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Digging into the soil metagenome

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If you have a question about this talk, please contact Mustapha Amrani.

Mathematical, Statistical and Computational Aspects of the New Science of Metagenomics

Co-authors: Elisa Loza (Rothamsted Research), Tim Mauchline (Rothamsted Research), Andy Neal (Rothamsted Research), Ian Clark (Rothamsted Research)

Soil is the most biodiverse environment on earth, typically containing 109 bacterial cells from 106 different species per g. At most, 1% of these cells can grow in the laboratory; the majority remained obscure until the recent development of culture-independent methods. Usually taken for granted, soil is an invaluable resource providing essential ecosystem services as well as food to sustain the growing human population. More information on the genetic diversity of soil communities, in particular functional genes for the biological processes that underpin soil quality, is needed to establish the resilience of the system to perturbation. How many individuals and phylogenetic groups are potentially capable of performing a function? How many of these are active in particular conditions? Are there multiple possible combinations that provide similar functionality? Does the system always return to one combination after perturbation? This is especially relevant to arable agriculture where soils are deliberately manipulated to support crop rotations, during conversion of land to different management systems or with increasingly unpredictable climate change.

The advent of NGS -based metagenomics and metatranscriptomics with quantitative data on the presence and activity of phylogenetic and functional groups provides an unprecedented opportunity to describe and interpret soil biological systems. Long-term field experiments at Rothamsted Research enable comparison of the relative impact of different fertilizer inputs, crops and cultivation on microbial communities. Data amassed on these soils including 16S rRNA gene amplicons, full metagenomes and transcriptomes will be presented. At present, the large volumes of the datasets, the lack of appropriate analytical pipelines and relevant statistics is a constraint on processing and analysing the data. Nevertheless, it has generated information on which groups respond to nitrogen fertilizer, ploughing and changes in plant cover.

This talk is part of the Isaac Newton Institute Seminar Series series.

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