## 2 Materials and Methods
### Illumina MiSeq and Data Processing  
After the field sampling, the 29 surface samples were freeze-dried for 48 h at \(-\)50 \({}^{\circ}\)C (F-20; NIHON Co., Shanghai, China) and sifted through a 2-mm nylon sieve to remove residual animal and plant matter, for analyzing the bacterial composition. The cetyltrimethylammonium ammonium bromide was widely used to extract the total bacterial and vegetal genomic DNA in the last decades [24], so it was used in our research. The detailed DNA extracting procedures referred to the report of [PERSON] et al. [25]. We quantified the extracted DNA by using Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) and checked the DNA quality with 1.2% agarose gel electrophoresis [26]. The purified DNA was diluted to 25 ng/\(\mu\)L, and then PCR amplification of the 16S rRNA genes V4 region was performed using the primers 515F and 806R [27]. Sample-specific 7-bp barcodes were incorporated into the primers for multiplex sequencing. The PCR was conducted using the Phusion High-Fidelity PCR Master Mix (Phusion High-Fidelity DNA Polymerase) with GC buffer (New England Biolabs Co., Ipswich, MA, USA) and concrete operations were showed in the report of [PERSON] et al. [28]. The PCR products were mixed in equal amounts, according to concentration, and the mixed products were purified with 2% agarose gel electrophoresis and quantified by using the PicoGreen dsDNA Assay Kit (Invitrogen, Carlsbad, CA, USA). Then, the paired-end 2 \(\times\) 300 bp sequencing was performed using the Illumina MiSeq platform with MiSeq Reagent Kit v3 at Shanghai Personal Biotechnology Co., Ltd. (Shanghai, China). The Quantitative Insights Into Microbial Ecology (QIIME, v1.8.0) pipeline was employed to process the sequencing data, as previously described [26; 27]. The nucleotide sequences we obtained were deposited in the National Center for Biotechnology Information, under the accession number PRJNA470781, PRJNA470783, and PRJNA470794.  
Raw sequencing reads with exact matches to the barcodes were assigned to the respective samples and identified as valid sequences in FLASH (version 1.2.7, Center for Computational Biology of Johns Hopkins University, Baltimore, Maryland, USA, 2011. [[http://ccb.jhu.edu/software/FLASH](http://ccb.jhu.edu/software/FLASH)]([http://ccb.jhu.edu/software/FLASH](http://ccb.jhu.edu/software/FLASH))) [26]. The chimeras were identified and removed by Uchime of Mother (version 4.1, The Department of Microbiology & Immunology at The University of Michigan, Detroit, MI, USA. 2011. [[http://www.mothur.org/](http://www.mothur.org/)]([http://www.mothur.org/](http://www.mothur.org/))), the low-quality sequences were filtered and the remaining high-quality sequences were clustered into operational taxonomic units (OTUs) at 97% sequence identity by UCLUST, and then representative OTU sequences were selected [16; 29]. These sequences were identified at the genus level, against the SILVA rRNA database in Mothur (version 1.31.2, The Department of Microbiology & Immunology at The University of Michigan, Detroit, MI, USA. 2009. [[http://www.mothur.org/](http://www.mothur.org/)]([http://www.mothur.org/](http://www.mothur.org/))) [30]. On the basis of the taxonomic information obtained, we determined the community composition of each sample at the different classification levels--kingdom, phylum, class, order, family, and genus [31]. To minimize the difference of sequencing depth across samples, an averaged, rounded rarefied OTU table was generated by averaging 100 evenly resampled OTU subsets, under 90% of the minimum sequencing depth.