In This Article Expand or collapse the "in this article" section Bacterial Diversity in Freshwater

  • Introduction
  • Historical Overview
  • Methods
  • Archaea and Bacteria
  • Marine and Freshwater Bacterioplankton
  • Typical Freshwater Bacteria

Ecology Bacterial Diversity in Freshwater
Eva S. Lindström
  • LAST REVIEWED: 25 September 2023
  • LAST MODIFIED: 25 September 2023
  • DOI: 10.1093/obo/9780199830060-0180


The tree of life, describing the evolutionary relationships among organisms, is totally dominated by bacteria. In a regular ecology textbook, the number of bacterial and Archaeal examples are, however, few. Microorganisms are in many respects understudied, and we do not yet know if they follow similar “rules” as other organisms: for instance, regarding patterns in diversity over time and space. Further, bacteria play important roles in biogeochemical cycles, and, therefore, it is also important to understand if and how this enormous diversity is related to the role bacteria play in ecosystems. Despite methodological developments (see Historical Overview and Methods) that led to an exponential increase in the amount of data over time, we are still only scratching the surface of the diversity of freshwater bacteria (see Measuring Alpha Diversity), and few general patterns in diversity have emerged. Some typical freshwater bacterial groups have been identified (see Marine and Freshwater Bacterioplankton and Typical Freshwater Bacteria), and some important environmental steering factors are known (see Biogeography of Freshwater Bacteria). Further, a consistent pattern appears to be that alpha diversity decreases along lake and river chains because of inoculation of bacteria from species-rich soils (see Patterns in Alpha Diversity). Some findings of bacterial alpha diversity further indicate that bacterial diversity may not always follow the same rules as in larger organisms, challenging some established textbook “truths” regarding what is influencing diversity in general. But more data are needed for certain conclusions. Future work should also include the identification of the true (active) players and their possible importance for ecosystem functioning (see Identifying Contributors to Community Functioning).

Historical Overview

The role bacteria and other microorganisms play in ecosystems and in biogeochemical cycles has been thoroughly investigated. For instance, the concept of the microbial loop is well established in lakes, meaning that microorganisms in the pelagic zone (i.e., bacterioplankton) play important roles as links between dissolved organic matter and higher trophic levels (Azam, et al. 1983; Jansson, et al. 1996). This activity is, for example, contributing to the important role lakes play in the global carbon cycle through consumption and emission of carbon dioxide and thereby in the regulation of the global climate (Tranvik, et al. 2009). In these studies, however, microbial communities have mostly been followed using bulk measurements of activities and abundances, paying little attention to the role of diversity and the contribution of individual populations and taxa. In contrast, the general knowledge of microbial diversity as well as its steering factors and importance for ecosystems is less clear. In fact, the study of the diversity of bacteria and many other microorganisms is in a stage that in larger organisms occurred several hundred years ago when “new” continents and their flora and fauna were described. The reason diversity studies of bacteria are lagging behind is that suitable methods for identification of microorganisms in nature were developed relatively recently. Classic microbiology has long relied on cultivation of the organism for identification in laboratories. However, as early as the 1950s (Jannasch and Jones 1959) it was concluded that cultivation underestimates the number of bacterial cells in nature, and, thus, also the diversity of communities. In the early 1990s cultivation-independent molecular tools started to be applied for the identification of microorganisms directly in nature (Giovannoni, et al. 1990; Ward, et al. 1990). Most of the methods developed then (and the ones we use today) rely on the analysis of nucleotide sequences of the 16S rRNA gene (see Methods). This gene was identified by Carl Woese in Woese 1987 as suitable for the delineation of evolutionary relationships among organisms and therefore also for identification. Bacteria and Archaea are often grouped into so-called operational taxonomic units (OTUs), based on their similarity in 16S rRNA, since a proper species definition is lacking (Achtman and Wagner 2008). More recently, the term ASV (Amplicon Sequence Variants) is more commonly used, as in Callahan, et al. 2017.

  • Achtman, M., and M. Wagner. 2008. Microbial diversity and the genetic nature of microbial species. Nature Reviews Microbiology 6:431–440.

    DOI: 10.1038/nrmicro1872

    A review paper discussing the lack of a unifying species concept in Bacteria and Archaea and possible solutions to that problem.

  • Azam, F., T. Fenchel, J. G. Field, et al. 1983. The ecological role of water-column microbes in the sea. Marine Ecology Progress Series 10.3: 257–263.

    DOI: 10.3354/meps010257

    A classical conceptual paper describing the concept of the microbial loop.

  • Callahan, B. J., P. J. McMurdie, and S. P. Holmes. 2017. Exact sequence variants should replace operational taxonomic units in marker-gene data analysis. The ISME Journal 11.12: 2639–2643.

    DOI: 10.1038/ismej.2017.119

    A description of ASVs and OTUs and the difference between the two approaches.

  • Giovannoni, S. J., T. B. Britschgi, C. L. Moyer, et al. 1990. Genetic diversity in Sargasso Sea bacterioplankton. Nature 345.6270: 60–62.

    DOI: 10.1038/345060a0

    One of the first papers in applying 16S rRNA gene-based tools directly on bacterial cells collected from the ocean.

  • Jannasch, H. W., and G. E. Jones. 1959. Bacterial populations in sea water as determined by different methods of enumeration. Limnology and Oceanography 4.2: 128–139.

    DOI: 10.4319/lo.1959.4.2.0128

    An early paper describing the differences in bacterial numbers obtained by cultivation techniques compared to microscopy.

  • Jansson, M., P. Blomqvist, A. Jonsson, et al. 1996. Nutrient limitation of bacterioplankton, autotrophic and mixotrophic phytoplankton, and heterotrophic nanoflagellates in Lake Örträsket. Limnology and Oceanography 41.7: 1552–1559.

    DOI: 10.4319/lo.1996.41.7.1552

    An early paper building on Azam, et al. 1983 suggesting a reversal of the microbial loop due to the bacterial utilization of humic matter in ecosystems dominated by bacteria.

  • Tranvik, L. J., J. A. Downing, J. B. Cotner, et al. 2009. Lakes and reservoirs as regulators of carbon cycling and climate. Limnology and Oceanography 54.2: 2298–2314.

    DOI: 10.4319/lo.2009.54.6_part_2.2298

    This synthesis paper showed lake ecosystems playing a much greater role in the global carbon cycle than previously known.

  • Ward, D. M., R. Weller, and M. M. Bateson. 1990. 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature 345.6270: 63–65.

    DOI: 10.1038/345063a0

    Another early paper in which the authors apply 16S rRNA gene-based tools directly on microbial cells collected from nature—in this case, hot springs.

  • Woese, C. R. 1987. Bacterial evolution. Microbiological Reviews 51.2: 221–271.

    DOI: 10.1128/mr.51.2.221-271.1987

    A classic paper evaluating the usage of 16S rRNA genes for delineating evolutionary relationships among organisms as well as for taxonomic identification.

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