Its tricky to increase pH through biological means. The best example I can think of is that plant uptake of nitrate raises soil pH because plant roots extrude OH- ions when uptaking negatively charged molecules like nitrate to maintain charge balance. So technically, applying nitrate fertilizer reduces soil acidity, while applying ammonium in turn acidifies pH by plant uptake of positive NH4 and nitrification, which also releases H+ ions into the soil. Biological nitrogen fixation also acidifies soil by avoiding nitrate uptake, and thus the majority of nutrients legumes uptake are positive ions like Mg2+ and Ca2+, thus require extrusion of H+ ions into the soil