An assessment of soil microbial community environmental stress in alpine marginal ecosystems using microbial indicators

•The phospholipid fatty acid contents have significantly altered.•Site effect had a considerably higher influence.•The soil microbial community was under environmental stress.•Microbial indicators can be used as potential biomarkers. Alpine marginal ecosystems above the natural tree line are considered to be the most vulnerable habitats for maintaining local biodiversity. The soil microbial community is crucial for ecosystem stability and function. However, our comprehension of the overall soil microbial community in alpine marginal ecosystems remains limited, particularly regarding environmental stress. We selected the Baima Mountain National Nature Reserve (BMNNR) in the northwest Yunnan provinces as our study area and collected soil samples from three different depth layers, in alpine marginal ecosystems. The phospholipid fatty acid (PLFA) analysis method was utilized to evaluate alterations in soil microbial communities. The results showed that: (1) the PLFA content gradually decreased with increasing soil depth; (2) on the whole, the variations in PLFA across alpine marginal ecosystems were obviously, the highest in alpine meadow (AM) and the lowest in alpine screes (AS); (3) the site effect exerted a greater direct influence than microhabitat effect and elevation (0–5 cm, 32 %, 16 % and 9 %, respectively; 20–40 cm, 46 %, 29 % and 0 %, respectively), with the direct impact of elevation decreasing as soil depth increased (0–5 cm, 5–20 cm and20-40 cm, 9 %, 1 % and 0 %, respectively); and (4) the ratio of cyclopropyl to precursors (Cy:Pre) in all communities was > 0.1, indicating that the soil microbial community was under environmental stress. This study demonstrates the potential of PLFA analysis to profile soil microbial communities and their stress status under field conditions and also provides a better understanding of the correlation between soil microbial communities and the function and health of alpine marginal ecosystems.