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Making Sense of Metagenomes

Final Report Summary - MASEM (Making Sense of Metagenomes)

The MASEM project focused on microbial communities involved in nitrate respiration. The turnover of nitrate plays a key role in all geochemical element cycling while its natural abundance is severely affected by human activity. The environmental fate of nitrate is currently unpredictable. The project aimed to deliver fundamental molecular understanding over the workings of natural selection for nitrate respiring communities. It aimed to express this understanding into useful, generalized metagenomic markers.
The project developed technology to study microbial communities for prolonged periods of time in the laboratory, at stable, environmentally relevant conditions. These communities were monitored by next generation DNA sequencing (metagenomics), combined with other -omics approaches. This enabled the reconstruction of near-complete genomes for each major community member and also enabled the reconstruction of the metabolism for each of these populations. The project also developed bio-informatic approaches to more effectively analyze these omics data in silico.
The project hypothesized that stable environmental conditions are a form of non-equilibrium thermodynamical steady states and would thus minimize entropy production. This hypothesis was falsified; it appeared that differences in substrate affinity governed communal metabolism which led to excess energy dissipation.
The studies led to observations of potentially high practical value. For example, in one study it was shown that differences between substrate affinities of the nitrite reductases of two different pathways for nitrate reduction was the key factor in the ecological selection for either pathway.
Most fixed nitrogen in the biosphere originates from anthropogenic sources such as the industrial production of ammonium fertilizer. Uptake of fertilizer by crops is only 17% efficient and 1-5% of fertilizer ammonium is converted biologically into nitrous oxide, a long-lived and powerful greenhouse gas. Microbial nitrification also converts a large portion of the fertilizer ammonium to nitrate in soil, where it subsequently runs off into surface waters and contributes to eutrophication in coastal zones. Nitrate emissions are partially remediated by denitrification in engineered environments such as waste-water treatment plants. If the end product of microbial nitrate reduction could be influenced by tuning environmental conditions this would yield significant ecological and economic benefits for both natural and engineered systems.
The MASEM project team showed which environmental conditions select for either process. Microbial generation time, supply of nitrite relative to nitrate and the carbon to nitrogen ratio were identified as key environmental controls that determine whether nitrate will be reduced to nitrogenous gas or ammonium.