Functional Assignment of Metagenomic Data: Insights for the Microbial Nitrogen Cycle
Vikas Sharma, Gaurav Chetal, Todd D. Taylor and Tulika Prakash
from: Metagenomics of the Microbial Nitrogen Cycle: Theory, Methods and Applications (Edited by: Diana Marco). Caister Academic Press, U.K. (2014)
Nitrogen is an essential component of basic bio-molecules. Atmospheric nitrogen is inaccessible to living organisms because of its inert nature but it can be fixed into usable forms by nitrogen-fixing microbial communities. The microbial nitrogen cycle is a complex process which occurs through the coordinated functioning of several microbial genes, many of which have been identified primarily from cultivable microbes. However, for unculturable microbes belonging to the community of a given environment, metagenomics is used as an alternative approach to the classical methods of genomics, including polymerase chain reaction based gene identification and restriction fragment length polymorphism. A few metagenomic studies of terrestrial and aquatic environments, including some under moderate and extreme conditions, have been carried out which focus on nitrogen-fixing microbial communities and their functional diversities. These studies highlighted the roles of the resident microbes and their genes in different steps of the nitrogen cycle. Other studies have shown that the use of nitrogen-based fertilizers on agricultural soil has led to alterations in the microbial populations due to increased nitrogen content in the soil. Recently scientists identified novel anammox bacteria which are responsible for the loss of fixed nitrogen from agricultural soil. Presence of anammox along with other non-anammox bacteria indicates a coordinated behaviour of these microbes in the nitrogen-cycling process; however, the complete mechanism of anammox process is not clearly understood. To gain a better understanding of the anammox and other processes of nitrogen-cycling, metagenomic studies should be combined with metatranscriptomic and functional metagenomic approaches which investigate the functional dynamics of a given community read more ...