Soil bacterial communities play a crucial role in nutrient cycling and ecosystem functioning in forested areas. Previous studies have reported that nitrogen deposition affects soil bacterial diversity and community structure. However, the responses to nitrogen deposition can be affected by local conditions such as soil type, so it remains unclear how important spatial location and soil type are in shaping bacterial communities under increasing nitrogen deposition. Here, we aimed to examine the responses of soil bacterial communities to long-term fertilization on five forest sites across Japan, representing both volcanic and non-volcanic soils, and to reveal the main drivers determining bacterial diversity and community variation.
For this purpose, we collected soil samples from two soil depths (organic and 0–5 cm mineral soils) in four to five forest stands dominated by Japanese oak on five sites seven years after initial fertilization. Each stand included two treatments (fertilized and control plots). The soil types include volcanic ash soils (3 sites) and non-volcanic soils (2 sites). These sites spanned a wide range of local conditions and spatial differences. We determined soil bacterial communities using 16S rRNA amplicon sequencing and analyzed community diversity and composition with Shannon diversity index, non-metric multidimensional scaling (NMDS), and permutational multivariate analysis of variance (PERMANOVA).
Relative abundance analysis revealed that Pseudomonadota and Actinobacteria dominated across all sites, with minor contributions from other phyla. Shannon diversity did not differ significantly between treatments. Further PERMANOVA analysis conducted separately for each site and soil depths showed that significant fertilization effects were observed only in the organic layers of two non-volcanic soils. Specifically, fertilization effects explained a relatively large proportion (16.6% and 19.4%) in respective sites. Furthermore, in the model using all data, we found that the effects of soil depths and sites emerged as the primary drivers of community variation. The effect of sites explained the largest proportion of variation in community structure (17.5%), followed by those of soil depths (8.0%). Due to the nesting of sites within soil types, the overall effect of soil types was confounded with site. When site effects were not included, soil types showed a significant effect.
These findings indicate that local environmental conditions affected more strongly on bacterial community composition than nitrogen fertilization, highlighting the resilience of the bacterial communities and the role of spatial heterogeneity in structuring soil bacterial community.