Linking phylotype & phenotype: genomic approach

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On way of linking microbial processes to specific organisms uses the genomic or metagenomic approach; fishing pieces of DNA out of environmental samples that contain both phylogenetic information (a copy of the ssu-rRNA gene) and phenotypic information (e.g. phototrophy, carbom fixation, whatever). Because both types of genes come from single pieces of DNA, they must be from the same organism, therefore linking the phylotype (from the rRNA sequence) and phenotype (from the metabolic gene) of that organism.

metagenomics
NCBI browser image of a portion of the EBAC31A08 sequence, showing the presence of both the rRNA operon (from which definitive phylogenetic information can be extracted) and the rhodopsin gene (from which phenotypic information can be inferred).