Strategies to Map the Microbiome of Freshwater Lakes: Sampling and Context

  • Stefan BertilssonEmail author
Part of the Springer Protocols Handbooks book series (SPH)


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.


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.


  1. 1.
    Lindeman RL (1941) Food cycle dynamics in a senescent lake. Am Midl Nat 26:636–673CrossRefGoogle Scholar
  2. 2.
    Williamson CE, Saros JE, Vincent WF, Smol JP (2009) Lakes and reservoirs as sentinels, integrators, and regulators of climate change. Limnol Oceanogr 54:2273–2282CrossRefGoogle Scholar
  3. 3.
    Newton RJ, Jones SE, Eiler A, McMahon KD, Bertilsson S (2011) A guide to the natural history of freshwater lake bacteria. Microbiol Mol Biol Rev 75:14–49CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Kalff J (2002) Limnology: inland water ecosystems. Prentice Hall, New Jersey, p 592Google Scholar
  5. 5.
    Wetzel RG (2001) Limnology - lake and river ecosystems, 3rd edn. Elsevier Academic Press, San DiegoGoogle Scholar
  6. 6.
    Madrid Y, Zayas ZP (2007) Water sampling: traditional methods and new approaches in water sampling strategy. Trends Anal Chem 26:293–299CrossRefGoogle Scholar
  7. 7.
    Prosser J (2010) Replicate or lie. Environ Microbiol 12:1806–1810CrossRefPubMedGoogle Scholar
  8. 8.
    ISO 5667-4 (1987) Water quality - sampling - guidance on sampling from lakes, natural and manmade. International Organization for StandardizationGoogle Scholar
  9. 9.
    Lindström ES, Forslund M, Algesten G, Bergström A-K (2006) External control of bacterial community structure in lakes. Limnol Oceanogr 51:339–342CrossRefGoogle Scholar
  10. 10.
    Cole JJ, Pace ML, Caraco NF, Steinhart GS (1993) Bacterial biomass and cell size distribution in lakes: more and larger cells in anoxic waters. Limnol Oceanogr 38:1627–1632CrossRefGoogle Scholar
  11. 11.
    Shade A, Jones SJ, McMahon KD (2008) The influence of habitat heterogeneity on freshwater bacterial community composition and dynamics. Environ Microbiol 10:1057–1067CrossRefPubMedGoogle Scholar
  12. 12.
    Stevenson LH, Wyman B (1991) Hypoxia. In: Dictionary of environmental science. Facts on File, Inc., New York, p 125Google Scholar
  13. 13.
    Peura S, Eiler A, Bertilsson S, Nykänen H, Tiirola M, Jones RI (2012) Distinct and diverse anaerobic bacterial communities in boreal lakes dominated by candidate division OD1. ISME J 6:1640–1652CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Evans D (1994) Empirical evidence of the importance of sediment resuspension in lakes. Hydrobiologia 284:5–12CrossRefGoogle Scholar
  15. 15.
    Simon M, Grossart HP, Schweitzer B, Ploug H (2002) Microbial ecology of organic aggregates in aquatic ecosystems. Aquat Microb Ecol 28:175–2011CrossRefGoogle Scholar
  16. 16.
    von Wachenfeld E, Tranvik LJ (2008) Sedimentation in boreal lakes-the role of flocculation of allochthonous dissolved organic matter in the water column. Ecosystems 11:803–814CrossRefGoogle Scholar
  17. 17.
    Allgaier M, Grossart HP (2006) Seasonal dynamics and phylogenetic diversity of free-living and particle-associated bacterial communities in four lakes in northeastern Germany. Aquat Microb Ecol 45:115–128CrossRefGoogle Scholar
  18. 18.
    Carrias JF, Serre JP, Sime-Ngando T, Amblard C (2002) Distribution, size, and bacterial colonization of pico- and nano-detrital organic particles (DOP) in two lakes of different trophic status. Limnol Oceanogr 47:1202–1209CrossRefGoogle Scholar
  19. 19.
    Sprules WG (1983) Size distribution of pelagic particles in lakes. Can J Fish Aquat Sci 40:1761–1769CrossRefGoogle Scholar
  20. 20.
    Cunliffe M, Upstil-Goddard RC, Murrell JC (2011) Microbiology of aquatic surface microlayers. FEMS Microbiol Rev 35:233–246CrossRefPubMedGoogle Scholar
  21. 21.
    Hervas A, Casamayor EO (2009) High similarity between bacterioneuston and airborne bacterial community composition in a high mountain lake area. FEMS Microbiol Ecol 67:219–228CrossRefPubMedGoogle Scholar
  22. 22.
    Schilling K, Zessner M (2011) Foam in the aquatic environment. Water Res 45:4355–4366CrossRefPubMedGoogle Scholar
  23. 23.
    Salonen K, Leppäranta M, Viljanen M, Gulati RD (2009) Perspectives in winter limnology: closing the annual cycle of freezing lakes. Aquat Ecol 43:609–616CrossRefGoogle Scholar
  24. 24.
    Bertilsson S, Burgin A, Carey CC, Fey SB, Grossart HP, Grubisic LM, Jones ID, Kirillin G, Lennon JT, Shade A, Smith RL (2013) The under-ice microbiome of seasonally frozen lakes. Limnol Oceanogr 58:1998–2012CrossRefGoogle Scholar
  25. 25.
    Eiler A, Heinrich F, Bertilsson S (2012) Coherent dynamics and association networks among lake bacterioplankton taxa. ISME J 6:330–342CrossRefPubMedGoogle Scholar
  26. 26.
    Shade AL, Kent AD, Jones SE, Newton RJ, Triplett EW, McMahon KD (2007) Inter-annual dynamics and phenology of bacterial communities in a eutrophic lake. Limnol Oceanogr 52:487–494CrossRefGoogle Scholar
  27. 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
  28. 28.
    Bertilsson S, Jones JB Jr (2003) Supply of dissolved organic matter to aquatic ecosystems: autochthonous sources. In: Findlay SEG, Sinsabaugh RL (eds) Aquatic ecosystems: interactivity of dissolved organic matter. Academic, New York, pp 3–24CrossRefGoogle Scholar
  29. 29.
    Schwarzenbach RP, Gschwend PM, Imboden DM (2003) Environmental organic geochemistry. Wiley, HobokenGoogle Scholar
  30. 30.
    Schmidt TC, Haderlein SB, Pfister R, Forster R (2004) Occurrence and fate modeling of MTBE and BTEX compounds in a Swiss lake used as drinking water supply. Water Res 38:1520–1529CrossRefPubMedGoogle Scholar
  31. 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
  32. 32.
    Phelps CD, Young LY (1999) Anaerobic biodegradation of BTEX and gasoline in various aquatic sediments. Biodegradation 10:15–25CrossRefPubMedGoogle Scholar
  33. 33.
    Kannan K, Johnson-Restrepo B, Yohn SS, Giesy JP, Long DT (2005) Spatial and temporal distribution of polycyclic aromatic hydrocarbons in sediments from Michigan inland lakes. Environ Sci Technol 39:4700–4706CrossRefPubMedGoogle Scholar
  34. 34.
    Jones SE, Chiu CY, Kratz TK, Wu JT, Shade A, McMahon KD (2008) Typhoons initiate predictable change in aquatic bacterial communities. Limnol Oceanogr 53:1319–1326CrossRefGoogle Scholar
  35. 35.
    Shade A, Read JS, Welkie DG, Kratz TK, Wu CH, McMahon KD (2011) Resistance, resilience and recovery: aquatic bacterial dynamics after water column disturbance. Environ Microbiol 13:2752–2767CrossRefPubMedGoogle Scholar
  36. 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
  37. 37.
    Shade A, Carey C, Kara E, Bertilsson S, McMahon KD, Smith M (2009) Can the black box be cracked? The augmentation of microbial ecology by high-resolution, automated sensing technologies. ISME J 3:881–888CrossRefPubMedGoogle Scholar
  38. 38.
    Kara EL, Hanson P, Hamilton D et al (2012) Time-scale dependence in numerical simulations: assessment of physical, chemical and biological predictions in a stratified lake at temporal scales of hours to months. Environ Model Software 35:104–121CrossRefGoogle Scholar
  39. 39.
    Schindler DW (1969) Two useful devices for vertical plankton and water sampling. J Fish Res Board Can 26:1948–1955CrossRefGoogle Scholar
  40. 40.
    Blakar IA (1979) A close interval water sampler with minimal disturbance properties. Limnol Oceanogr 24:983–988CrossRefGoogle Scholar
  41. 41.
    Tranvik LJ, Tranvik PH (1993) A simple water sampler, and a chamber for in situ incubation of plankton samples at discrete depths. Freshw Biol 30:235–238CrossRefGoogle Scholar
  42. 42.
    Field D, Garrity G, Gray T et al (2008) The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 26:541–547CrossRefPubMedPubMedCentralGoogle Scholar
  43. 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. 44.
    Mudroch A, McKnight SD (eds) (1994) Handbook of techniques for aquatic sediments, 2nd edn. CRC Press/Lewis Publishers, Boca RatonGoogle Scholar
  45. 45.
    Agogué H, Casamayor EO, Joux F et al (2004) Comparison of samplers for the biological characterization of the sea surface microlayer. Limnol Oceanogr Meth 2:213–225CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  1. 1.Department of Ecology & GeneticsLimnology and Science for Life Laboratory, Uppsala UniversityUppsalaSweden

Personalised recommendations