Mots-Clés

Single-cell omics phylogenomics population genomics metagenomics

Description

Within the burning issue of how to feed the world during the next decades, soil acidification is a growing problem worldwide putting at risk agricultural sustainability. This soil acidification is accelerated by intensive farming and is known to increase metals and mineral toxicities while limiting P, K, and Mn bioavailability. Thus, soil acidification limits crop productivity in agricultural soils. Effects on soil microorganisms have also been evidenced, especially changes in the microbial community composition. Thus, it is also the plant microorganisms’ symbiotic reservoir that is likely to be affected by soil acidification and ultimately the functions supported by these microorganisms. For generalist microorganisms able to live across a pH gradient, mutations syndrome (i.e. set of mutations similarly modifying one or more functions between organisms) is expected related to this persistent environmental pressure.

Microbial population analyses from environmental samples are rare because of technical difficulties and, to our knowledge, the hypothesis of a mutation syndrome has never been assessed. Elsewhere, the analyses will allow predicting putative functions which would possibly lead to the prediction of changes in soil-based ecosystem supporting functions.

To address these hypotheses, a revolutionary approach to directly assess the individual cells’ genomic variations and the use of a long-term established pH gradient are both needed.

The experimental field station is located in Aberdeen, Scotland, where the soil acidity has been manipulated for 60+ years with crop rotation. The soil has been sampled last spring. Intact bacterial cells were extracted from the soil with a pH of 4.5, 6, and 7.5 and individually sequenced (at the whole genome scale).

The goals of this project are the following:

• to assess the genetic variation at the genome scale to test the prediction of an existing mutation syndrome
• at the community level, to assess changes in the supported ecological functions

The internship is inserted within a bigger project. The internship will be supervised by 2 young experts (one post-doctoral researcher and one PhD student).