## 3 Results
### Microbial Diversity of the Samples from Production and Control Wells  
Using high-throughput sequencing technology based on the Illumina platform, 42,074 bacterial sequences and 66,428 archaeal sequences from the production well W226 and 40,795 bacterial sequences and 29,302 archaeal sequences from the control well W202 were clustered to 711, 499, 445, and 262 different OTUs, respectively (Table 3). In each sample, the number of bacterial OTUs was greater than that of the archaeal OTUs. Figure 2a,c show the rarefaction curve with a dissimilarity cut-off of 3% to indicate microbial diversity within each sample. As the number of sequences increases, the number of OTUs obtained gradually increases. The number of bacterial OTUs in the production well W226 and the control well W202 was higher than the number of archaeal OTUs, indicating that the diversity of bacteria in both samples was higher than that of archaea. For bacteria, when the number of sequences from samples W226 and W202 was greater than 25,000, the number of OTUs did not differ between the samples; for archaea, when the number of sequences from sample W202 was greater than 10,000, the increase in OTUs exhibited a flat pattern, and when the number of sequences in the sample was greater than 20,000, the number of OTUs in W226 exhibited a gradual plateau pattern. Overall, the OTUs did not increase as the number of sequences increased, which indicated that the number of the obtained sequences in our study was sufficiently large to reflect the diversity of microorganisms (bacteria and archaea) contained in each sample, and the analysis results obtained based on these data reflected the actual composition of the microorganisms in each sample. All the OTUs of both bacteria and archaea could be taxonomically assigned to the phylum level. On the contrary, only 81.7% and 78.6% of bacterial OTUs were assigned to the genus level from the W226 and W202 samples, respectively. Furthermore, 89.2% and 78.2% of bacterial OTUs were assigned to the genus level from the W226 and W202 samples, respectively (Figure 2b).  
\begin{table}
\begin{tabular}{c c c c c c} \hline \hline \multirow{2}{*}{**Well No.**} & \multicolumn{5}{c}{**Ion Concentrations/(mg\(\cdot\)L\({}^{-1}\))**} \\ \cline{2-6}  & **Ca\({}^{2+}\)** & **Na\({}^{+}\)** & **K\({}^{+}\)** & **TN** & **TP** \\ \hline W202 & 11,600 & 10,300 & 81.9 & 20 & 0.50 \\ W226 & 3070 & 40,900 & 164.0 & 26 & 0.56 \\ \hline \hline \end{tabular}
\end{table}
Table 2: Dissolved ion content in the water samples.  
To reduce the impact of the number of obtained sequences of different samples on diversity analysis, an alpha diversity index was introduced to reflect OTU abundance at a consistent sequencing depth, which included the Chao1, ACE, Simpson, and Shannon indices (Table 3). The Chao1 and ACE indices focus on reflecting the richness of the community, whereas the Simpson and Shannon indices take the evenness of the community into account [29]. For bacteria, the Chao1 and ACE indices of the W226 sample were higher than those of the corresponding W202 sample, indicating that the richness of the bacterial community of the W226 sample was significantly higher than that of the W202 sample. However, both the Simpson and Shannon indices of bacteria in the production W226 sample were lower than those in the control W202 sample, which suggests that the community evenness of the W226 sample was lower than that of the W202 sample. One of the potential interpretations of this phenomenon is that the injected nutrients increased the community richness, but reduced the community evenness of bacteria in the production well W226. Therefore, several specific bacterial populations in the production well W226 were enriched significantly when compared to that in the control well W202. The Chao1, ACE, Shannon, and Simpson indices of the archaeal sequences from the W226 sample were all higher than those of the W202 sample. This result indicated that both the archaeal community richness and evenness were increased after flooding.