Background: Soil microbes exist throughout the soil profile and those inhabiting topsoil (0–20 cm) are believed to play a key role in nutrients cycling. However, the majority of the soil microbiology studies have exclusively focused on the distribution of soil microbial communities in the topsoil, and it remains poorly understood through the subsurface soil profile (i.e., 20–40 and 40–60 cm). Here, we examined how the bacterial community composition and functional diversity changes under intensive fertilization across vertical soil profiles [(0–20 cm (RS1), 20–40 cm (RS2), and 40–60 cm (RS3)] in the red soil of pomelo orchard, Pinghe County, Fujian, China. Results: Bacterial community composition was determined by 16S rRNA gene sequencing and interlinked with edaphic factors, including soil pH, available phosphorous (AP), available nitrogen (AN), and available potassium (AK) to investigate the key edaphic factors that shape the soil bacterial community along with different soil profiles. The most dominant bacterial taxa were Proteobacteria, Acidobacteria, Actinobacteria, Chloroflexi, Crenarchaeota, and Bacteriodetes. Bacterial richness and diversity was highest in RS1 and declined with increasing soil depth. The distinct distribution patterns of the bacterial community were found across the different soil profiles. Besides, soil pH exhibited a strong influence (pH ˃AP ˃AN) on the bacterial communities under all soil depths. The relative abundance of Proteobacteria, Actinobacteria, Crenarchaeota, and Firmicutes was negatively correlated with soil pH, while Acidobacteria, Chloroflexi, Bacteriodetes, Planctomycetes, and Gemmatimonadetes were positively correlated with soil pH. Co-occurrence network analysis revealed that network topological features were weakened with increasing soil depth, indicating a more stable bacterial community in the RS1. Bacterial functions were estimated using FAPROTAX and the relative abundance of functional bacterial community related to metabolic processes, including C-cycle, N-cycle, and energy production was significantly higher in RS1 compared to RS2 and RS3, and soil pH had a significant effect on these functional microbes. Conclusions: This study provided the valuable findings regarding the structure and functions of bacterial communities in red soil of pomelo orchards, and highlighted the importance of soil depth and pH in shaping the soil bacterial population, their spatial distribution and ecological functioning. These results suggest the alleviation of soil acidification by adopting integrated management practices to preserve the soil microbial communities for better ecological functioning.

Soil fungi play a critical role in plant performance and soil nutrient cycling. However, the understanding of soil fungal community composition and functions in response to different nutrients management practices in red soils remains largely unknown. Here, we investigated the responses of soil fungal communities and functions under conventional farmer fertilization practice (FFP) and different nutrient management practices, i.e., optimization of NPK fertilizer (O) with soil conditioner (O + C), with lime and mushroom residue (O + L + M), and with lime and magnesium fertilizer (O + L + Mg). Illumina high-throughput sequencing was used for fungal identification, while the functional groups were inferred with FUNGuild. Nutrient management practices significantly raised the soil pH to 4.79–5.31 compared with FFP (3.69), and soil pH had the most significant effect (0.989 ***) on fungal communities. Predominant phyla, including Ascomycota, Basidiomycota, and Mortierellomycota were identified in all treatments and accounted for 94% of all fungal communities. The alpha diversity indices significantly increased under nutrients management practices compared with FFP. Co-occurrence network analysis revealed the keystone fungal species in the red soil, i.e., Ascomycota (54.04%), Basidiomycota (7.58%), Rozellomycota (4.55%), and Chytridiomycota (4.04%). FUNGuild showed that the relative abundance of arbuscular mycorrhizal fungi and ectomycorrhizal fungi was higher, while pathogenic fungi were lower under nutrient management practices compared with FFP. Our findings have important implications for the understanding of improvement of acidic soils that could significantly improve the soil fungal diversity and functioning in acidic soils.

Root system plays a crucial role in plant growth and development by uptake of soil nutrients, which is affected by intensive use of NPK fertilizer. However, it is unknown how integrated nutrient management (INM) could affect the root growth and its nutrient uptake in the red soils of southern China. For this, the impacts of different INM practices on root morphological traits and root nutrient uptake were investigated in the pomelo tree. First, we investigated the spatial root distribution of various tree ages (i.e., 8, 13, 18, and 23 years old) and found the optimum root growth at 20–80 cm around the tree trunk in topsoil (0–20 cm). Hence, the pomelo trees were fertilized at 20–80 cm around the trunk, i.e., FFP (farmer fertilization practice), optimization NPK fertilizer (O) combined with lime (L) and mushroom residue (M) known as O+L+M treatment, and O+L combined with Mg fertilizer called as O+L+Mg treatment. We found that root length (RL) significantly increased by application of O+L+M (108.5 and 219.1 cm) and O+L+Mg (73.6, 66.8 cm) in topsoil and subsoil, respectively, in 2019. Similarly, root surface area (RSA) was significantly higher under INM, i.e., O+L+Mg > O+L+M > FFP. For root diameter (RD), O+L+M (0.8 mm) and O+L+Mg (1.5 mm) showed significantly lower diameter than FFP (2.54 mm). The root tips (RT) also improved considerably under INM practices compared with FFP. Besides, root nutrient contents (N, P, K, Ca, and Mg) also significantly improved under O+L+M and O+L+Mg over FFP. Similar trends of root growth and nutrients uptake were recorded in 2020. Overall, these findings suggest that INM plays a significant role in root development and nutrient uptake under acidic soil, which could be useful for maximizing crop productivity.