# Contrasting Methane, Sulfide and Nitrogen‐Loading Regimes in Bioreactors Shape Microbial Communities Originating From Methane‐Rich Coastal Sediment of the Stockholm Archipelago

## TL;DR

This study explores how microbial communities from methane-rich coastal sediment respond to different nutrient and sulfide conditions in bioreactors.

## Contribution

The study reveals novel microbial diversity and functional pathways in methane oxidation under fluctuating coastal conditions.

## Key findings

- Sulfide-dependent denitrification dominates under eutrophic conditions, while dissimilatory nitrate reduction to ammonium occurs under oligotrophic conditions.
- Methane oxidation is driven by Methylobacter and Methylomonas in eutrophic bioreactors, with more diverse methane-oxidizing communities under oligotrophic conditions.
- Novel putative copper-dependent membrane-bound monooxygenases (Cu-MMOS) are identified in MBAE14 and Rugosibacter genomes.

## Abstract

Coastal ecosystems are increasingly exposed to high nutrient loads and salinity intrusions due to rising seawater levels. Microbial communities, key drivers of elemental cycles in these ecosystems, consequently, experience fluctuations. This study investigates how the methane‐rich coastal sediment microbiome from the Stockholm Archipelago copes with high and low nitrogen and sulfide loading by simulating coastal conditions in two methane‐saturated anoxic brackish bioreactors. Over a year, the bioreactors were subjected to the same ratio of nitrate, ammonium and sulfide (2:1:1) under eutrophic or oligotrophic conditions and monitored using 16S rRNA gene amplicon and metagenomic sequencing. Sulfide was depleted in both conditions. Sulfide‐dependent denitrification was the predominant process in eutrophic conditions, whereas dissimilatory nitrate reduction to ammonium dominated under oligotrophic conditions. Methane oxidation was driven by Methylobacter and Methylomonas in eutrophic conditions, whereas a more diverse methane‐oxidising microbial community developed under oligotrophic conditions, which likely competed for nitrate with anaerobic methanotrophic archaea and the gammaproteobacterial MBAE14. Novel putative copper‐dependent membrane‐bound monooxygenases (Cu‐MMOs) were identified in MBAE14 and co‐enriched Rugosibacter genomes, suggesting the need for further physiological and genetic characterisation. This study highlights the importance of understanding coastal anoxic microbiomes under fluctuating conditions, revealing complex interactions and novel pathways crucial for ecosystem functioning.

In this study, microbial communities are enriched in brackish anoxic bioreactors with methane, sulfide, nitrate and ammonium. Novel diversity is identified and functionally analysed.