The grazing activity of animals has a significant role on the environmental modification of land. In the coastal wetlands of eastern China, long-term David deer (Elaphurus davidianus) grazing has caused the degradation of various ecological elements in the area. Still, few studies have been reported concerning the effects of David deer grazing on the soil microorganisms of their habitats. We analyzed the community structure of soil bacteria and fungi in an area of continuous annual grazing and another area without traces of David deer grazing so as to learn about the effects of deer grazing on the soil microbial community structure in a spatial instead of temporal way, in preparation for improving the environment for deer survival. David deer grazing drastically changed the physicochemical characteristics of the soil, accelerating the alkalinization process and inhibiting the buildup of nutrients. There were differences in the microbial community structure between the grazed and the control areas, with bacteria predominating. The control had a higher level of bacterial and fungal alpha-diversity than the grazed area. The makeup of the soil’s microbial community was also influenced, except for the dominant microbial at the phylum level. In addition to the establishment of numerous complex fungal functional types, David deer grazing increased the number of bacterial functional types linked to the carbon cycle. The impacts of soil pH and urease activity on bacterial and fungi populations were highlighted using the redundancy analysis. This study demonstrates that David deer grazing changes and complicates microbial functional kinds of composition, as well as modifies the composition of the soil’s microbial community, improving the soil nutrient cycling process, mainly the carbon element.

Although significant progress has been made in the conservation of Père David’s deer (Elaphurus davidianus) populations, rapid population growth in coastal wetlands has caused severe habitat degradation. This highlights the urgent challenge of balancing ungulate population dynamics with wetland restoration efforts, particularly considering the limited data available on post-disturbance ecosystem recovery in these environments. In this study, we evaluated soil quality and bacterial community dynamics at an abandoned feeding site and a nearby control site within the Dafeng Milu National Nature Reserve during 2020–2021. The goal was to provide a theoretical basis for the ecological restoration of Père David’s deer habitat in coastal wetlands. The main findings are as follows: among the measured indicators, bulk density (BD), soil water content (SWC), sodium (Na⁺), total carbon (TC), total nitrogen (TN), total phosphorus (TP), available potassium (AK), microbial biomass nitrogen (MBN), and the Chao index were selected to form the minimum data set (MDS) for calculating the soil quality index (SQI), effectively reflecting the actual condition of soil quality. Overall, the SQI at the feeding site was lower than that of the control site. Based on the composition of bacterial communities and the functional prediction analysis of bacterial communities in the FAPROTAX database, it is shown that feeding sites are experiencing sustained soil carbon loss, which is clearly caused by the gathering of Père David’s deer. Co-occurring network analyses demonstrated the structure of the bacterial community at the feeding site was decomplexed, and with a lower intensity than the control. In RDA, Na⁺ is the main soil property that affects bacterial communities. These findings suggest that the control of soil salinity is a primary consideration in the development of Père David’s deer habitat restoration programmes, followed by addressing nitrogen supplementation and carbon sequestration.