ABSTRACT
Another aspect of comparative biology that has benefited from advances in high- throughput sequencing is the field of environmental biology, which requires obtaining samples and identifying the microbes or other species that live in these samples. Essentially, any biome can be examined for its microbial makeup. Amplicon sequencing, microbiomes, metagenomics, and e-DNA are described in this chapter. Next-generation sequencing (NGS) approaches have been essential in advancing these kinds of studies. We describe the format and data processing steps that microbiome and eDNA data need for proper analysis. Storage of eDNA and microbiome short reads can be accomplished at NCBI Short Read Archives (SRA). The various kinds of software and data analyses than can be applied to eDNA and microbiome data are also described. Higher analytical goals of eDNA studies can include testing a specific ecological hypothesis, assessing the roles of species in different communities, community dynamics, and network reconstruction.
