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Saline groundwater irrigation is commonly used in arid regions of the Middle East and North Africa for date palm (Phoenix dactylifera) cultivation, yet little is known about its impact on communities of root-associated fungi (RAF). We investigated the impact of irrigation water sources (freshwater versus saline groundwater) on date palm RAF diversity, communities, and their assembly processes. RAF richness was lower in roots under saline groundwater irrigation and was significantly related to soil and water electrical conductivity (EC), and only 25.3% of the total operational taxonomic units (OTUs) were strictly found in roots under saline groundwater irrigation. Overall, the RAF communities were distinct among irrigation water sources, wherein water pH and EC were the major structuring factors. The relative importance of drift assembly was higher for RAF distribution under saline groundwater irrigation. Saprotrophic and pathotrophic communities were also distinct between irrigation water sources and shaped by irrigation water pH. In addition, we found higher abundance of saprotrophic OTUs Acrocalymma vagum, Coprinopsis sp., and Myrothecium sp. in roots under saline groundwater irrigation. In summary, we show that saline groundwater irrigation lowers RAF richness and alters overall and guild level RAF communities (saprotroph and pathotroph), which assemble mainly through drift process, wherein overall communities are shaped by irrigation water pH and EC, while saprotrophic and pathotrophic communities are structured by water pH. The high abundance of specific saprotrophs under saline groundwater irrigation indicates their potential role in nutrient cycling and plant growth promotion in arid agroecosystems.

Abstract Saline water irrigation has been used in date palm (Phoenix dactylifera L.) agriculture as an alternative to non-saline water due to water scarcity in hyper-arid environments. However, the knowledge pertaining to saline water irrigation impact on the root-associated bacterial communities of arid agroecosystems is scarce. In this study, we investigated the effect of irrigation sources (non-saline freshwater vs saline groundwater) on date palm root-associated bacterial communities using 16S rDNA metabarcoding. The bacterial richness, Shannon diversity and evenness didn’t differ significantly between the irrigation sources. Soil electrical conductivity (EC) and irrigation water pH were negatively related to Shannon diversity and evenness respectively, while soil organic matter displayed a positive correlation with Shannon diversity. 40.5% of total Operational Taxonomic Units were unique to non-saline freshwater irrigation, while 26% were unique to saline groundwater irrigation. The multivariate analyses displayed strong structuring of bacterial communities according to irrigation sources, and both soil EC and irrigation water pH were the major factors affecting bacterial communities. The genera Bacillus, Micromonospora and Mycobacterium were dominated while saline water irrigation whereas contrasting pattern was observed for Rhizobium, Streptomyces and Acidibacter. Taken together, we suggest that date-palm roots select specific bacterial taxa under saline groundwater irrigation, which possibly help in alleviating salinity stress and promote growth of the host plant.

The irrigation of date palms (Phoenix dactylifera) with saline groundwater is routinely practiced in the agroecosystems of arid environments because of freshwater scarcity. This leads to salts deposition in topsoil layers and increases soil salinization. However, how different irrigation sources affect soil microbiota is poorly understood. Bulk soil samples were collected from date farms receiving non-saline water and saline groundwater to examine bacterial communities using metabarcoding. Overall, bacterial diversity measures (Shannon diversity index, richness, and evenness) did not vary between irrigation sources. Bacterial communities were structured based on irrigation water sources and were significantly associated with their electrical conductivity. Of 5,155 operational taxonomic units (OTUs), 21.3% were unique to soil irrigated with saline groundwater, 31.5% received non-saline water irrigation, and 47.2% were shared. The Proteobacteria abundance was higher in soil under saline groundwater irrigation while Actinobacteriota abundance was lower. A compositional shift at the genera level was also evident; the abundance of Subgroup_10 and Mycobacterium was higher under saline groundwater irrigation. Mycobacterium was a key indicator of OTU under saline groundwater irrigation while Solirubrobacter was an indicator of non-saline water irrigation. Functional gene analyses showed enrichment of fatty acid, cell wall, and starch biosynthesis pathways in soil under saline groundwater irrigation. These findings provide insights into how “salinity filtering” influences bacterial communities, key taxa, and the potential metabolic function in soil under increasing irrigation water salinities, and have broad implications for arid agroecosystems.