Bottom trawling is one of the most destructive fishing methods currently in use, with acute impacts on benthic ecosystems and chronic impacts on macrofauna communities. However, the long-term effects of chronic bottom trawling on smaller components of benthic communities and on sediment biogeochemistry are less well understood. To address this knowledge gap, we examined the effects of bottom trawling and environmental variables (bottom water and sediment properties) on alpha diversity and community structure of prokaryotes, meiofauna (including metazoans and foraminifera), and macrofauna over a spatial gradient of commercial bottom trawling, including a marine protected area which has been unfished for 12 years after >100 years of chronic trawling. Our results showed that chronic trawling affected the four organism groups in different ways. Prokaryote and foraminifera diversities were slightly higher at sites with higher trawling intensities, due to a greater number of rare species. Community composition was affected by trawling in all groups except meiofaunal metazoans. Sedimentary carbon played a significant role in shaping all four communities, as well as carbon degradation rates, but was not itself affected by trawling. Our results highlight that the complex interactions between environmental variables and disturbances from bottom trawling affect different components of the benthic fauna in different ways. Differences in organism size, population turnover rates, metabolic and ecological plasticity, feeding traits, and sensitivity to physical disturbance probably explain these differences.

Elevated methane concentrations in seawater have been reported over extensive areas of the East Siberian Arctic Seas, overlying thawing subsea permafrost. However, observed methane concentrations of the ephemeral seawater are highly variable across both space and time, compromised by both the timing of rare measurements and storm-driven exchanges to the atmosphere. Here, we applied time-integrated signals of the δ¹³C-composition of specific C₃₀ hopanoids (diploptene, hop-17(21)-ene, neohop-13(18)-ene and diplopterol) in surface sediments to trace aerobic methane oxidation as a proxy for enhanced methane cycling. Interpretations of hopanoids and possible sources were further assessed by 16S-rRNA analyses in the surface sediments. The consistently low δ¹³C-C₃₀ hopenes signals, ranging between −57.5 ‰ to −37.1 ‰ (n=23) across the Laptev Sea shelf indicated aerobic methane oxidation. This suggests ubiquitous methane cycling with the most pronounced intensities in the outer shelf region, broadly consistent with the observed methane concentrations. Notably, depleted δ¹³C-C₃₀ hopenes were also found in the mid-shelf region of the Laptev Sea, earlier thought to be an area of comparatively low methane cycling. High methane concentrations were also observed in the vicinity of the Lena River delta, yet the isotopically heavier δ¹³C-C₃₀ hopenes may here reflect a combination of lower aerobic methane oxidation, a greater relative abundance of type II methanotrophs (lower isotope fractionation during hopanoid production) and isotope dilution from non-methanotrophic sources. While this complicates the biomarker interpretation in the unique setting near the Lena River delta, the δ¹³C-C₃₀ hopenes were still much lower than δ¹³C-organic carbon, indicating aerobic methane oxidation and a clear methane cycling signal also in this regime. Taken together, the results unravel the wider cross-shelf patterns of enhanced methane cycling in the Laptev Sea through probing of methane fossilised in membrane lipids of aerobic methanotrophs, with the molecular-isotopic pattern being preserved in the sedimentary archive.

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.

Antimicrobial resistance (AMR) in marine environments poses intricate challenges due to the ecological complexity of microbial communities and environmental gradients. This study compares various antimicrobial resistance gene (ARG) annotation tools and databases, focusing on deep learning approaches versus traditional alignment-based methods, to evaluate their effectiveness in profiling the resistome of a complex marine ecosystem. Our report not only highlights the utility of deep learning methods for environmental applications but also proposes pathways for future improvements that can bridge the gap between comprehensive detection and clinically relevant risk interpretation.

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.

The effect of micropollutant discharges from increased river urbanization could disrupt planktonic food webs; however, the extent to which micropollutants impact these webs remains unstudied. In this study, downstream areas of the north and west tributaries of the Jiulong River (Fujian, China), which differ in their urbanization status (north: ∼25 % built land area; west: ∼65 %), were sampled for eleven consecutive days during both dry and wet seasons. We quantified micropollutant compounds and constructed a planktonic food web consisting of bacteria, algae, protozoa, and microzooplankton using DNA metabarcoding. Significantly higher concentrations of nutrients and micropollutants were detected in the more urbanized west tributary than in the north tributary. Structural equation modeling showed that the food webs in both tributaries were similarly affected by physico-chemical factors. However, micropollutants exerted a stronger influence on the food web in the west tributary than in the north tributary. Both direct and indirect effects of micropollutants on the planktonic food webs were identified in the west tributary. More importantly, the indirect (cascade) effect of micropollutants on consumers in the food web (protozoa and microzooplankton) was mediated by algae, not bacterial communities.

Background  Antimicrobial resistance is a major global health concern, with the environment playing a key role in its emergence and spread. Understanding the relationships between environmental factors, microbial communities, and resistance mechanisms is vital for elucidating environmental resistome dynamics. In this study, we characterized the environmental resistome of the Baltic Sea and evaluated how environmental gradients and spatial variability, alongside its microbial communities and associated functional genes, influence resistome diversity and composition across geographic regions.

Results  We analyzed the metagenomes of benthic sediments from 59 monitoring stations across a 1,150 km distance of the Baltic Sea, revealing an environmental resistome comprised of predicted antimicrobial resistance genes (ARGs) associated with resistance against 26 antibiotic classes. We observed spatial variation in its resistance profile, with higher resistome diversity in the northern regions and a decline in the dead zones and the southern areas. The combined effects of salinity and temperature gradients, alongside nutrient availability, created a complex environmental landscape that shaped the diversity and distribution of the predicted ARGs. Salinity predominantly influenced microbial communities and predicted ARG composition, leading to clear distinctions between high-saline regions and those with lower to mid-level salinity. Furthermore, our analysis suggests that microbial community composition and mobile genetic elements might be crucial in shaping ARG diversity and composition.

Conclusions  We presented that salinity and temperature were identified as the primary environmental factors influencing resistome diversity and distribution across geographic regions, with nutrient availability further shaping these patterns in the Baltic Sea. Our study also highlighted the interplay between microbial communities, resistance, and associated functional genes in the benthic ecosystem, underscoring the potential role of microbial and mobile genetic element composition in ARG distribution. Understanding how environmental factors and microbial communities modulate environmental resistomes will help predict the impact of future environmental changes on resistance mechanisms in complex aquatic ecosystems.

Meiofauna (all invertebrates smaller than 1 mm) are not only sensitive to environmental changes but also contribute significantly to nutrient cycling and energy transfer to higher trophic levels. Despite their importance, meiofauna distribution and ecology in the Siberian seas remain understudied. Here, we employ sediment environmental DNA metabarcoding to characterize meiofauna diversity across the unexplored Siberian seas. We show that meiofauna community structure is primarily driven by river discharge and coastal erosion, which are heavily influenced by climate change, rather than geographical distinctions between the seas. We observed higher meiofauna diversity in nearshore areas where river plumes promoted colonizer nematode communities that are resilient to disturbances. Yet, their dominance may lead to decreased ecosystem stability in the future. This study provides a valuable baseline for meiofauna diversity in remote Siberian seas undergoing rapid environmental change, which will be useful for assessing the future direction and pace of benthic ecological trajectories.

This paper identifies the top-50 priority questions for meiofaunal research, highlighting their critical roles in biogeochemical cycles and biodiversity. It calls for a balanced research agenda, international cooperation, and advances in technology to overcome current challenges and unlock meiofauna’s full potential.