3.2 Description of Illumina Miseq dataset and bacterial richness and diversity
Ranging from 187,097 to 395,864 sequences with an average of 299,394 sequences per sample, a total of 4,790,305 high-quality sequences were obtained from sixteen soil samples treated with different N fertilization rates. The average length of the sequences analyzed was 376 bases, approximate 80% of the sequences analyzed were assigned at the Phylum level, 45-50% of the sequences at the Order level, and only 30-35% of the sequences were assigned to the Genus level. Figure 3 displays the description of the number of assignments by RDP classifier at each taxonomic level and for each soil sample.
Figure 3
In total, 9358 OTUs occurred with a frequency of at least 10 reads in the dataset. Figure 4 presents the bacterial community richness and diversity indexes calculated from the 16S rRNA gene amplicon sequencing. In comparison with the control soil samples, the OTUs increased by 3.67%, 8.14 and 15.05% at treatments of 150, 300 and 450 kg N hm−2 y-1 rates, respectively. Alpha diversity based on species richness varied among samples (p <0.05) (Fig. 4). Chao1 and ACE, the community richness indexes, increased with the N fertilization rates, and samples at NF3 (450 kg N hm-2 y-1) treatment had significantly higher Chao1 and ACE indexes than those at CK and NF1 (150 kg N hm-2 y-1) treatments. The average ratio of OTUs/Chao1 was 83.27% ± 1.86%, implying that the sequencing efforts were not exhaustive. Shannon index showed similar trend with coverage index, i.e., increasing with the N fertilization rates, whereas Simpson index decreased with N rates. The comparison of the samples based on the richness and diversity indexes showed that bacterial community structures well responded to the N fertilization rates, and greatest bacterial richness occurred in NF3 and NF2 treatments, followed byNF1 and CK treatments.
Figure 4