Micro-RIP -  Functional analysis of uncultivated microbes 
using radioisotope probing
(PI Marja tiirola, University of Jyväskylä, European Research Council (ERC) Consolidator project 2014-2019) 

"This project has received funding from the European Union’s Seventh Framework Programme for research, technological development and demonstration under grant agreement no 615246. The area of the activity is life sciences."

Metaomics are emerging fields in applied microbiology to study diversity and functions of microbial assemblages using high-throughput methodologies. Even if the currently available omics-approaches are excellent tools for generating new hypotheses, massive sequencing alone is not the most economical or informative way for resolving microbial functions or regulation in environmental samples. Environmental microbiology calls for more advanced research methods to study these topics.

The proposed project introduces an unconventional technology, radioisotope probing (RIP). This approach is based on the invention of radioactivity measurement via pH analysis. When the analysis of radioactivity is now combined with semiconductor sequencing, the technology offers two-dimensional analysis of millions of molecules on a sequencing chip. Actually, it is staggering that next-generation sequencing (NGS) plates are currently wasted after the sequencing effort. Hybridization of experimentally labelled RNA and radioactivity measurement would provide a second dimension for the sequencing analysis, facilitating various new applications in environmental microbiology, as well as potential applications for the needs of biochemistry and medical research.

The aim of this project is to develop and test RIP applications for studying regulation of microbial decomposition, which is the key question, when predicting the effects of climate change. It is hypothesized that more frequent flood, droughts and redox fluctuations can prime the biodegradation of boreal carbon stores. Regulation of microbial processes, including decomposition, includes 1) the structure of microbial communities, which is dependent of the etiology of the sample; 2) regulation of gene expression, and 3) mRNA processing and half-life. We aim to explore these mechanisms in community-level analysis, using novel applications of the RIP technology and interpreting the results of experimental manipulations by systems biology tools.

The project develops and tests three novel radioisotope probing applications to analyse functional diversity, transcriptional regulation and mRNA processing in microbial communities, especially focusing on prokaryotic species. Functional diversity of microbes utilizing model and complex substrates is studied in terrestrial and aquatic communities using time-series sampling and labelling experiments. Prevailing mechanisms in the cellular regulation of microbial communities are investigated using community-level methylation and regulatory RNA patterns. The effect of external stressor (redox fluctuations and toxicans) on these patterns is analysed using sequencing and RIP to reveal the mechanisms regulating the processes beyond mere community composition.

The project improves our understanding of the genetics and epigenetics of microbial communities, aiming to shed light on the burning question, how the decomposition of organic matter is regulated.