr, Staley JT (1978) Patchiness in the distribution of planktonic heterotrophic bacteria in lakes. Appl Environ Microbiol 31:1003–1005Google Scholar
- 44.Mudroch A, McKnight SD (eds) (1994) Handbook of techniques for aquatic sediments, 2nd edn. CRC Press/Lewis Publishers, Boca RatonGoogle Scholar