Metagenomic and Metatranscriptomic Analysis of Methanogenesis from Coal Degradation by Compounded Microflora

doi:10.13560/j.cnki.biotech.bull.1985.2024-0050

Abstract

Abstract:

【Objective】Aromatic compound metabolism is considered a limiting factor for the generation of biogenic coalbed methane. To increase biomethane production from coal, the compounded microflora（CM）was obtained by compounding raw inoculum（RI）with ability of producing methane by degrading coal and phenanthrene-degrading functional microflora enriched from produced water. 【Method】A combined metagenome and metatranscriptome approach was used to analyze the differences in the community structure and metabolic pathways of CM and RI. 【Result】The methane yield of CM increased significantly by 114.55%. Compounding significantly increased the proportion of aromatics-degrading bacteria, such as Pseudomonas, accounting for 63.49%, and also increased the metabolic activity of the dominant bacteria as well as the synthesis and expression of the key enzymes in the metabolic pathway of aromatic compounds. Gene abundance of the aromatics-degrading pathway in CM was 1.65 times higher than that of RI, and the gene expression abundance was 6.34 times higher than that of RI（P<0.05）. The gene abundance and expression abundance of EC:1.13.11.2 were 2.24 and 62 times higher than those of RI, respectively. The increased expression abundance of these enzymes prompted the transformation of aromatic compounds to pyruvate. Compounding also enhanced the gene expression during the process of pyruvate metabolism to acetyl-CoA. The expression abundance of EC:1.2.4.1 reached 14.70-fold of the RI in CM. The gene expression abundance of the respective methanogenic pathways in CM was 2.66 to 7.10-fold of the RI. 【Conclusion】The compounding enriched the aromatics-degrading bacteria and significantly increased gene abundance, especially gene expression abundance, in the whole metabolic pathway of degrading aromatics to methane generation, resulting in the increased methane production.

Key words: coal bed methane, compounded microflora, aromatic compounds, metagenomic, metatranscriptomic

LIU Ding-rui, GUO Hong-guang, GONG Kai-yi. Metagenomic and Metatranscriptomic Analysis of Methanogenesis from Coal Degradation by Compounded Microflora[J]. Biotechnology Bulletin, 2024, 40(9): 270-281.

Figures/Tables 10

Fig. 1 Biomethane yield in CM and RI

Fig. 2 Distribution of RI and CM at domain level A: Distribution of RI and CM at the level of metagenomic domains; B: Distribution of RI and CM at the level of metatranscriptomic domains

Fig. 3 Microbial composition maps of three parallel groups of RI and CM samples at phylum（A）, bacterial genus（B）, and archaeal genus（C） MG: Metagenomic; MT: metatranscriptomic,the same below

Fig. 4 Absolute abundance of gene presence and expression between primary（A）and secondary（B）metabolic systems in bioreactor RI and CM The Y-axis scale refers to the logarithm of sequence abundance（sequences with annotations）for each category

Fig. 5 Differential analysis of RI and CM metabolic pathways on tertiary pathways A:Volcano plot of KEGG in metagenomic in tertiary pathways. B: Volcano plot of KEGG in metatranscriptomic in tertiary pathways. C: Comparison of abundance of coal-degrading methane-producing metabolic pathways in metagenomic. D: Comparison of abundance of coal-degrading methane-producing metabolic pathways in metatranscriptomic

Fig. 6 Aromatic compound metabolic pathways and plots of gene abundance and gene expression abundance The bar graphs refer to the logarithm of abundance and expression abundance for each gene, the same below

Fig. 7 Pyruvate metabolic pathways and plots of gene abundance and gene expression abundance

Table 1 Main production pathways of acetyl coenzyme A and abundance of genes and expression abundance of genes in the routes

模块Module	RI-MG	RI-MT	CM-MG	CM-MT	功能描述 Function
M00422	7578	1453.027	2252	6649.955	Acetyl-CoA pathway, CO₂ => acetyl-CoA
M00569	15455.33	114.273	34242	2434.298	Catechol meta-cleavage, catechol => acetyl-CoA / 4-methylcatechol => propanoyl-CoA
M00036	79514	704.217	98381.33	1709.537	Leucine degradation, leucine => acetoacetate + acetyl-CoA
M00013	10171.33	16.876	21789.33	957.577	Malonate semialdehyde pathway, propanoyl-CoA => acetyl-CoA
M00032	32807.33	343.8167	37454.67	2953.905	Lysine degradation, lysine => saccharopine => acetoacetyl-CoA
M00307	70726	1861.692	64192	3460.332	Pyruvate oxidation, pyruvate => acetyl-CoA
M00086	42996	780.0583	50578	1389.26	Beta-oxidation, acyl-CoA synthesis

Fig. 8 Methane metabolic pathways and plots of gene abundance and gene expression abundance

Table 2 Gene content and expression of each pathway of methane production

样本名称Sample	M00357	M00356	M00567	M00563
RI-MG	72573	48854	50116	46484
RI-MT	7123	1821	2040	1703
CM-MG	63086	28250	30324	28090
CM-MT	18937	12936	11077	10457

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