Page 167 - Microbial methane cycling in a warming world From biosphere to atmosphere Michiel H in t Zandt

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4oC 10oC 4oC 10oC
Flavobacteriales Sphingobacteriales Methylococcales Nitrosomonadales Bacteroidetes vadinHA Anaerolineales Methylophilales Frankiales Burkholderiales Micrococcales Rhodobacterales Rhizobiales Caulobacterales KD4.96
Gracilibacteria Others
Figure 5. Phylogenetic classification of amplified bacterial 16S rRNA genes in the methanotrophic cultures after 62 days of incubation. The maximum taxonomy depth is on family level. Taxonomic groups with less than 2% abundance are grouped in others.
Analysis of single-end reads revealed the presence of the Soil Crenarchaeotic Group
All sequencing results presented above were obtained from Illumina paired-end data. However, as 16S rRNA gene amplicon sequencing depends on primer-based amplification, a bias can be introduced due to primer specificity. Amplification biases may result in single-end amplification. Therefore, single-end data were analyzed separately to quantify the bias for our datasets. The single-end sequences showed the same amount of OTUs as for paired-end data, with a total input of nearly 1 million single-end reads. Single-end data indicated the presence of the Soil Crenarchaeota Group (SCG), whereas paired-end data did not. The relative abundance of SCG in the archaeal single-end reads of the original core was 22%-48%. Their relative abundance ranged between 16% and 23% for the methanogenic enrichments amended with H2/CO2, H2/MeOH and the control. SCG relative abundance in acetate and TMA incubations was lower (3%-6%). For the aerobic methanotrophic cultures, between 39% and 69% of the archaeal single-end reads were affiliated to the SCG. Recently it was found that the forward primer Arc349F, mostly used for Illumina 16S rRNA gene sequencing of Archaea and also used in this study, only matches 53% of Archaea and missed almost all Crenarchaea and unclassified Archaea (Hugerth et al. 2014). Single-end data suggest that SCG might play an important role in this ecosystem.
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Relative abundance (%)