Using controlled soil incubations, the study found that moderate soil moisture enhanced nitrification under higher ammonium supply, while waterlogged conditions suppressed aerobic nitrifiers because of limited oxygen. The work reveals that nitrite accumulation is not simply a chemical outcome, but the result of mismatched microbial activities between ammonia oxidizers and nitrite oxidizers.
Soil nitrification is a central process in the nitrogen cycle, converting ammonia (NH3) first to nitrite (NO2−) and then to nitrate (NO3−). This process is driven by ammonia-oxidizing microorganisms, including ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), followed by nitrite-oxidizing bacteria (NOB). Under stable conditions, the two steps are usually well coupled, preventing excessive nitrite buildup. However, soil moisture can alter oxygen diffusion, substrate movement, microbial activity, and redox conditions. Previous studies have recognized that water content affects nitrification, but how moisture and ammonium supply together regulate the balance between ammonia oxidation and nitrite oxidation in soils has remained insufficiently understood.
A study (DOI: 10.48130/ebp-0026-0005) published in Environmental and Biogeochemical Processes on 29 April 2026 by Shurong Liu's team, Shenzhen Campus of Sun Yat-Sen University, reports that moderate moisture and high ammonium input promote AOB-driven ammonia oxidation faster than nitrite oxidation can proceed, causing nitrite accumulation, whereas waterlogging shifts the system toward oxygen-limited nitrogen transformation.
The researchers collected topsoil from an unfertilized peach orchard in Yuncheng City, Shanxi Province, China, and conducted a laboratory incubation experiment. Soils were adjusted to four water-holding capacity (WHC) levels: 40%, 60%, 90%, and 120%, representing relatively dry, moderate, moist, and waterlogged conditions. Three ammonium nitrogen levels were added: 50, 100, and 200 mg NH4+–N kg−1. Soil samples were collected over nine days to track changes in ammonium, nitrite, and nitrate. The team also used quantitative polymerase chain reaction (qPCR) and complementary DNA (cDNA)-based analyses to measure both the abundance and activity of key microbial functional genes, including amoA for ammonia oxidizers and nxrB for nitrite oxidizers. The chemical data showed that when ammonium supply was low, soil moisture had limited influence on ammonia oxidation. Under higher ammonium input, however, ammonia oxidation increased markedly at 60%–90% WHC, while it declined under 120% WHC, indicating oxygen limitation in saturated soils. Nitrite accumulated most strongly under high nitrogen input and moderate moisture, especially when rapid ammonia oxidation produced nitrite faster than it could be converted to nitrate. Microbial analyses explained this imbalance. AOB activity was strongest under high nitrogen and moderate moisture, making AOB the main driver of ammonia oxidation in these treatments. In contrast, Nitrobacter, a key nitrite oxidizer, was highly sensitive to saturated conditions and declined sharply at 120% WHC. Nitrospira was more abundant overall and showed broader tolerance to moisture extremes, but its transcriptionally active fraction was limited under some high-substrate conditions. Correlation analyses further showed that nitrite accumulation was positively associated with the ratio of ammonia oxidation to nitrite oxidation and with the AOB-to-Nitrobacter abundance ratio, confirming that microbial imbalance was the main mechanism behind nitrite buildup.
Overall, the study demonstrates that soil moisture controls nitrogen cycling not only by changing oxygen availability, but also by reshaping the microbial partnerships that link ammonia and nitrite oxidation. Moderate moisture can accelerate nitrification when ammonium is abundant, but it may also create a temporary bottleneck if nitrite oxidizers cannot keep pace. In contrast, waterlogging suppresses aerobic nitrification and may increase the role of denitrification. The authors note that future studies using selective inhibitors, isotope tracing, and direct gas measurements will be needed to separate the contributions of different microbial groups under field conditions.
