Suitability of six extraction methods for isolating a large quantity of high-quality RNA from New Zealand free-draining stony soil

ABSTRACT

High-quality RNA from soil is essential for investigating the functionality of soil microbial communities. The affordability the RNA-Seq method enables innovative studies of whole ecosystems but relies on a high quality and quantity of RNA. Different types of soils have different physicochemical properties, and therefore RNA extraction methods are usually investigated for each soil type separately. This study investigated six RNA extraction methods from a free-draining Balmoral/Lismore stony silt loam soil. Four commercial RNA extraction kits and two manual RNA extraction methods were assessed for their suitability for high throughput, purity, integrity, and quantity of RNA and its suitability for RNA-Seq applications, processing time, and toxicity. Three RNA extraction methods satisfied the majority of the criteria, thus allowing large-scale functional studies of soil microbiome.

KEYWORDS:

• RIN score
• homogenisation
• pasture
• stony
• silt

Acknowledgements

We thank Lincoln University for permission to collect samples from the Ashley Dene Research and Development Station, Carina Davis for sample collection, Leah Kearns, Manpreet K Dhami and one anonymous reviewer for helpful comments on the manuscript.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

This work was supported by the Ministry for Business, Innovation and Employment via Manaaki Whenua – Landcare Research’s Strategic Science Investment Fund, and by the National Science Challenge Our Land & Water via the Innovative Agricultural Microbiomes project A24085.