Investigation of Pine Wilt Disease in Chongqing: From Field Occurrence and Genetic Diversity to Endophytic Microbial Composition and Functional Analysis

Pine wilt disease (PWD), caused by <i>Bursaphelenchus xylophilus</i>, is a destructive forest disease leading to rapid mortality. Although Chongqing is a major epidemic region in China, the population genetic structure of <i>B. xylophilus</i> and the ecological interactions among nematode occurrence, blue stain formation, and microbial community dynamics remain insufficiently clear. This study systematically surveyed nematode incidence and performed morphological and molecular identification, revealing strong correlations between nematode presence, blue stain, and insect infestation (<i>p</i> < 0.0001). Within <i>Monochamus alternatus</i>, nematodes were mainly distributed in the abdomen and thorax (<i>p</i> < 0.0001). High-throughput sequencing showed significantly higher fungal (e.g., <i>Leptographium</i>) and bacterial (e.g., <i>Burkholderia-Caballeronia-Paraburkholderia</i>) diversity in diseased than healthy pinewood, indicating pronounced microbial shifts during disease progression. <i>mtCOI</i>-based genetic analyses of 162 nematodes from 11 populations revealed five haplotypes, with Hap1 shared across all populations. AMOVA indicated that over 80% of genetic variation occurred within populations, and neutrality and mismatch analyses suggested recent expansion in some populations (Beibei, Jiangbei, Rongchang). These findings clarify nematode epidemiology, microbial shifts, and genetic characteristics in Chongqing, providing a scientific basis for precise sampling, rapid detection, and integrated management of PWD, and suggest that microbial community changes may contribute to rapid pine decline.