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Updated: Feb 2, 2026

Exploring the Root Microbiome: Extracting Bacterial Community Data from the Soil, Rhizosphere, and Root Endosphere
Published on: May 2, 2018
Root microbiome response to treated wastewater irrigation
Avihai Zolti1, Stefan J Green2, Evyatar Ben Mordechay3
1Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization - Volcani Center, Rishon Lezion 7528809, Israel; Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel.
Irrigating crops with treated wastewater (TWW) alters soil properties and plant growth. TWW significantly impacts soil microbial communities in both soil and root environments, affecting plant-soil interactions.
Area of Science:
- Environmental Science
- Microbiology
- Agronomy
Background:
- Freshwater (FW) scarcity is increasing globally, leading to wider use of treated wastewater (TWW) for crop irrigation.
- While TWW offers a water alternative, potential long-term impacts on soil health, plant performance, and the rhizosphere microbiome require thorough investigation.
Purpose of the Study:
- To evaluate the effects of irrigation water quality (FW vs. TWW) on soil and root microbial community structure.
- To assess the impact of TWW irrigation on edaphic properties, plant performance, and the rhizosphere microbiome in different soil types and plant species.
Main Methods:
- Comparison of soil and root microbiomes (total and active communities) of tomato and lettuce grown in two soils, irrigated with either FW or TWW.
- Analysis of soil physicochemical properties (pH, EC, K, Na, DOC) and plant biomass (fruit and shoot weight).
- Calculation of effect sizes for plant species, soil type, and irrigation water quality on microbial community structure.
Main Results:
- TWW irrigation significantly increased soil pH, EC, K, Na, and DOC compared to FW irrigation.
- TWW irrigation led to decreased plant fruit and shoot weight.
- Both plant species and irrigation water quality were dominant factors shaping root-associated microbial communities, while soil type and irrigation water quality shaped soil microbial communities.
Conclusions:
- Irrigation water quality is a major determinant of root-associated microbiome structure.
- TWW irrigation significantly alters soil properties and microbial communities, impacting the plant-soil interface.
- Understanding these microbial shifts is crucial for sustainable agriculture with TWW irrigation.
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