# Changes in Soil Chemical Properties Due to Long-Term
## 3 Results
\begin{table}
\begin{tabular}{c c c c c c c c c c c} \hline \hline \multirow{2}{*}{**Treatment**} & **pH** & **EC** & **OM** & **TN** & **P\({}_{2}\)O\({}_{5}\)** & **K** & **Ca** & **Mg** & **DOC** & _mcrA_ & _pmoA_ \\ \cline{2-10}  & **(1:5)** & **(4S m\({}^{-1}\))** & **(\%)** & **(\%)** & **(mg kg\({}^{-1}\))** & & **(mg kg\({}^{-1}\))** & **Copy Number g\({}^{-1}\) Dry Soil** \\ \hline NF & 5.80 ab & 0.90 a & 2.1 b & 0.15 b & 28 c & 0.13 b & 5.7 b & 1.13 b & 53 b & \(1.20\times 10^{6}\) b & \(1.60\times 10^{6}\) b \\ NPKCom & 5.99 a & 1.23 a & 2.9 a & 0.22 a & 141 a & 0.53 a & 7.3 a & 1.71 a & 74 ab & \(3.47\times 10^{6}\) a & \(4.08\times 10^{6}\) a \\ Com & 5.64 b & 1.09 a & 2.7 a & 0.21 a & 63 b & 0.49 a & 6.5 ab & 1.22 b & 99 a & \(3.42\times 10^{6}\) a & \(4.31\times 10^{6}\) a \\ \hline \hline \end{tabular} Mean values in the same column followed by the same letter are not significantly different at 0.05% (Tukey’s, n = 9); NF—unfertilized control; NPKCom—chemical fertilizer (NPK)+compost; Com—compost; EC—electrical conductivity; OM—organic matter; TN—total nitrogen; DOC—dissolved organic carbon.  
\end{table} 
Table 2: Soil chemical properties and abundance of methane cycling related genes of long-term compost-fertilized paddy fields. contributed the greatest loading for PC1 followed by OM, Ca, and an equal contribution from \(mcrA\) and \(pmnoA\), with these variables mainly attributing to the 62.28% variability. For the PC2, pH and DOC gave the highest loading, contributing mainly to the 16.90% overall variability. The soil EC is the highest loading factor in PC3, which potentially gave an additional 10.40% overall variability. The PCA ordination plot showed the grouping of the soil treatments according to their soil chemical properties and the abundance of the \(mcrA\) and \(pmnoA\) genes (Figure 1). The distinct clustering of the Com treatments is partly influenced by DOC. The distinct clustering of the NPKCom treatment is party influenced by pH. The combined effects of the different soil chemical parameters (OM, TN, P, K, EC, Mg and Ca) and the gene abundance (\(mcrA\), \(pmnoA\)) add to the overall clustering of the different treatments under long-term compost fertilization. Similar clustering as shown through k-means clustering was also observed between the treatments due to soil chemical properties (Figure S1). The sequencing of genes derived from PCR-amplified genomic DNA from paddy fields with compost fertilization showed distantly and closely related reference sequences attributed to methanogenesis and methane oxidation. For the \(mcrA\) gene, all the sequences are distantly related to Methanobacteriaceae, which were also from environmental samples from the methanogenic archaeal community on the rice roots (Figure 2). The \(pmnoA\) gene sequences showed more diverse reference strains associated with methane oxidation (Figure 3). The gene sequences have high similarity with reference strains containing the particulate methane monooxygenase gene. The most abundant gene sequences are attributed to _Methylomonas_ sp. (8/20), followed by _Methylobacter_ sp. (5/20), _Methylocystis_ sp. (3/20), _Methylomicrobion_ sp. (1/20), each representative of _Methyloscrina_ sp. (1), and a distant relative of _Methylglobus_ sp. (1). One of the sequences (\(pmnoA\) 7) was unidentified.