Xiyuan River Metagenome (PRJCA011688)

The impacts of human-induced microbial homogenization may be underestimated by using the taxonomic diversity (e.g. 16S rRNA gene high-throughput sequencing), because microorganisms have enormous diversity and high functional redundancy which may lead to homogeneous function but heterogeneous taxonomic diversity. In this study, metagenomic and 16S rRNA gene high-throughput sequencing were used to investigate the planktonic microbial communities in a nitrogen-polluted subtropical river. We found that the human activities in downstream sites (nitrogen-polluted area) significantly decreased the a- and ß-diversity of total taxonomic communities (16S rRNA gene ASVs). However, this decrease was mainly contributed by the rare taxonomic communities, while the non-rare taxonomic communities did not show clearly decline. Furthermore, the fractions of observed metagenome-assembled genomes (MAGs) showed that the nitrifier and denitrifier MAGs accounted for 21.38% and 41.71% of the total observed MAGs abundance in downstream sites, but only accounted for 4.16% and 30.02% in upstream sites. This indicated that the downstream microbial communities were functional homogenization. Interestingly, human activities increased the taxonomic a- and ß-diversity of nitrifier and denitrifier MAGs in downstream sites, although the taxonomic a- and ß-diversity of total downstream MAGs showed decline. Overall, our findings bring a new insight in human-induced biotic homogenization and indicated that the biotic homogenization may have previously been underestimated by using the taxonomic diversity which may lead to negative consequences for ecosystem functional homogenization.