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Objective The microbial communities preserved within vertebrate bone remains serve as crucial biological archives recording their burial processes and environmental histories. However, how bone microbial communities respond to environmental changes across different geographical and chronological scales, as well as their specific indicative potential in paleoenvironmental reconstruction, remains unclear. This study aims to reveal the spatio-temporal variation patterns of vertebrate bone microbial communities in northern China and evaluate their feasibility as paleoenvironmental biomarkers. Methods Ancient DNA extraction and shotgun metagenomic sequencing techniques were employed to analyze the microbial community composition of 43 animal bone fossil or subfossil samples collected from different geographical regions (Northeast and Northwest China) and geological periods (Late-Pleistocene and Holocene) in northern China. Diversity statistics and differential species identification were combined to systematically compare the spatio-temporal variation characteristics of community structures. Results Microbial communities exhibited significant differences across both geographical regions and geological periods. Samples from Northeast China showed higher microbial diversity, being dominated by soil-derived taxa such as Acidobacteria sp. GGB63485, while samples from Northwest China were dominated by freshwater and chemoautotrophic taxa including Curvibacter and Sulfuricaulis. Cold-tolerant and oligotrophic taxa were enriched in Late-Pleistocene samples, while taxa associated with aquatic environments and plant degradation were more prominent in Holocene samples. Conclusion The compositional differences of microbial communities in bone remains are jointly driven by local environmental factors and temporal climate change. The structural characteristics can effectively reflect paleoenvironmental conditions including soil type, hydrological status, redox potential, and temperature changes. This study provides empirical evidence and methodological approaches for paleoenvironmental reconstruction with skeletal microbiomes, expands the boundaries of traditional paleoenvironmental indicator systems, and offers new perspectives for understanding the assembly mechanisms and ecological responses of microbial communities during long-term burial.
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| 科 Family | 属数 Number of genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) | 属 Genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) |
|---|---|---|---|---|---|---|
| 鹅膏菌科Amanitaceae | 2 | 11 | 5.26 | 鹅膏菌属 Amanita | 10 | 4.78 |
| 小菇科 Mycenaceae | 2 | 12 | 5.74 | 丝盖伞属 Inocybe | 5 | 2.39 |
| 多孔菌科 Polyporaceae | 8 | 14 | 6.70 | 蜡蘑属 Laccaria | 5 | 2.39 |
| 红菇科 Russulaceae | 3 | 23 | 11.00 | 小皮伞属 Marasmius | 6 | 2.87 |
| 小菇属 Mycena | 11 | 5.26 | ||||
| 光柄菇属 Pluteus | 5 | 2.39 | ||||
| 红菇属 Russula | 17 | 8.13 | ||||
| 栓菌属 Trametes | 5 | 2.39 |
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