Irrigation Effects on Soil Microbial Communities

Irrigation practices shape the composition, diversity and function of the soil microbiome, with consequences for nutrient cycling, crop health and ecosystem resilience. Variations in water source—ranging from freshwater and treated effluent to desalinated seawater—and in irrigation technique or intensity modulate soil moisture, salinity and chemical inputs. These drivers select for distinct bacterial and fungal assemblages, alter enzyme activities involved in carbon, nitrogen and phosphorus transformations and influence the prevalence of beneficial symbionts or plant pathogens. In arid and semi-arid regions a shift towards alternative water resources often enhances microbial biomass and stimulates community reorganisation, yet may also introduce salts or phytotoxic elements that impair sensitive host–microbe interactions. Water-saving technologies further shape rhizosphere processes by redistributing moisture and nutrients, reinforcing the importance of integrated management to sustain agricultural productivity under growing water scarcity.

Research from Nature Portfolio

Investigations in semi-arid drylands have characterised how conversion from shrubland to irrigated agriculture with freshwater, dam-stored water or untreated wastewater drives both total and active bacterial communities. Soil moisture, sodium concentration and pH emerge as primary determinants of taxonomic shifts, while predicted functional gene profiles for nitrogen, carbon and phosphorus cycling vary markedly among systems. Freshwater-irrigated soils display strong seasonal sensitivity in community composition, whereas wastewater-irrigated soils exhibit taxonomic shifts but maintain functional resistance to environmental fluctuations. A second study of aquaculture wastewater irrigation in arid soils reveals a pronounced decline in microbial functional diversity, chiefly attributed to increased soil salinity. Concurrently, taxonomic composition shifts towards Actinobacteria, Chloroflexi, Acidobacteria and Gemmatimonadetes, underscoring the need for targeted water and salinity management to preserve microbial processes in water-limited regions.

Irrigation Effects on Soil Microbial Communities publication trend

The graph below shows the total number of articles in irrigation effects on soil microbial communities across all publications each year (not limited to Nature Index journals).

Technical terms

Soil microbiome: The collective community of microorganisms, including bacteria, fungi and archaea, inhabiting the soil environment.

Rhizosphere: The narrow zone of soil influenced by root exudates and associated microbial interactions.

Amplicon sequencing: A method for profiling microbial taxa based on selectively amplifying and sequencing marker genes (e.g. 16S rRNA).

Microbial functional diversity: The range of metabolic capabilities and ecological functions performed by soil microorganisms.

References

1. Drylands soil bacterial community is affected by land use change and different irrigation practices in the Mezquital Valley, Mexico. Scientific Reports (2018).
2. Impacts of aquaculture wastewater irrigation on soil microbial functional diversity and community structure in arid regions. Scientific Reports (2017).
3. Balancing the scales: assessing the impact of irrigation and pathogen burden on potato blackleg disease and soil microbial communities. Microbiome (2024).
4. Agro-physiological and soil microbial responses to desalinated seawater irrigation in two crops. Ecotoxicology and Environmental Safety (2023).
5. Short-term effect of reclaimed wastewater quality gradient on soil microbiome during irrigation. The Science of The Total Environment (2023).