Three ways ‘Omic’ technologies are lifting the lid on the soil microbiome

Omic technologies allow us to better understand organisms’ genes (genomics), RNA (transcriptomics), proteins (proteomics) and metabolites (metabolomics). A multidisciplinary approach using these technologies is particularly important to understanding the soil microbiome as it is an incredibly complex and dynamic community. Read more in this blog, part two of a series by Research Assistant for Genomics and Molecular Diagnostics, Dr Victoria Woolley.

1.Genomic technologies

Genomic technologies, in particular DNA sequencing, have revolutionised our understanding of the soil microbiome. DNA sequencing has allowed identification of microorganisms present in the soil, even when it is not possible to culture them. These technologies include amplicon sequencing of housekeeping genes (e.g. 16S and ITS genes), which can be performed using next generation sequencing (NGS) technologies including CHAP’s Illumina MiSeq, hosted at its partner NIAB.

Long-read sequencing can also be used in conjunction with amplicon amplification but generates longer DNA sequences that are more likely to be able to identify a species of microorganism. Nanopore sequencing is an example of a long-read sequencing technology and there are multiple platforms available that vary in size and throughput. For example, the MinION is a small, portable sequencing device, the GridION is a mid-range equivalent and the PromethION is the largest, high throughput long-read sequencer for genome sequencing experiments.

Long-read sequencing technology, as well as other high throughput NGS platforms, can also be used to perform metagenomics and provide a DNA fingerprint for a microbial community. This is the direct analysis of all DNA in an environmental sample to better understand the diversity of organisms as well as their functional diversity.


2. Transcriptomic technologies

Transcriptomics is the study of an organism’s transcriptome (all of its RNA transcripts), which gives information about gene expression. This is important for the soil microbiome because different conditions affect which genes are expressed and this may impact community structure and interactions with other microorganisms or interactions with larger organisms e.g. crop plants.

RNA-Seq is the technique used for measuring the transcriptome. It requires similar technologies to those described above, but instead of sequencing DNA, RNA is sequenced. RNA-Seq of the whole transcriptome usually requires higher throughput technologies than the targeted DNA sequencing technologies described above. Platforms such as the Illumina Hi-seq and PromethION are most suitable for this type of analysis.


 3. Proteomic technologies

Studying proteins (proteomics) is important in understanding the soil microbiome at integrated levels such as pathways and functional analysis. It can also be used to identify microorganisms based on the unique suite of proteins that they produce.

Mass spectrometry techniques including MALDI-TOF MS can be used to identify microorganisms based on their unique proteins present in the soil microbiome.  A major limitation of this analysis is that proteins degrade rapidly in the environment so samples for analysis need to be relatively fresh.

Other proteomics tools such as LC-MS/MS would be capable to characterise protein composition deeper in case protein content from a soil sample can be extracted with sufficient purity. This is often a limitation and highlights the need to use a multi-analytical approach for the soil microbiome research.

In the next article of this series, you can read about the importance of soil microbiome in sustainable agriculture.


To find out more information on how you can work with CHAP using some of the equipment described above, including the Illumina MiSeq, please contact enquiries@chap-solutions.co.uk .