Data from: Roles of soil microbes in shaping the nutrient accumulation of dietary bamboo of giant pandas
Data files
Sep 13, 2025 version files 1.87 GB
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README.md
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Soil_microbes_data.zip
1.87 GB
Abstract
Soil microbes play key roles in the nutrient acquisition of plants, and plant nutrients are a key determinant of herbivore foraging behavior and nutritional physiology which would further affect their life history strategies. Giant pandas (Ailuropoda melanoleuca), as obligate bamboo herbivores, rely heavily on bamboo for sustenance. We here evaluate the potential impact of soil microbes on the dietary bamboo of giant panda by monitoring bamboo growth dynamics alongside soil properties and microbial community patterns. Our results revealed that soil bacterial and fungal composition significantly influence the availability of soil available phosphorus (AP), ammonium nitrogen (NH4^+-N), and nitrate nitrogen (NO3^--N). Notably, bacterial and fungal genera associated with nitrogen (N) and phosphorus (P) acquisition were significantly enriched during the new shoot season. Higher soil AP and NH4^+-N level were found to significantly enhance the growth of new bamboo shoots. Combined with the life histories of giant pandas and the nutrient contents of bamboo, it is evidenced that the soil microbes provide essential nutritional foundations for the foraging and reproductive timing of giant pandas during the new shoot season. This study offers novel insights into the critical role of soil microbes in the soil-plant-herbivore system, which plays an indirect role in shaping the foraging and reproductive strategies of a large mammalian herbivore.
Dataset DOI: 10.5061/dryad.rfj6q57ph
Description of the data and file structure
File: Soil_microbes_data.zip
This study was conducted in Foping Nature Reserve, located in Shaanxi Province, China. We sampled soil at 12 sites scattered around the wood bamboo forest of the Foping Nature Reserve. We sampled every two months in a whole year, specifically in March, May, July, September, November and January from 2019 to 2020. Within each site, three randomly located soil cores with a diameter of 5 cm were collected at a depth of 0 to 10 cm. The top of the bulk soil was collected in six months, resulting in a total of 72 soil samples (12 sites in 6 months).
Extraction of DNA from fresh soil samples (0.5 g) was performed using the Power-Soil® DNA Isolation Kit (MO BIO Laboratories, USA) according to the manufacturer’s manual. A region of the 16S rRNA/ITS genes for bacteria (V4 - V5 regions) and fungi (ITS1 regions) were amplified by primer pairs, 515F/907R and ITS1F/ITS2R, respectively, that included 12 bp barcodes. Sequencing was conducted on an Illumina MiSeq PE300 platform (Illumina Inc., San Diego, CA, USA) according to the standard protocols by Majorbio Bio-Pharm Technology Co. Ltd. (Shanghai, China).
Raw fastq files of bacterial and fungal reads obtained from MiSeq sequencing were quality-filtered by Trimmomatic and merged by FLASH. Operational taxonomic units (OTUs) with a 97% similarity cutoff were clustered using UPARSE version 7.1. The taxonomy of each OTU representative sequence of bacteria was analyzed by RDP Classifier version 2.2 against the 16S rRNA database (version 138/16S-bacteria database) using a confidence threshold of 70%. The taxonomy of the fungal sequences was analyzed by the RDP Classifier algorithm against the United States database (version 7.2/its-fungi database) using a confidence threshold of 70% (Wang et al., 2007).