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 is 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).
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 why 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 as suitable for the delineation of evolutionary relationships among organisms (Woese 1987) and therefore also for identification. Today 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).
Achtman, M., and M. Wagner. 2008. Microbial diversity and the genetic nature of microbial species. Nature Reviews Microbiology 6:431–440.
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. 10:257–263.
A classical conceptual paper describing the concept of the microbial loop.
Giovannoni, S. J., T. B. Britschgi, C. L. Moyer, et al. 1990. Genetic diversity in Sargasso Sea bacterioplankton. Nature 345:60–62.
One of the first papers 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 4:128–139.
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.
An early paper building on the work by Azam, et al., 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.
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 345:63–65.
Another early paper applying 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.
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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- Accounting for Ecological Capital
- Allocation of Reproductive Resources in Plants
- Animals, Functional Morphology of
- Animals, Reproductive Allocation in
- Animals, Thermoregulation in
- Antarctic Environments and Ecology
- Applied Ecology
- Aquatic Conservation
- Aquatic Nutrient Cycling
- Archaea, Ecology of
- Assembly Models
- Bacterial Diversity in Freshwater
- Benthic Ecology
- Biodiversity and Ecosystem Functioning
- Biodiversity Patterns in Agricultural Systms
- Biological Chaos and Complex Dynamics
- Biome, Alpine
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- Biome, Savanna
- Biome, Tundra
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- Bryophyte Ecology
- Butterfly Ecology
- Carson, Rachel
- Chemical Ecology
- Classification Analysis
- Coastal Dune Habitats
- Communities and Ecosystems, Indirect Effects in
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- Community Concept, The
- Community Ecology
- Community Genetics
- Community Phenology
- Competition and Coexistence in Animal Communities
- Competition in Plant Communities
- Complexity Theory
- Conservation Biology
- Conservation Genetics
- Coral Reefs
- Darwin, Charles
- De-Glaciation, Ecology of
- Disease Ecology
- Drought as a Disturbance in Forests
- Early Explorers, The
- Earth’s Climate, The
- Eco-Evolutionary Dynamics
- Ecological Dynamics in Fragmented Landscapes
- Ecological Informatics
- Ecology, Microbial (Community)
- Ecosystem Engineers
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- Elton, Charles
- Endophytes, Fungal
- Energy Flow
- Environments, Extreme
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- Fern and Lycophyte Ecology
- Fire Ecology
- Food Webs
- Foraging Behavior, Implications of
- Foraging, Optimal
- Forests, Temperate Coniferous
- Forests, Temperate Deciduous
- Freshwater Invertebrate Ecology
- Genetic Considerations in Plant Ecological Restoration
- Genomics, Ecological
- Geographic Range
- Gleason, Henry
- Greig-Smith, Peter
- Gymnosperm Ecology
- Habitat Selection
- Harper, John L.
- Heavy Metal Tolerance
- Himalaya, Ecology of the
- Host-Parasitoid Interactions
- Human Ecology
- Human Ecology of the Andes
- Hutchinson, G. Evelyn
- Insect Ecology, Terrestrial
- Introductory Sources
- Invasive Species
- Island Biogeography Theory
- Island Biology
- Kin Selection
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- Leopold, Aldo
- Lichen Ecology
- Life History
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- MacArthur, Robert H.
- Mangrove Zone Ecology
- Marine Fisheries Management
- Mathematical Ecology
- Mating Systems
- Maximum Sustainable Yield
- Metabolic Scaling Theory
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- Metapopulations and Spatial Population Processes
- Mutualisms and Symbioses
- Mycorrhizal Ecology
- Natural History Tradition, The
- Networks, Ecological
- Niche Versus Neutral Models of Community Organization
- Nutrient Foraging in Plants
- Ordination Analysis
- Organic Agriculture, Ecology of
- Parental Care, Evolution of
- Patch Dynamics
- Phenotypic Selection
- Philosophy, Ecological
- Phylogenetics and Comparative Methods
- Physiological Ecology of Nutrient Acquisition in Animals
- Physiological Ecology of Photosynthesis
- Physiological Ecology of Water Balance in Terrestrial Anim...
- Plant Disease Epidemiology
- Plant Ecological Responses to Extreme Climatic Events
- Polar Regions
- Pollination Ecology
- Population Dynamics, Density-Dependence and Single-Species
- Population Dynamics, Methods in
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- Predation and Community Organization
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- Religion and Ecology
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- Ricketts, Edward Flanders Robb
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- Shelford, Victor
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- Species Extinctions
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- Stoichiometry, Ecological
- Stream Ecology
- Systems Ecology
- Tansley, Sir Arthur
- Terrestrial Resource Limitation
- Thermal Ecology of Animals
- Tragedy of the Commons
- Trophic Levels
- Vegetation Classification
- Vegetation Mapping
- Weed Ecology
- Whittaker, Robert H.
- Wildlife Ecology