Genome (DNA) sequencing and metagenomics (e.g. bacterial environmental samples) are differ in a sense that in genome sequencing the DNA is derived from one particular organism (species), while in metagenomic study the DNA for sequencing is the mix of many genomes from different species and even viruses/phages.

The processing of the output and interpretation will be different in these two cases. In genome sequencing, researcher deals only with one genome, but there is a number of genomes in metagenomic study. Thus, in metagenomics it is often hard to tell species apart. There methods to identify species down to their phyla, for example. One can simply use rRNA data for that.

Dear I believe that is the same, total microrganisms can be do by sequ in ilumina plataform associated to culture techinics 

Genome (DNA) sequencing and metagenomics (e.g. bacterial environmental samples) are differ in a sense that in genome sequencing the DNA is derived from one particular organism (species), while in metagenomic study the DNA for sequencing is the mix of many genomes from different species and even viruses/phages.

The processing of the output and interpretation will be different in these two cases. In genome sequencing, researcher deals only with one genome, but there is a number of genomes in metagenomic study. Thus, in metagenomics it is often hard to tell species apart. There methods to identify species down to their phyla, for example. One can simply use rRNA data for that.

To answer your last question: 16S rDNA sequencing give all detetable species. Alternatively, single-cell genomics will also provide the samplable composition and identity mirobes in soil. both have their own limits and strengths.