85 Contrasting methane, sulfide and nitrogen regimes in coastal sediment bioreactors the middle (month 7) and end (month 14.5-15.5) of the monitoring, respectively (Figure 1C). Overall, denitrification marker genes showed a higher coverage in the eutrophic system compared to the oligotrophic system (Figure 1C). eu. 7 14.5 15.5 eu. bf. 7 14.5 15.5 ol. 7 14.5 15.5 ol. bf. 7 14.5 15.5 sqr nrfA narG napA nirS nirK norB nosZ A B C Metagenomic coverage −1 0 1 2 Time (days) Time (days) NH4 + med. (mmol/day) NH4 + med. (µmol/day) NH4 + br. (µM) NH4 + br. (mM) eu. 7 14.5 15.5 eu. bf. 7 14.5 15.5 ol. 7 14.5 15.5 ol. bf. 7 14.5 15.5 sqr nrfA narG napA nirS nirK norB nosZ A B C Metagenomic coverage −1 0 1 2 Figure 1. A-B Ammonium added to the bioreactor (in mmol/day or in µmol/day) (medium or med.) and measured in situ in the bioreactor (br.) (in mM or µM) weekly over the course of the experiment in the eutrophic (A) and oligotrophic system (B). Both primary and secondary y-axis indicate the same scale but with different units C Z-score normalized gene coverage of selected functional markers for sulfide detoxification (sqr), Dissimilatory Nitrate Reduction to Ammonium (DNRA, nfrA) and denitrification (narG, napA, nirS, nirK, norB, nosZ). Note that the high and low coloring scheme sustains the green (high) and low (pink) pattern for all panels. Eutrophic (eu.) to oligotrophic (oli.) and biofilm (bf.). Substrate loading affects microbial community composition dominated by gammaproteobacterial groups First, we verified that the microbial community of the inoculum was representative of the original mixture from depths of 9–16 cm (referred to as “raw”) (see Supplementary Tables 2 - 3). By month 2, the bacterial community showed a marked difference compared to the inoculum in both systems, accompanied by a strong decrease in richness and diversity (Figure 2A-B, Supplementary Figure 4). The diversity decrease took longer in the archaeal community (Supplementary 3
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