Supplemental Note 1 Quality control and preparation for analyses in QIIME: 1) Pair forward and reverse files using PEAR (pear-0.9.10-bin-64) 2) Trim paired files using Trimmomatic (trimmomatic-0.36.jar) 3) Convert paired and trimmed .fastq to .fasta using the custom code: cat [input .fastq] | paste Ð - - - | cut -f 1,2 | sed 's/^/>/'| tr "\t" "\n" >[output .fasta] 4) Validate tab-delimited mapping file using Ôvalidate_mapping_file.pyÕ 5) Generate meta-.fasta files using Ôadd_qiime_labels.pyÕ 6) Detect chimeras using usearch and the Ôrdp_gold.faÕ database from the meta-.fasta (called, Ôcombined_seqs.fnaÕ). 7) Filter chimeras using Ôfilter_fasta.pyÕ 8) Pick OTUs with a 99% clustering using Ôpick_open_reference_otus.pyÕ and the Ôsilva_132_99_16S.fnaÕ database 9) Filter OTUs with <10 reads and ÔunassignedÕ using Ôfilter_otus_from_otu_table.pyÕ 10) Determine rarefaction depth using Ôbiom summarize-tableÕ 11) Rarefaction depth was visualized using Ôalpha_rarefaction.pyÕ Community-level dynamics: 12) All beta diversity via PCoA were calculated using Ôjackknifed_beta_diversity.pyÕ 13) Two-dimensional PCoA were created from the ÔpcoaÕ sub-directory of the Ôjackknifed_beta_diversity.pyÕ output using Ômake_2d_plots.pyÕ 14) Alpha diversity estimates were calculated using Ôalpha_diversity.pyÕ 15) Filtered .biom tables for beta diversity analyses using sub-sets of samples were split using Ôsplit_otu_table.pyÕ Composition of the bacterial community: 16) Community composition plots were generated using Ôsummarize_taxa_through_plots.pyÕ 17) Differentially abundant OTUs were determined using Ôdifferential_abundance.pyÕ using ÔDESeq2_nbinomÕ and dark-dark as ÔxÕ and light-dark as ÔyÕ Shared taxa between LD and DD: 18) Core bacterial communities were determined using Ôcompute_core_microbiome.pyÕ 19) Beta diversity comparisons were performed using Ôjackknifed_beta_diversity.pyÕ and statistics were completed using Ôcompare_categories.pyÕ 20) Community composition plots of the ÔcoreÕ bacterial community were generated using Ôsummarize_taxa_through_plots.pyÕ