Metagenomic <scp>16S rDNA I</scp>llumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities

<jats:title>Summary</jats:title><jats:p>Sequencing of <jats:styled-content style="fixed-case">16S rDNA</jats:styled-content> polymerase chain reaction (<jats:styled-content style="fixed-case">PCR</jats:styled-content>) amplicons is the most common approach for investigating environmental prokaryotic diversity, despite the known biases introduced during <jats:styled-content style="fixed-case">PCR</jats:styled-content>. Here we show that <jats:styled-content style="fixed-case">16S rDNA</jats:styled-content> fragments derived from Illumina‐sequenced environmental metagenomes (<jats:styled-content style="fixed-case"><jats:italic><jats:sub>mi</jats:sub>tag</jats:italic></jats:styled-content>s) are a powerful alternative to <jats:styled-content style="fixed-case">16S rDNA</jats:styled-content> amplicons for investigating the taxonomic diversity and structure of prokaryotic communities. As part of the <jats:italic><jats:styled-content style="fixed-case">T</jats:styled-content>ara</jats:italic> <jats:styled-content style="fixed-case">O</jats:styled-content>ceans global expedition, marine plankton was sampled in three locations, resulting in 29 subsamples for which metagenomes were produced by shotgun Illumina sequencing (ca. 700 Gb). For comparative analyses, a subset of samples was also selected for <jats:styled-content style="fixed-case">R</jats:styled-content>oche‐454 sequencing using both shotgun (<jats:styled-content style="fixed-case"><jats:italic><jats:sub>m454</jats:sub>tag</jats:italic></jats:styled-content>s; 13 metagenomes, ca. 2.4 Gb) and 16S rDNA amplicon (<jats:styled-content style="fixed-case"><jats:italic><jats:sub>454</jats:sub>tag</jats:italic></jats:styled-content>s; ca. 0.075 Gb) approaches. Our results indicate that by overcoming <jats:styled-content style="fixed-case">PCR</jats:styled-content> biases related to amplification and primer mismatch, <jats:styled-content style="fixed-case"><jats:italic><jats:sub>mi</jats:sub>tag</jats:italic></jats:styled-content>s may provide more realistic estimates of community richness and evenness than amplicon <jats:styled-content style="fixed-case"><jats:italic><jats:sub>454</jats:sub>tag</jats:italic></jats:styled-content>s. In addition, <jats:styled-content style="fixed-case"><jats:italic><jats:sub>mi</jats:sub>tag</jats:italic></jats:styled-content>s can capture expected beta diversity patterns. Using <jats:styled-content style="fixed-case"><jats:italic><jats:sub>mi</jats:sub>tag</jats:italic></jats:styled-content>s is now economically feasible given the dramatic reduction in high‐throughput sequencing costs, having the advantage of retrieving simultaneously both taxonomic (<jats:styled-content style="fixed-case">B</jats:styled-content>acteria, <jats:styled-content style="fixed-case">A</jats:styled-content>rchaea and <jats:styled-content style="fixed-case">E</jats:styled-content>ukarya) and functional information from the same microbial community.</jats:p>