DOI: 10.5061/dryad.rfj6q57ph
title: Data from: Roles of soil microbes in shaping the nutrient accumulation of dietary bamboo of giant pandas

description: 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.
description: # Data from: Roles of soil microbes in shaping the nutrient accumulation
 of dietary bamboo of giant pandas Dataset DOI:
 [10.5061/dryad.rfj6q57ph](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).