Fig. 2.

Phylogenomic trees of MAGs affiliated with the Syntrophomodaceae and Methanocellaceae and linear correlation graphs showing their NPs-induced metagenomic abundance increases in the black soil and the red soil. a Phylogenomic trees of MAGs that were recovered from black and red soils and exhibited significant changes in their metagenomic abundance between the different treatments (CK, 0.5% NPs, and 5% NPs). Multiple sequence alignments of 120 bacterial and 122 archaeal marker genes by GTDB-Tk were used to construct the phylogenomic trees of bacteria and methanogens, respectively. The maximum-likelihood phylogenies were calculated for the multiple sequence alignments (MSAs) in the format of an IQ-TREE using the LG + F + R10 model. b Graphs showing the significant correlation between the NPs-induced metagenomic abundance increases of MAGs affiliated with the Syntrophomodaceae (y-axis) and Methanocellaceae (x-axis). The correlation analysis of Syntrophomonadaceae and Methanocellaceae MAGs did not involve dereplication, because our focus was on the genomic variations among the taxa of interest. “***” means P < 0.001