The ecology and biogeochemistry of stream biofilms

Key Points

  • Biofilms dominate microbial life in stream ecosystems. These matrix-enclosed and surface-attached microbial communities are ubiquitous, prolific and highly active at the interfaces of the streambed. The biofilm mode of life is advantageous in streams with a fast flow of water and continuous export of nutrients and organic matter.

  • Biofilms in streams can be considered a 'microbial skin', regulating the processing and export of nutrients and organic matter from catchments and influencing the dispersal of microorganisms and their biodiversity dynamics at the scale of entire stream networks.

  • Interactions between the growth of biofilms, streamwater flow and substratum chemistry produce emergent environmental complexity in the streambed.

  • Proteobacteria and Bacteroidetes often dominate the communities of stream biofilms. Flavobacteriia and Sphingobacteriia seem to be especially important members of these communities. Archaea are found within niche microenvironments established by the metabolic activity of other microorganisms.

  • High biodiversity in stream biofilms is supported by continuous input of microorganisms from upstream catchments, environmental sorting induced by habitat heterogeneity (ranging from the scale of the biofilm to large stream networks) and episodic disturbance from streamwater flow.

  • New interdisciplinary approaches are needed to link structure and function of biofilms to their environment and, ultimately, to ecosystem processes and biogeochemical fluxes in streams. This is crucial to understand and predict implications of global ecosystem change and climate change on the microbial ecology and functioning of stream ecosystems.


Streams and rivers form dense networks, shape the Earth's surface and, in their sediments, provide an immensely large surface area for microbial growth. Biofilms dominate microbial life in streams and rivers, drive crucial ecosystem processes and contribute substantially to global biogeochemical fluxes. In turn, water flow and related deliveries of nutrients and organic matter to biofilms constitute major constraints on microbial life. In this Review, we describe the ecology and biogeochemistry of stream biofilms and highlight the influence of physical and ecological processes on their structure and function. Recent advances in the study of biofilm ecology may pave the way towards a mechanistic understanding of the effects of climate and environmental change on stream biofilms and the biogeochemistry of stream ecosystems.

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Figure 1: Biodiversity of a benthic biofilm across all three domains of life.
Figure 2: Major bacterial classes in stream biofilms.
Figure 3: Physical structure and 'building blocks' of stream biofilms.
Figure 4: Controls on the complexity of stream biofilms.


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The authors thank A. Ulseth and M. Bogard for critically reading an earlier version of the manuscript. Financial support came from the Austrian Science Foundation (P23420-B17, START Y420-B17) and the Swiss Science Foundation (205321_159958 / 1) to T.J.B., from the Austrian Science Foundation (J3542-B22) to K.B. and from the Spanish Ministry of Economy and Competitiveness (FLUMED-HOTSPOT) to A.R.

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Correspondence to Tom J. Battin.

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Traditionally considered to be a phototrophic biofilm that coats benthic substrates in stream ecosystems.


Traditionally considered to be a biofilm that grows on stones in stream ecosystems.


Invertebrates living in aquatic ecosystems that have a body size typically not exceeding one millimetre.

Ecosystem respiration

The respiration by both heterotrophic and autotrophic organisms within an ecosystem, in which heterotrophic respiration generates carbon dioxide from the breakdown of organic compounds.

Primary production

The generation of organic carbon from carbon dioxide by photosynthesis, which uses light as an energy source.


Drainage basin of streams or rivers delineated by the watershed and within which water from rain, snow or ice melt converges at the valley bottom to contribute to streamwater flow.

Hyporheic zone

The zone in the streambed sediment in which streamwater interacts with groundwater, as driven by hydrodynamic exchange. Typically considered to be a habitat with high rates of biodiversity and biogeochemical reaction.

Reflective characteristics

The ability of an interface, or ecological boundary, to partially or entirely return matter, energy or organisms.


The microbial communities colonizing the above-ground surfaces that are provided by terrestrial plants.

Benthic zone

The upper zone of the streambed; the benthic zone is notable for its direct interface with streamwater flow and its exposure to light.

Humic substances

A complex and heterogeneous mixture of polydispersed materials formed by biochemical and chemical reactions during the decay of plant tissue. This mixture is a major contributor to dissolved organic matter in aquatic ecosystems.

Co-occurrence networks

Graphical visualization of potential relationships, between species or other entities, that have been derived from correlation analyses.

Operational taxonomic units

(OTUs). Classification of microorganisms on the basis of an operational definition for species distinction that applies a percentage similarity threshold to 16S rRNA sequences.

Flow fields

Flow patterns that are generated by a moving liquid over and around solids.


Geomorphological features that develop at the interface of fluid and a movable bed, such as dunes and ripples on the beds of streams and rivers. Bedforms affect near-bottom hydraulics and hydrodynamic exchange with porewater in the streambed.


The compositional similarity of ecological communities and the species turnover therein.

Neutral models

In the context of biodiversity, models that assume that individuals of all ecologically similar species are competitively equal and that the stochasticity of demographic processes, such as immigration, birth and death, drive local community assembly.


Local species diversity in a habitat or ecosystem, often referred to as species richness or Shannon or Simpson diversity.

Competitive exclusion

Ecological process whereby two (or more) species that use the same resources cannot stably coexist.


The smallest streams in a fluvial network and where streamflow is generated.

Laminar flow

The flow of water in parallel layers that are not disrupted. Laminar flow often fosters copious biofilm growth, as turbulence-induced erosion of microbial biomass is low.

Drag force

A force that acts on any solid objects exposed to water flow; the drag comes from forces caused by pressure distributions over the surface of the object.

Hydrodynamic exchange

The exchange of water masses driven by the pressure differences that occur over rough streambeds.

Priming effect

Phenomenon in which labile dissolved organic matter (DOM) compounds facilitate the breakdown of apparently recalcitrant DOM compounds by microbial heterotrophs. The mechanism is unclear but may involve the provision of energy for the expression of extracellular enzymes that degrade recalcitrant DOM.

Recalcitrant DOM

Dissolved organic matter (DOM) that is resistant to degradation by microbial heterotrophs.

Functional plasticity

The capacity of an ecological community to accommodate environmental changes by adjusting the overall performance of dominant phylotypes.

Functional redundancy

A concept that relates changes in ecosystems to species loss, in which species that perform similar roles in communities can substitute for one another with little effect on the functioning of the community and ecosystem.

Functional gene arrays

DNA array technology for assessing functional gene diversity and distribution in microbial communities.


Method that visualizes and quantifies the uptake of a radioactively labelled compound at the level of single cells.


The process in which increased nutrient inputs drive an increase in algal biomass in aquatic systems, which in turn causes anoxia as a result of the breakdown of these algae by microbial heterotrophs.

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Battin, T., Besemer, K., Bengtsson, M. et al. The ecology and biogeochemistry of stream biofilms. Nat Rev Microbiol 14, 251–263 (2016).

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