Brackish water irrigation differentially modulates rhizosphere microbial communities and metabolites under two biochar feedstocks in cotton

Rhizosphere microbe–metabolite associations under biochar amendment may influence crop responses to salt stress, but how biochar feedstock type shapes these associations under brackish water irrigation remains unclear. We investigated the responses of cotton rhizosphere bacterial communities, soil metabolites, soil nutrient availability, plant physiological traits, and seed cotton yield to wheat straw biochar (B1) and apple wood biochar (B2) under freshwater irrigation (S0) and brackish water irrigation (S1) in the field. Brackish water irrigation differentially altered rhizosphere bacterial communities and metabolite profiles under the two biochar treatments. Under B1, S1 was associated with Nitrobacter enrichment and higher predicted nitrification-related functions, with soil NO₃⁻-N decreasing by 14.7%, compared with 30.2% in the non-biochar treatment. These bacterial responses were accompanied by higher levels of soluble sugars and organic acids, with enrichment of starch and sucrose metabolism, citrate cycle, and carbon metabolism. In contrast, B2 maintained higher alkaline phosphatase activity and was more closely associated with lipid-, phenolic-, and flavonoid-related metabolic responses. Although S1 reduced cotton root growth, photosynthesis, and yield, B1 maintained higher specific root length, aboveground dry biomass, seed cotton yield, and net photosynthetic rate than B2 under brackish water irrigation. Compared with S1B0, B1 increased net photosynthetic rate by 30.3%, whereas B2 increased it by 17.0%. These results suggest that different biochar feedstocks were associated with distinct short-term rhizosphere responses under brackish water irrigation: B1 was mainly linked to soluble sugar and organic acid metabolism, predicted N-cycling functions, and yield maintenance, whereas B2 was more closely associated with lipid- and phenolic-related stress responses.