The diversity of hydrogen-producing bacteria and methanogens within an in situ coal seam

Abstract

Background: Biogenic and biogenic-thermogenic coalbed methane (CBM) are important energy reserves for unconventional natural gas. Thus, to investigate biogenic gas formation mechanisms, a series of fresh coal samples from several representative areas of China were analyzed to detect hydrogen-producing bacteria and methanogens in an in situ coal seam. Complete microbial DNA sequences were extracted from enrichment cultures grown on coal using the Miseq high-throughput sequencing technique to study the diversity of microbial communities. The species present and differences between the dominant hydrogen-producing bacteria and methanogens in the coal seam are then considered based on environmental factors.

Results: Sequences in the Archaea domain were classified into four phyla and included members from Euryarchaeota, Thaumarchaeota, Woesearchaeota, and Pacearchaeota. The Bacteria domain included members of the phyla: Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, Acidobacteria, Verrucomicrobia, Planctomycetes, Chloroflexi, and Nitrospirae. The hydrogen-producing bacteria was dominated by the genera: Clostridium, Enterobacter, Klebsiella, Citrobacter, and Bacillus; the methanogens included the genera: Methanorix, Methanosarcina, Methanoculleus, Methanobrevibacter, Methanobacterium, Methanofollis, and Methanomassiliicoccus.

Conclusion: Traces of hydrogen-producing bacteria and methanogens were detected in both biogenic and non-biogenic CBM areas. The diversity and abundance of bacteria in the biogenic CBM areas are relatively higher than in the areas without biogenic CBM. The community structure and distribution characteristics depend on coal rank, trace metal elements, temperature, depth and groundwater dynamic conditions. Biogenic gas was mainly composed of hydrogen and methane, the difference and diversity were caused by microbe-specific fermentation of substrates; as well as by the environmental conditions. This discovery is a significant contribution to extreme microbiology, and thus lays the foundation for research on biogenic CBM.

Keywords: Biogenic; Coalbed methane; Diversity; Environment factors; Hydrogen-producing bacteria; Methanogens.

Fig. 1

The Venn diagram showing the number of shared and unique OTUs between different Groups for bacterial community (a) and archaea community (b). Group 1: C1, C7; Group 2: C2, C3, C6, C10; Group 3: C4, C9; Group 4: C5, C8

Fig. 2

Principal component analysis (PCA) base on OTUs for bacterial community (a) and archaeal community (b). The higher the degree of similarity between samples, the more aggregated in the graph

Fig. 3

Genus level taxonomic composition of the top 10 most abundant genus from 10 coal samples for the bacterial community. Total summed abundances of the remaining genus are indicated by the “other” group and unclassified

Fig. 4

Genus level taxonomic composition of the top 10 most abundant genus from four Groups for the bacterial community. Total summed abundances of the remaining genus are indicated by the “other” group and unclassified

Fig. 5

Genus level taxonomic composition of the top 10 most abundant genus from 10 coal samples for the archaeal community. Total summed abundances of the remaining genus are indicated by the “other” group and unclassified

Fig. 6

Genus level taxonomic composition of the top 10 most abundant genus from four Groups for the archaeal community. Total summed abundances of the remaining genus are indicated by the “other” group and unclassified

Fig. 7

The RDA (redundancy analysis) based on the level of bacteria (a) and archaea (b) with the coal bed environmental factors and coal characteristics. The length of the impact factor is longer, the contribution of the impact is higher, and conversely, when the impact factor is shorter, the contribution of the impact is lighter. When the environmental factor is acutely angled with the sample, there is a positive correlation, and when the environmental factor and the sample angle are obtuse, there is a negative correlation

Fig. 8

Chao1′s (dark grey) and Shannon’s (light grey) index for the four groups (Coal samples were divided into four groups according to the value of RO for the bacterial community (a) and archaea community (b), Group 1 represents a value less than 0.6%, Group 2 represents the value between 0.8 and 1.1%, Group 3 represents the value between 1.4 and 1.8%, Group 4 represents the value between 2.67 and 3.15%) derived from regions. 25th and 75th percentiles are indicated by the outer edges of boxes while the maximum and minimum values are showed by the ends of the whiskers and the median by a horizontal line within each box

Fig. 9

The trace metal elements content of Fe, Co, Ni in coal samples

Fig. 10

The location of coal samples