Using NGS technologies to understand methanogenic hydrocarbon degradation by an archaeal species

Introduction

The use of NGS technologies has revealed that in addition to their methogenic activity, the archaeal species Candidatus Methanoliparum can also break down hydrocarbons. This exciting discovery could have several important applications for recovering energy from subsurface oil reservoirs. The study is a collaborative effort led by Lei Cheng from the Institute of Biogas Science of the Ministry of Agriculture and Rural Affairs, Professor Li Meng of Shenzen University, and Professor Gunter Wegener of the Max Planck Institute of Marine Microbiology. These exciting findings were made possible by using NGS technology provided by Novogene.

Using NGS technologies, the researchers uncovered previously unknown facts about Candidatus Methanoliparum (Ca. Methanoliparum), a prokaryote that belongs to the domain Archea. These microorganisms are methanogens, which means that they produce methane as a metabolic byproduct under hypoxic conditions. The methanogenic degradation of hydrocarbons found in oil is usually carried out by hydrocarbon-degrading bacteria in partnership with methogenic archea, with both parties reaping the benefit. However, this study’s use of sequencing technologies has helped shed light on how these methanogens can work in isolation to degrade the hydrocarbons found in oil and what mechanims they use that set them aside from other methanogens. This research revealed that Ca. Methanoliparum contains and overexpresses genes that encode alkyl-coenzyme M reductases and methyl-coenzyme M reductases, genes involved in archeal multicarbon alkane and methane metabolism, demonstrating the critical role that Ca. Methanoliparum plays in oil hydrocarbon degradation.

Experimental Design

To understand the role these microrganisms have in oil hydrocarbon degradation, Ca. Methanoliparum was cultured from a subsurface oil reservoir, and samples were supplemented with the hydrocarbon hexadecane before sequencing was carried out to look at the functioning genes.
The results from the 16S RNA amplicon sequencing data demonstrate that Ca. Methanoliparum made up 75% of archaea found in hexadecane-degrading cultures. The high presence of Ca. Methanoliparum in the samples was confirmed by metagenomic sequencing, which showed that Ca. Methanoliparum accounted for approximately 30-40% of the microbial community in these cultures.

Once it was established that these cultures contained high numbers of Ca. Methanoliparum, metatranscriptomics was performed to quantify gene expression to assess what genes were functional and if they were related to methanogenic hexadecane degradation. The data demonstrated that Ca. Methanoliparum has a high number of transcripts related to genes involved in the methanogenic hexadecane degradation pathway. Genes encoding this pathway ranked among the top 10 – 25% of all genes transcribed by these archea. More specifically, Ca. Methanoliparum was shown to overexpress genes that encode both alkyl-coenzyme M reductases and methyl-coenzyme M reductases which are genes involved in multi-carbon and methan metabolism. This exciting finding demonstrates that Ca. Methanoliparum performs both the degradation of hexadecane and the formation of methane.

The Benefits of Novogene for the Study

Novogene is very honored to be selected as a reliable NGS service provider and provided 16S, metagenomics & macrotranscriptome sequencing technologies for this study. Novogene is a world leader in sequencing technologies and has vast experience with amplicon projects. New pipelines have been developed that enable Novogene to sequence amplicons using both short and long reads for 16S amplicons. In addition, Novogene’s metagenomic sequencing services offer researchers flexibility in their experimental design by providing analysis and clustering using both OUT (operational taxonomic units) and ASV(DADA2) pipelines.

Metatranscriptome sequencing enables researchers to look at the whole expression profile of transcripts at a given time using next-generation sequencing (NGS). This enables researchers to quantify changes in gene expression patterns in microbial communities over time which helps to improve our understanding of the structure and function of these communities and examine adaptive mechanisms.

Conclusions

The novel results from this collaborative study show that, unlike other archea, Ca. Methanoliparum can perform both the degradation of hydrocarbons and the formation of methane. The use of NGS sequencing provided key results that demonstrate that Ca. Methanoliparum makes up a significant portion of the microbial community. Metatranscriptomics confirmed that the top 10 – 25% of all transcribed genes were involved in pathways associated with hydrocarbon degradation and methane formation. These results indicate that Ca. Methanoliparum may play a crucial role in transforming hydricarbons into methane and would not have been possible without NGS technologies.

References

Zhou, Z., Zhang, C. J., Liu, P. F., Fu, L., Laso-Pérez, R., Yang, L., … & Cheng, L. (2021). Non-syntrophic methanogenic hydrocarbon degradation by an archaeal species. Nature, 1-6.