Background  Cable bacteria are filamentous sulphide-oxidisers capable of cm-scale electron transport. They are generally considered restricted to the upper few oxic–suboxic cm of marine sediments, where they couple sulphide oxidation to oxygen or nitrate reduction. Despite their influence on redox gradients, trace metal mobility, and nutrient cycling, their presence and activity in deeper anoxic sediment layers remain unknown. The presence and activity of marine cable bacteria (Candidatus Electrothrix) were investigated at four stations in Sweden and Finland, including deep vertical profiles of anoxic sediment layers, to assess their presence and activity under different environmental contexts.

Results  Using metatranscriptomic data for rRNA-based community profiling and gene expression combined with porewater geochemistry, evidence of abundant and active cable bacteria was found, peaking below 20 cm depth in deep anoxic sediment layers of Koljö Fjord on the Swedish West Coast. This zone coincided with elevated gene expressions related to sulphide oxidation (including sqr) and nitrate reduction (napA), as well as an abundant presence of sulphide and a sharp nitrate peak. Phylogenetic analyses revealed a diverse assemblage of Ca. Electrothrix includes several potential novel taxa. The co-occurrence of cable bacteria activity, sulphide availability, and a nitrate peak at depth suggests that these organisms may be supported by local nitrate production under anoxic conditions.

Conclusions  Our findings challenge the prevailing view that cable bacteria are restricted to shallow sediment horizons and demonstrate their activity and diversity in deep, anoxic layers. This expands the known ecological niche of cable bacteria and suggests that locally produced nitrate under anoxic conditions may facilitate their activity at depth. This discovery advances our understanding of ecology in anoxic marine environments, providing new insights into marine cable bacteria, sediment biogeochemistry, and analogues of early Earth microbial ecosystems.

Microbial communities in coastal sediments sustain key biogeochemical processes but face growing pressures from metal contamination and oxygen depletion. In this study, we derived the quantitative thresholds for effects of sediment pollutants on microbial diversity and their functions using the pollution-induced community tolerance (PICT) concept. Ecotoxicological EC10 thresholds for sediment microbiomes were calculated based on both biodiversity loss and functional gene expression measured through metatranscriptomics. A 10-day mesocosm experiment was conducted with sediments from a historically Cu-contaminated harbour (Oskarshamn) and a pristine reference site (Askö) in the Baltic Sea, exposed to five Cu doses (50–700 mg L⁻¹) under oxic and hypoxic conditions. Communities from Oskarshamn showed consistently higher EC10 threshold values for both diversity and Cu resistance/efflux gene expression, indicating functional pre-adaptation to long-term contamination. Under hypoxic condition, gene-based EC10 values were up to five times higher than under oxic conditions. Random Forest modelling further identified porewater Cu and dissolved oxygen as dominant predictors of Cu partitioning and microbial sensitivity. This study establishes, for the first time, a microbial species sensitvity distribution (SSD) framework linking geochemical drivers with molecular and community responses to derive site-specific EC10 thresholds for improved sediment risk assessment.

Coastal ecosystems play a crucial role in greenhouse gas (GHG) dynamics but are less studied than open oceans or terrestrial systems. This study measured concentrations of carbon dioxide (CO₂), methane (CH₄), and nitrous oxide (N₂O) in six shallow bays of the wider Stockholm Archipelago during spring (April) and autumn (September–October) 2024 using cavity ring-down spectroscopy combined with a water equilibration system. We explored how GHG levels relate to bay physical characteristics (i.e. topographic openness, sediment properties vegetation cover) and seawater properties (temperature, salinity, dissolved-oxygen saturation, chlorophyll-a, organic carbon, and nutrient concentrations), revealing significant seasonal variation of concentrations. Surface water pCO₂ ranged from 225–1372 ppm, CH₄ from 3.6–580 nmol L⁻¹, and N₂O from 8–20.8 nmol L⁻¹ with pCO₂ and CH₄ higher in autumn and N₂O higher in spring. CH₄ concentrations below 250 nmol L⁻¹ were negatively correlated with N₂O, while higher CH₄ levels showed a positive correlation, suggesting differences in the dominant sedimentary microbial pathways. Most bays acted as net GHG sinks in April and sources in September, with only one bay showing net source behaviour in both seasons. One bay that is subject to substantial human impacts (e.g. dredging, high nutrient loading, reduced vegetation cover) showed CO₂-equivalent CH₄ emissions that surpassed CO₂ uptake in this particular bay. CO₂-equivalent fluxes ranged from −195.2 to 793.6 mg CO₂ eq. m⁻² d⁻¹ (median: 131.5 mg CO₂ eq. m⁻² d⁻¹). This study is distinctive in simultaneously measuring all three major GHGs across multiple bays in relation to diverse environmental controls, offering a uniquely integrated understanding of coastal GHG dynamics. These findings highlight the variability and complexity of coastal ecosystems and demonstrate the importance of high-resolution measurements for accurate up-scaling of fluxes from these dynamic environments.

Methylated micropollutants such as naproxen and caffeine persist in wastewater effluents and accumulate in coastal sediments, including Hakefjorden, Skagerrak Sea, yet their anaerobic fate and role in methane emissions remain unresolved. In particular, it is unclear whether pollutant-derived methyl groups are routed mainly to CO₂ or can be transformed into CH₄ in sulfate-rich coastal sediments. Our primary objective was to resolve this routing by tracing the fate and microbiome responses to ¹³C-labeled naproxen and caffeine in sediment microcosms. We show that naproxen underwent rapid O-demethylation to desmethylnaproxen, with 90% ± 15.5% removed within 25 days, producing primarily ¹³CO₂ and some ¹³CH₄. Naproxen enriched methylotrophic and hydrogenotrophic Methanomicrobia, alongside Lokiarchaeia, Bathyarchaeia, and bacterial taxa like Eubacterium (Alkalibaculum A sporogenes) and Syntrophomonadaceae. Metagenomics revealed O-demethylation genes in enriched bacterial MAGs affiliated with uncultured Thermoanaerobaculia, indicating a bacterial demethylation potential. In contrast, caffeine was largely recalcitrant to degradation (∼85% ± 5% remaining), yet its ¹³C-labeled N-methyl groups fueled trace ¹³CH₄ production. These results show that methylated micropollutants can activate both bacterial and archaeal demethylation pathways in coastal sediment microbiomes.

Various morphotypes of large filamentous bacteria were isolated through micromanipulation from sulphidic sediment mats in the Bay of Concepción, central Chile. This study employed DNA amplification, whole-genome sequencing and bioinformatics analyses to unveil the taxonomic and genomic features of previously unidentified bacteria. The results revealed several novel genera, families and species, including three specimens belonging to Beggiatoales (Beggiatoaceae family), five to Desulfobacterales (Desulfobacteraceae family), two to the Chloroflexi phylum and one to the phylum Firmicutes. Metabolically, Beggiatoaceae bacteria exhibit a flexible and versatile genomic repertoire, enabling them to adapt to variable conditions at the sediment–water interface. All the bacteria demonstrated a mixotrophic mode, gaining energy from both inorganic and organic carbon sources. Except for the Firmicutes bacterium, all others displayed the ability to grow chemolithoautotrophically using H₂ and CO₂. Remarkably, the reverse tricarboxylic acid (rTCA) and Calvin–Benson–Bassham (CBB) pathways coexisted in one Beggiatoaceae bacterium. Additionally, various defence systems, such as CRISPR-Cas, along with evidence of viral interactions, have been identified. These defence mechanisms suggest that large filamentous bacteria inhabiting sulphidic sediments frequently encounter bacteriophages. Thus, robust defence mechanisms coupled with multicellularity may determine the survival or death of these large bacteria.