Bacterial diversity in subbituminous coal and soil from coal mine of South Sumatra, Indonesia

Coal and soil around coal seam environment provide potential factors that support bacterial life. Study of environmental metagenome to determine relationship among the bacteria that make up the community in coal and soil layers is reported. DNA extractions were performed in three different methods, namely direct extraction, filtration, and filtration with blending. The DNA of coal and soil samples were subject to PCRamplification to get V5-V6 16S rRNA gene fragments, then separated by denaturing gradient gel electrophoresis (DGGE). Results showed that the indirect methods are advantageous and can detect more bands compared to the direct method. Among the samples tested, a high number of bacterial ribotypes (Shannon diversity index), but low evenness of the bacterial community were observed in the coal samples. Cluster analysis of DGGE bands showed that the coal mixed soil clustered separate from its parent, the coal seam and the soil samples. Phylogenetic trees of their sequences showed that the coal boomed more Firmicutes and Actinobacteria compared to the soil samples. It confirmed that the physico-chemical properties of soil strongly influence evolutionary distance of coal and soil bacteria though they are separated by little physical distance. This is the first report in which the disturbed coal which is represented by coal mixed soil was not artificially reconstructed as a microcosm, and is in a natural situation in which the virgin coal seam is compared to the adjacent virgin soil layers and soil mixed coal as the disturbed soil.

煤系地层周围煤与土壤环境提供了支持细菌生命存在的潜在因素。本研究报道了对煤与土壤层中构成群落细菌之间关系的环境宏基因组学研究。DNA提取采用三种不同的方法进行，即直接提取、过滤以及混合过滤。煤与土壤样本的DNA经过PCRamplification获得V5-V6 16S rRNA基因片段，随后通过变性梯度凝胶电泳（DGGE）进行分离。结果显示，相较于直接方法，间接方法具有优势，能够检测到更多条带。在所测试的样本中，煤样中观察到细菌表型多样性指数（Shannon多样性指数）较高，但细菌群落的均匀度较低。DGGE条带的聚类分析表明，煤混土壤与母体煤系地层及土壤样本聚类分离。其序列的进化树显示，与土壤样本相比，煤中富集了更多厚壁菌门（Firmicutes）和放线菌门（Actinobacteria）。这证实了土壤的物理化学性质强烈影响了煤与土壤细菌的进化距离，尽管它们之间仅有微小的物理距离。这是首次报告，其中被扰动的煤，以煤混土壤为代表，并未作为人工微生态系统进行重建，而是处于自然状况中，其中原始煤系地层与相邻的原始土壤层以及土壤混煤被作为扰动的土壤。