DOI: 10.57760/sciencedb.20583
title: Soil microbial dataset in the western karst region of China
title: Soil microbial dataset in the western karst region of China

description: A 0.5 g soil sample was used for DNA extraction of soil bacteria and fungi, following the instructions provided with the Hi Pure Stool DNA Kit for Soil (Magen, Guangzhou, China). The V3-V4 region of the bacterial 16S rRNA gene was amplified using primers 341F (CCTACGGGGGNGGCWGCAG) and 785R (GACTACHVGGGGTATCTAATCC). The PCR amplification conditions were as follows: pre-denaturation at 95°C for 3 minutes, denaturation at 95°C for 30 seconds, annealing at 55°C for 30 seconds, and extension at 72°C for 45 seconds, repeated for 35 cycles, followed by a final extension at 72°C for 10 minutes. Each reaction was performed in triplicate. For fungal DNA, the internal transcribed spacer (ITS) region was amplified using primers ITS1F (CTTGGTCATTTAGAGGAAGTAA) and ITS2R (GCTGCGTTCTTCATCGATGC). The amplification conditions included pre-denaturation at 95°C for 3 minutes, denaturation at 95°C for 30 seconds, annealing at 55°C for 30 seconds, and extension at 72°C for 45 seconds, repeated for 27 cycles, followed by a final extension at 72°C for 10 minutes. Each reaction was also performed in triplicate. The gel-purified PCR products were used to construct sequencing libraries, which were subjected to paired-end sequencing on the Illumina MiSeq PE250 platform of Majorbio.co.The original 16S rRNA gene sequences were filtered by extracting non-repetitive sequences from the optimized dataset and removing single-occurrence sequences. For bacterial sequences, clean tags were processed using the SILVA 16S rRNA database, while fungal sequences were processed using the Unite fungal database. Operational Taxonomic Unit (OTU) clustering was performed on non-repetitive sequences (excluding single-occurrence sequences) at 97% similarity. During clustering, chimeric sequences were removed to obtain representative OTU sequences. All optimized sequences were mapped to the OTU representative sequences, and sequences with ≥97% similarity to the representative OTU sequences were designated as the representative sequences of each OTU. Alpha diversity indices, including Sobs, Shannon, Simpson, Chao1, ACE, and Pielou's evenness, were calculated using QIIME (v.1.9.1). Taxonomic classification of microbial sequences was performed with the RDP Classifier (version 2.11, http://sourceforge.net/projects/rdp-classifier/) at a confidence threshold of 0.7.The tabular data were divided into two groups of data, bacterial and fungal: C (corn field), CC (intercropped corn and cabbage field), E (economic fruit forests), P (plantation), and R (restored forest). Overall, the tabular data contained barcodes, microbial diversity indices, and microbial community composition.
description: A 0.5 g soil sample was used for DNA extraction of soil bacteria and fungi, following the instructions provided with the Hi Pure Stool DNA Kit for Soil (Magen, Guangzhou, China). The V3-V4 region of the bacterial 16S rRNA gene was amplified using primers 341F (CCTACGGGGGNGGCWGCAG) and 785R (GACTACHVGGGGTATCTAATCC). The PCR amplification conditions were as follows: pre-denaturation at 95°C for 3 minutes, denaturation at 95°C for 30 seconds, annealing at 55°C for 30 seconds, and extension at 72°C for 45 seconds, repeated for 35 cycles, followed by a final extension at 72°C for 10 minutes. Each reaction was performed in triplicate. For fungal DNA, the internal transcribed spacer (ITS) region was amplified using primers ITS1F (CTTGGTCATTTAGAGGAAGTAA) and ITS2R (GCTGCGTTCTTCATCGATGC). The amplification conditions included pre-denaturation at 95°C for 3 minutes, denaturation at 95°C for 30 seconds, annealing at 55°C for 30 seconds, and extension at 72°C for 45 seconds, repeated for 27 cycles, followed by a final extension at 72°C for 10 minutes. Each reaction was also performed in triplicate. The gel-purified PCR products were used to construct sequencing libraries, which were subjected to paired-end sequencing on the Illumina MiSeq PE250 platform of Majorbio.co.The original 16S rRNA gene sequences were filtered by extracting non-repetitive sequences from the optimized dataset and removing single-occurrence sequences. For bacterial sequences, clean tags were processed using the SILVA 16S rRNA database, while fungal sequences were processed using the Unite fungal database. Operational Taxonomic Unit (OTU) clustering was performed on non-repetitive sequences (excluding single-occurrence sequences) at 97% similarity. During clustering, chimeric sequences were removed to obtain representative OTU sequences. All optimized sequences were mapped to the OTU representative sequences, and sequences with ≥97% similarity to the representative OTU sequences were designated as the representative sequences of each OTU. Alpha diversity indices, including Sobs, Shannon, Simpson, Chao1, ACE, and Pielou's evenness, were calculated using QIIME (v.1.9.1). Taxonomic classification of microbial sequences was performed with the RDP Classifier (version 2.11, http://sourceforge.net/projects/rdp-classifier/) at a confidence threshold of 0.7.The tabular data were divided into two groups of data, bacterial and fungal: C (corn field), CC (intercropped corn and cabbage field), E (economic fruit forests), P (plantation), and R (restored forest). Overall, the tabular data contained barcodes, microbial diversity indices, and microbial community composition.