## 3 Results
### Microbial Community Profile of the Samples from Production and Control Wells  
The microbial community profiles from the production and control wells were compared for the following two taxonomies: phylum and class. For bacteria (Figure 3), Proteobacteria was the predominant phylum, accounting for more than 80% of all bacterial  
Figure 2: Community diversity of each sample. Rarefaction curves of observed bacterial (**a**) and archaeal (**c**) OTUs for the control and sampling wells. Distribution of bacterial (**b**) and archaeal (**d**) OTUs at different classification levels. \begin{table}
\begin{tabular}{c c c c c c c c c} \hline \hline
**Microorganism** & **Well No.** & \begin{tabular}{c} **Qualified** \\ **Sequences** \\ \end{tabular} & \
\begin{tabular}{c} **Observed** \\ **OTUs** \\ \end{tabular} & **Chao1** & **ACE** & **Shannon** & **Simpson** &
\begin{tabular}{c} **Good’s** \\ **Average** \\ \end{tabular} \\ \hline Bacteria & W226 & 42,074 & 711 & 711.02 & 712.52 & 3.30 & 0.58 & 0.98 \\  & W202 & 40,795 & 499 & 500.00 & 500.00 & 4.14 & 0.76 & 0.97 \\ \hline Archaea & W226 & 66,428 & 445 & 473.66 & 498.15 & 4.88 & 0.92 & 0.97 \\  & W202 & 29,302 & 262 & 268.00 & 268.00 & 3.15 & 0.62 & 0.97 \\ \hline \hline \end{tabular}
\end{table} 
Table 3: The observed OTUs and alpha diversity indices of the samples. sequences retrieved from both samples. After nutrient treatment, the proportion of Firmicutes in the W226 sample increased to 12% compared to the 1.5% in W202, which indicated that bacteria from the Firmicutes phylum were enriched after flooding. At the class level, \(\varepsilon\)-Proteobacteria increased from 71.0% in the W226 sample to 60.4% in the W202 sample. In the control well W202, \(\delta\)-proteobacteria was the second dominant class, with an abundance of 21.6%, followed by Spirochaetes (4.2%) and \(\alpha\)-proteobacteria (4.0%). For the production well W226, the abundance of \(\delta\)-proteobacteria dropped sharply from 21.6% to 3.9% in W202, whereas another class of Proteobacteria-\(\gamma\)-proteobacteria rose from 1.3% to 7.0%. Moreover, Clostridia, which belongs to the Firmicutes phylum, increased to 10.6% and became the second most abundant class. The above results suggested that bacteria from three classes, \(\varepsilon\)-Proteobacteria, Clostridia, and \(\gamma\)-proteobacteria, were fully enriched through flooding, since the proportion of these three classes was more than 88% of all the sequences retrieved from well W226. The archaeal compositions of the production well W226 and control well W202 were similar at the phylum level (Figure 4). The Euryarchaeota phylum was the most abundant group, representing more than 95% of the retrieved sequences in both samples; most of these were methanogenic archaea. Some differences in the composition were also observed. For example, the abundance of the Thaumarchaeota phylum, which contains most of the ammonia-oxidizing archaea, increased from 0.13% in the W202 sample to 3.85% in the W226 sample. However, the archaeal composition in the production well W226 and control well W202 showed larger differences at the class level. The most extreme difference in the sample was the composition of Methanomicrobia, which accounted for 93.8% of the retrieved sequences in W202, but only 57.9% in W226. On the contrary, there was a significant increase in the abundance of Methanococci from 0.6% in the control well to 30.9% in the production well. Furthermore, some classes from the W202 sample, such as Thermococci, Archaeoglobi, Thaumarchaeota Incertae Sedis, and Aenigmarchaeota Incertae Sedis, could not be detected in the W226 samples. These results indicate that the richness and evenness of the archaeal community in W226 was higher than that of W202, which is consistent with the alpha diversity analysis. Figure 3: Community compositions of bacterial populations from the production and control well at the phylum and class level.