Sediments polluted with hydrophobic organic contaminants (HOCs) and metals can pose environmental risks, yet effective remediation remains a challenge. We investigated a new composite sorbent comprising granular activated carbon (GAC) and a calcium-silicate (Polonite®, PO) for thin-layer capping of polluted sediment, with the aim to sequester both HOCs and metals. Box cores were collected in polluted Oskarshamn harbor, Sweden, and the sediments were treated with GAC and/or Polonite in a 10-week mesocosm study to measure endpoints ranging from contaminant immobilization to ecological side effects on native fauna and biogeochemical processes. The GAC particle size was 300–500 μm to reduce negative effects on benthic fauna (by being non-ingestible) and of biogenic origin (coconut) to have a small carbon footprint compared with traditional fossil ACs. The calcium-silicate was a fine-grained industrial by-product used to target metals and as a carrier for GAC to improve the cap integrity.

GAC decreased the uptake of dioxins (PCDD/Fs) in the bivalve Macoma balthica by 47 % and the in vitro bioavailability of PCB by 40 %. The composite cap of GAC + Polonite decreased sediment-to-water release of Pb < Cu < Ni < Zn < Cd by 42–98 % (lowest to highest decrease) and bioaccumulation of Cd < Zn < Cu in the worm Hediste diversicolor by 50–65 %. Additionally, in vitro bioavailability of Pb < Cu < Zn, measured using digestive fluid extraction, decreased by 43–83 %.

GAC showed no adverse effects on benthic fauna while Polonite caused short-term adverse effects on fauna diversity and abundance, partly due to its cohesiveness, which, in turn, can improve the cap integrity in situ. Fauna later recovered and bioturbated the cap. Both sorbents influenced biogeochemical processes; GAC sorbed ammonium, Polonite decreased respiration, and both sorbents reduced denitrification. In conclusion, the side effects were relatively mild, and the cap decreased the release and bioavailability of both HOCs and metals effectively, thus offering a promising sustainable and cost-effective solution to remediating polluted sediments.

Biogeochemical processes at the sediment–water interface are essential for the functioning of marine ecosystems. It is a central question in benthic ecology how these processes are controlled and mediated by biotic factors. Particularly, the role of meiobenthos, the most abundant and diverse faunal component in these systems, is little understood and requires more attention. In this chapter, we discuss the impact of meiofauna bioturbation inmarine sediments on significant mechanisms and processes in (a) carbon degradation and oxygen penetration, (b) sulfide dynamics, and (c) nitrogen cycling. Particularly in the growing hypoxic areas of the seafloor where meiofauna is often the only animal group present, the role and bioturbative activities of this central component of the benthos need further scrutiny regarding the decrease of oxygen and increase of toxic hydrogen sulfide. These knowledge gaps in the interaction between meiofauna and marine biogeochemistry are the background for our concluding outlines: We present current research frontiers in order to assess the role of meiofauna as regulators of geochemical processes and microbial activities. These goals require combination of quantitative and qualitative meiobenthos investigations with state-of-the-art experimental work.

Coastal and shelf sediments are central in the global nitrogen (N) cycle as important sites for the removal of fixed N. However, this ecosystem service can be hampered by ongoing deoxygenation in many coastal areas. Natural reoxygenation could reinstate anoxic sediments as sites where fixed N is removed efficiently. To investigate this further, we studied benthic N cycling in previously long-term anoxic sediments, following a large intrusion of oxygenated water to the Baltic Sea. During three campaigns in 2016-2018, we measured in situ sediment-water fluxes of ammonium (NH), nitrate (NO), oxygen (O₂), dissolved inorganic carbon, and NO reduction processes using benthic chamber landers. Sediment microprofiles of O₂, nitrous oxide (N₂O), and hydrogen sulfide were measured in sediment cores. At a permanently oxic station, denitrification to N₂ was the main NO reduction process. Benthic N₂O production appeared to be linked to nitrification, although no net N₂O fluxes from the sediment were detected. At newly oxygenated sites, dissimilatory NO reduction to NH comprised almost half of the total NO reduction. At these stations, the removal of fixed N was inefficient due to high effluxes of NH. Sedimentary N₂O production was associated with incomplete denitrification, accounting for 41-88% of the total denitrification rate. Microprofiling revealed algae aggregates as potential hotspots of seafloor N₂O production. Our results show that transient oxygenation of euxinic systems initiates benthic NO reduction, but may not lead to efficient sedimentary removal of fixed N. Instead, recycling of N compounds is promoted, which may accelerate the return to anoxia.

Human-induced expansion of oxygen-deficient zones can have dramatic impacts on marine systems and its resident biota. One example is the formation of the potent neurotoxic methylmercury (MeHg) that is mediated by microbial methylation of inorganic divalent Hg (Hg^II) under oxygen-deficient conditions. A negative consequence of the expansion of oxygen-deficient zones could be an increase in MeHg production due to shifts in microbial communities in favor of microorganisms methylating Hg. There is, however, limited knowledge about Hg-methylating microbes, i.e., those carrying hgc genes critical for mediating the process, from marine sediments. Here, we aim to study the presence of hgc genes and transcripts in metagenomes and metatranscriptomes from four surface sediments with contrasting concentrations of oxygen and sulfide in the Baltic Sea. We show that potential Hg methylators differed among sediments depending on redox conditions. Sediments with an oxygenated surface featured hgc-like genes and transcripts predominantly associated with uncultured Desulfobacterota (OalgD group) and Desulfobacterales (including Desulfobacula sp.) while sediments with a hypoxic-anoxic surface included hgc-carrying Verrucomicrobia, unclassified Desulfobacterales, Desulfatiglandales, and uncharacterized microbes. Our data suggest that the expansion of oxygen-deficient zones in marine systems may lead to a compositional change of Hg-methylating microbial groups in the sediments, where Hg methylators whose metabolism and biology have not yet been characterized will be promoted and expand. 

Thin-layer capping using activated carbon (AC) has been described as a cost-effective in situ sediment remediation method for organic contaminants. In this study, we compare the capping efficiency of powdered AC (PAC) against granular AC (GAC) using contaminated sediment from Oskarshamn harbor, Sweden. The effects of resuspension on contaminant retention and cap integrity were also studied. Intact sediment cores were collected from the outer harbor and brought to the laboratory. Three thin-layer caps, consisting of PAC or GAC mixed with clay, or clay only, were added to the sediment surface. Resuspension was created using a motor-driven paddle to simulate propeller wash from ship traffic. Passive samplers were placed in the sediment and in the water column to measure the sediment-to-water release of PAHs, PCBs, and metals. Our results show that a thin-layer cap with PAC reduced sediment-to-water fluxes of PCBs by 57 % under static conditions and 91 % under resuspension. Thin-layer capping with GAC was less effective than PAC, but reduced fluxes of high-molecular weight PAHs. Thin-layer capping with AC was less effective in retaining metals, except for Cd, which release was significantly reduced by PAC. Resuspension generally decreased water concentrations of dissolved cationic metals, perhaps due to sorption to suspended sediment particles. Sediment resuspension in treatments without capping increased fluxes of PCBs with log Kow > 7 and PAHs with log Kow 5 6, but resuspension reduced PCB and PAH fluxes through the PAC thin-layer cap. Overall, PAC performed better than GAC, but adverse effects on the benthic community and transport of PAC to non-target areas are drawbacks that favor the use of GAC.

1. Tube-dwelling chironomid larvae are among the few taxa that can withstand and thrive in the organic-rich sediments typical of eutrophic freshwater ecosystems. They can have multiple effects on microbial nitrogen (N) cycling in burrow environments, but such effects cease when chironomid larvae undergo metamorphosis into flying adults and leave the sediment.

2. Here we investigated the ecological role of Chironomus plumosus by exploring the effect of its different life stages (as larva and adult midge) on microbial N transformations in a shallow freshwater lagoon by means of combined biogeochemical and molecular approaches. Results suggest that sediment bioturbation by chironomid larvae produce contrasting effects on nitrate (NO3-)-reduction processes.

3. Denitrification was the dominant pathway of NO3- reduction (>90%), primarily fuelled by NO3- from bottom water. In addition to pumping NO3--rich bottom water within the burrows, chironomid larvae host microbiota capable of NO3- reduction. However, the contribution of larval microbiota is lower than that of microbes inhabiting the burrow walls. Interestingly, dinitrogen fixation co-occurred with NO3- reduction processes, indicating versatility of the larvae's microbial community.

4. Assuming all larvae (averaging 1,800 ind./m(2)) leave the sediment following metamorphosis into flying adults, we estimated a displacement of 47,787 mu mol of organic N/m(2) from the sediment to the atmosphere during adult emergence. This amount of particulate organic N is similar to the entire N removal stimulated by larvae denitrification over a period of 20 days.

5. Finally, the detection of N-cycling marker genes in flying adults suggests that these insects retain N-cycling microbes during metamorphosis and migration to the aerial and terrestrial ecosystems. This study provides evidence that chironomids have a multifaceted role in shaping the N cycle of aquatic ecosystems.

1. Meiofauna (invertebrates that pass through a 1-mm mesh sieve, but are retained on a 40-µm mesh) represent the most abundant and diverse animal group on Earth, but empirical evidence of their role in benthic respiration, production and carbon cycling across ecosystems is not well documented. Moreover, how meiofauna respond to changing oxygen conditions is poorly understood.

2. We further developed an incubation system, in which oxygen and temperature conditions are easily controlled and single meiofaunal nematode respiration is resolved in glass capillary tubes, using Clark-type oxygen microsensor. We performed the respiration measurements after exposing nematodes to different ambient oxygen concentrations, which resulted in 3–60 µM O2 during hypoxic and 80–210 µM O2 during oxic incubations in close proximity to the respective nematodes.

3. Individual nematode respiration rates ranged from 0.02 to 1.30 nmol O2 ind.−1 day−1 and were 27% lower during hypoxic than oxic incubations. Rates derived from established allometric relations were on average fourfold higher than our direct measurements.

4. The presented method is suitable for single nematode respiration measurements and can be adapted to a wide range of experimental conditions. Therefore, it can be used to assess meiofauna contribution to ecosystem processes and investigate species-specific responses to changing environmental conditions, for example, oxygen stress, increasing water temperature.

Since the start of synthetic fertilizer production more than a hundred years ago, the coastal ocean has been exposed to increasing nutrient loading, which has led to eutrophication and extensive algal blooms. Such hypereutrophic waters might harbor anaerobic nitrogen (N) cycling processes due to low-oxygen mi- croniches associated with abundant organic particles, but studies on nitrate reduction in coastal pelagic environments are scarce. Here, we report on 15 N isotope-labeling experiments, metagenome, and RT-qPCR data from a large hypereutrophic lagoon indicating that dissimilatory nitrate reduction to ammonium (DNRA) and denitrification were active processes, even though the bulk water was fully oxygenated ( > 224 μM O 2 ). DNRA in the bottom water corresponded to 83% of whole-ecosystem DNRA (water + sedi- ment), while denitrification was predominant in the sediment. Microbial taxa important for DNRA accord- ing to the metagenomic data were dominated by Bacteroidetes (genus Parabacteroides ) and Proteobac- teria (genus Wolinella ), while denitrification was mainly associated with proteobacterial genera Pseu- domonas, Achromobacter , and Brucella . The metagenomic and microscopy data suggest that these anaero- bic processes were likely occurring in low-oxygen microniches related to extensive growth of filamentous cyanobacteria, including diazotrophic Dolichospermum and non-diazotrophic Planktothrix . By summing the total nitrate fluxes through DNRA and denitrification, it results that DNRA retains approximately one fifth (19%) of the fixed N that goes through the nitrate pool. This is noteworthy as DNRA represents thus a very important recycling mechanism for fixed N, which sustains algal proliferation and leads to further enhancement of eutrophication in these endangered ecosystems.

Up to 20% of prokaryotic organisms in the oceans are estimated to die every day due to viral infection and lysis. Viruses can therefore alter microbial diversity, community structure, and biogeochemical processes driven by these organisms. Cyanophages are viruses that infect and lyse cyanobacterial cells, adding bioavailable carbon and nutrients into the environment. Cyanobacteria are photosynthesizing bacteria, with some species capable of N₂ fixation, which are known to form large blooms as well as resistant resting cells known as akinetes. Here, we investigated cyanophage diversity and community structure plus cyanobacteria in dead zone sediments. We sampled surface sediments and sequenced DNA and RNA, along an oxygen gradient—representing oxic, hypoxic, and anoxic conditions—in one of the world’s largest dead zones located in the Baltic Sea. Cyanophages were detected at all stations and, based on partial genome contigs, had a higher alpha diversity and different beta diversity in the hypoxic-anoxic sediments, suggesting that cyanobacteria in dead zone sediments and/or environmental conditions select for specific cyanophages. Some of these cyanophages can infect cyanobacteria with potential consequences for gene expression related to their photosystem and phosphate regulation. Top cyanobacterial genera detected in the anoxic sediment included Dolichospermum/Anabaena, Synechococcus, and Cyanobium. RNA transcripts classified to cyanobacteria were associated with numerous pathways, including anaerobic carbon metabolism and N₂ fixation. Cyanobacterial blooms are known to fuel oxygen-depleted ecosystems with phosphorus (so-called internal loading), and our cyanophage data indicate the potential for viral lysis of cyanobacteria which might explain the high nutrient turnover in these environments.

Seasonally nitrogen-limited and phosphorus-replete temperate coastal waters generally host dense and diverse diazotrophic communities. Despite numerous studies in marine systems, little is known about diazotrophs and their functioning in oligohaline estuarine environments. Here we applied a combination of nifH transcript and metagenomic shotgun sequencing approaches to investigate temporal shifts in taxonomic composition and nifH activity of size-fractionated diazotrophic communities in a shallow and mostly freshwater coastal lagoon. Patterns in active nifH phylotypes exhibited a clear seasonal succession, which reflected their different tolerances to temperature change and nitrogen (N) availability. Thus, in spring, heterotrophic diazotrophs (Proteobacteria) dominated the nifH phylotypes, while increasing water temperature and depletion of inorganic N fostered heterocystous Cyanobacteria in summer. Metagenomic data demonstrated four main N-cycling pathways and three of them with a clear seasonal pattern: denitrification (spring) → N2 fixation (summer) → assimilative NO3− reduction (fall), with NH4+ uptake into cells occurring across all seasons. Although a substantial denitrification signal was observed in spring, it could have originated from the re-suspended benthic rather than planktonic community. Our results contribute to a better understanding of the realized genetic potential of pelagic N2 fixation and its seasonal dynamics in oligohaline estuarine ecosystems, which are natural coastal biogeochemical reactors.