Microbial Community Dynamics in Intermittent Water Systems

Intermittent water systems—rivers, streams and channels that alternate between flowing and dry phases—are widespread across arid, temperate and alpine regions. During dry intervals, sediments and hyporheic zones retain pockets of moisture, supporting specialised microbial assemblages. When flow resumes, rapid community shifts occur, driven by rewetting pulses that reshape biogeochemical activity. Key drivers include hydrological regime (duration and intensity of drying), substrate quality (organic matter availability and recalcitrance), temperature fluctuations and nutrient concentrations. Interactions among bacteria, archaea and fungi regulate carbon and nitrogen cycling, underpinning ecosystem functions such as organic‐matter decomposition, nitrification, denitrification and greenhouse-gas emissions. Oligotrophic taxa typically thrive under prolonged dryness, whereas copiotrophic and denitrifying groups bloom upon rewetting. Biotic interactions—competition, facilitation and successional turnover—often exert stronger control on community assembly than dispersal alone. Understanding these dynamics has global significance for water-resource management, mitigating emissions of CO₂ and N₂O, enhancing nutrient retention and informing restoration strategies in catchments exposed to climate change and human water extraction.

Research from Nature Portfolio

Large-scale environmental DNA metabarcoding across non-perennial rivers reveals that both direct factors (nutrient and carbon availability) and indirect climate variables shape microbial biodiversity during dry phases. Co-variation among bacteria, fungi, algae and protozoa explains more spatial variation in community composition than hydrological gradients, suggesting a prominent role for biotic interactions and unmeasured ecological filters. Experimental manipulation of extended drought and episodic rewetting demonstrates that archaea show greater phylogenetic shifts under severe hydrological disturbance than bacteria or fungi. Recovery following water return induces larger community realignments in surface sediments than those observed during drying, highlighting the importance of microhabitat moisture retention in modulating resilience.

Microbial Community Dynamics in Intermittent Water Systems publication trend

The graph below shows the total number of articles in microbial community dynamics in intermittent water systems across all publications each year (not limited to Nature Index journals).

Technical terms

Environmental DNA (eDNA) metabarcoding: Molecular technique for assessing biodiversity by sequencing DNA fragments from environmental samples.

Hyporheic zone: Subsurface region beneath and alongside a stream bed where surface water and groundwater mix, housing active microbial biofilms.

Oligotrophic taxa: Organisms adapted to low-nutrient environments, often dominating during prolonged dryness.

Denitrification: Microbial reduction of nitrate to gaseous forms (N₂, N₂O), influencing nitrogen fluxes and greenhouse-gas emissions.

Extracellular enzymatic activity: Release of enzymes by microbes to degrade complex substrates (e.g., polysaccharides, proteins) into utilizable molecules.

Microbial respiration: Conversion of organic substrates to CO₂ by microorganisms, serving as a proxy for overall metabolic activity.

References

1. Unravelling large-scale patterns and drivers of biodiversity in dry rivers. Nature Communications (2024).
2. Distinct responses from bacterial, archaeal and fungal streambed communities to severe hydrological disturbances. Scientific Reports (2019).
3. Hidden Decomposers: the Role of Bacteria and Fungi in Recently Intermittent Alpine Streams Heterotrophic Pathways. Microbial Ecology (2023).
4. Role of dry watercourses of an arid watershed in carbon and nitrogen processing along an agricultural impact gradient. Journal of Environmental Management (2023).
5. Small rain events during drought alter sediment dissolved organic carbon leaching and respiration in intermittent stream sediments. Biogeochemistry (2022).