Improving ecological insights from sequencing
Consequently, the majority of sequencing studies remain highly descriptive due to their design and the limitations of the nature of the data. Microbial ecology as a field should bridge microbiological isolation approaches and characterization of microbial communities, while reconciling the heterogeneity of soil systems in which microorganisms live. Improving the quantitative nature of sequencing studies, and applying amplicon sequencing of functional genes are two approaches toward expanding the insights researchers are able to gain into soil microbial communities. Recent studies are beginning to combine other forms of data with amplicon sequencing data to improve investigations of ecological patterns.
Combinations of amplicon sequencing and stable-isotope probing have been used as a viable option to link microbial activity to microbial abundance (54).
Other researchers have combined sequencing approaches in order to improve inferences made from amplicon sequencing data (55). Since vertical gains and losses of genetic information are common in prokaryotic world, there is a substantial probability of error associated with functional assignment of taxa based solely on 16S identities. To circumvent this recognized limitation, metagenomic and metatranscriptomics analyses are increasingly being used to describe the functional gene diversity and expression in various environmental samples, although both sequencing and bioinformatic efforts needed for gaining functionally relevant insights into ecosystem processes by these approaches are usually magnitudes higher than those needed for analyzing amplicon sequencing data.