Genomic DNA was extracted from 0.5 to 1.0 g of sediment from each sample using the DNeasy PowerLyzer PowerSoil Kit (12855-100, QIAGEN) according to manufacturer protocol with minor modifications for the step of homogenization and cell lysis, i.e., cells were lysed by bead beating at 6 m s−1 for 45 s using a Bead Ruptor 24 (OMNI). Extraction blanks were performed alongside the samples to assess laboratory contamination during the extraction process. DNA concentrations were assessed fluorometrically using a Qubit 2.0 fluorometer (Thermo Fisher Scientific). The v3-4 region of the bacterial 16S rRNA gene and the v4-5 region of the archaeal 16S rRNA gene were amplified using the primer pairs SD-Bact-0341-bS17/SD-Bact-0785-aA21 and SD-Arch-0519-aS15/SD-Arch-0911-aA20, respectively (45 (link)), followed by post-PCR cleanup and indexing. Indexed amplicon samples were sequenced using Illumina’s v3 600-cycle (paired-end) reagent kit on an Illumina MiSeq benchtop sequencer (Illumina Inc.) after all DNA extraction blanks and PCR reagent blanks were confirmed for negative amplification. Raw sequences were quality controlled and further processed to construct an ASV table. Detailed methods for PCR conditions, amplicon cleanup, indexing, sequence processing, ASV taxonomy assignment, estimation of alpha and beta diversity, and associated statistical analyses are described in SI Appendix.