Long-Term Pollution Does Not Inhibit Denitrification and DNRA by Adapted Benthic Microbial Communities.

Denitrification in sediments is a key microbial process that removes excess fixed nitrogen, while dissimilatory nitrate reduction to ammonium (DNRA) converts nitrate to ammonium. Although microorganisms are responsible for essential nitrogen (N) cycling, it is not yet fully understood how these microbially mediated processes respond to toxic hydrophobic organic compounds (HOCs) and metals. In this study, we sampled long-term polluted sediment from the outer harbor of Oskarshamn (Baltic Sea), measured denitrification and DNRA rates, and analyzed taxonomic structure and N-cycling genes of microbial communities using metagenomics. Results showed that denitrification and DNRA rates were within the range of a national reference site and other unpolluted sites in the Baltic Sea, indicating that long-term pollution did not significantly affect these processes. Furthermore, our results indicate an adaptation to metal pollution by the N-cycling microbial community. These findings suggest that denitrification and DNRA rates are affected more by eutrophication and organic enrichment than by historic pollution of metals and organic contaminants.

High throughput shotgun sequencing of eRNA reveals taxonomic and derived functional shifts across a benthic productivity gradient.

Benthic macrofauna is regularly used in monitoring programmes, however the vast majority of benthic eukaryotic biodiversity lies mostly in microscopic organisms, such as meiofauna (invertebrates < 1 mm) and protists, that rapidly responds to environmental change. These communities have traditionally been hard to sample and handle in the laboratory, but DNA sequencing has made such work less time consuming. While DNA sequencing captures both alive and dead organisms, environmental RNA (eRNA) better targets living organisms or organisms of recent origin in the environment. Here, we assessed the biodiversity of three known bioindicator microeukaryote groups (nematodes, foraminifera, and ciliates) in sediment samples collected at seven coastal sites along an organic carbon (OC) gradient. We aimed to investigate if eRNA shotgun sequencing can be used to simultaneously detect differences in (i) biodiversity of multiple microeukaryotic communities; and (ii) functional feeding traits of nematodes. Results showed that biodiversity was lower for nematodes and foraminifera in high OC (6.2%-6.9%), when compared to low OC sediments (1.2%-2.8%). Dissimilarity in community composition increased for all three groups between Low OC and High OC, as well as the classified feeding type of nematode genera (with more nonselective deposit feeders in high OC sediment). High relative abundant genera included nematode Sabatieria and foraminifera Elphidium in high OC, and Cryptocaryon-like ciliates in low OC sediments. Considering that future sequencing technologies are likely to decrease in cost, the use of eRNA shotgun sequencing to assess biodiversity of benthic microeukaryotes could be a powerful tool in recurring monitoring programmes.

Quality of phytoplankton deposition structures bacterial communities at the water-sediment interface.

Phytoplankton comprises a large fraction of the vertical carbon flux to deep water via the sinking of particulate organic matter (POM). However, despite the importance of phytoplankton in the coupling of benthic-pelagic productivity, the extent to which its deposition in the sediment affects bacterial dynamics at the water-sediment interface is poorly understood. Here, we conducted a microcosm experiment in which varying mixtures of diatom and cyanobacteria, representing phytoplankton-derived POM of differing quality, served as inputs to sediment cores. Characterization of 16S rRNA gene of the bacterial communities at the water-sediment interface showed that bacterial α-diversity was not affected by POM addition, while bacterial ß-diversity changed significantly along the POM quality gradient, with the variation driven by changes in relative abundance rather than in taxon replacement. Analysing individual taxa abundances across the POM gradient revealed two distinct bacterial responses, in which taxa within either diatom- or cyanobacteria-favoured groups were more phylogenetically closely related to one another than other taxa found in the water. Moreover, there was little overlap in taxon identity between sediment and water communities, suggesting the minor role played by sediment bacteria in influencing the observed changes in bacterial communities in the overlying water. Together, these results showed that variability in phytoplankton-originated POM can impact bacterial dynamics at the water-sediment interface. Our findings highlight the importance of considering the potential interactions between phytoplankton and bacteria in benthic-pelagic coupling in efforts to understand the structure and function of bacterial communities under a changing climate.

Salinity drives meiofaunal community structure dynamics across the Baltic ecosystem.

Coastal benthic biodiversity is under increased pressure from climate change, eutrophication, hypoxia, and changes in salinity due to increase in river runoff. The Baltic Sea is a large brackish system characterized by steep environmental gradients that experiences all of the mentioned stressors. As such it provides an ideal model system for studying the impact of on-going and future climate change on biodiversity and function of benthic ecosystems. Meiofauna (animals < 1 mm) are abundant in sediment and are still largely unexplored even though they are known to regulate organic matter degradation and nutrient cycling. In this study, benthic meiofaunal community structure was analysed along a salinity gradient in the Baltic Sea proper using high-throughput sequencing. Our results demonstrate that areas with higher salinity have a higher biodiversity, and salinity is probably the main driver influencing meiofauna diversity and community composition. Furthermore, in the more diverse and saline environments a larger amount of nematode genera classified as predators prevailed, and meiofauna-macrofauna associations were more prominent. These findings show that in the Baltic Sea, a decrease in salinity resulting from accelerated climate change will probably lead to decreased benthic biodiversity, and cause profound changes in benthic communities, with potential consequences for ecosystem stability, functions and services.

The importance of benthic-pelagic coupling for marine ecosystem functioning in a changing world.

Benthic-pelagic coupling is manifested as the exchange of energy, mass, or nutrients between benthic and pelagic habitats. It plays a prominent role in aquatic ecosystems, and it is crucial to functions from nutrient cycling to energy transfer in food webs. Coastal and estuarine ecosystem structure and function are strongly affected by anthropogenic pressures; however, there are large gaps in our understanding of the responses of inorganic nutrient and organic matter fluxes between benthic habitats and the water column. We illustrate the varied nature of physical and biological benthic-pelagic coupling processes and their potential sensitivity to three anthropogenic pressures - climate change, nutrient loading, and fishing - using the Baltic Sea as a case study and summarize current knowledge on the exchange of inorganic nutrients and organic material between habitats. Traditionally measured benthic-pelagic coupling processes (e.g., nutrient exchange and sedimentation of organic material) are to some extent quantifiable, but the magnitude and variability of biological processes are rarely assessed, preventing quantitative comparisons. Changing oxygen conditions will continue to have widespread effects on the processes that govern inorganic and organic matter exchange among habitats while climate change and nutrient load reductions may have large effects on organic matter sedimentation. Many biological processes (predation, bioturbation) are expected to be sensitive to anthropogenic drivers, but the outcomes for ecosystem function are largely unknown. We emphasize how improved empirical and experimental understanding of benthic-pelagic coupling processes and their variability are necessary to inform models that can quantify the feedbacks among processes and ecosystem responses to a changing world.

Joint Toxicity of Cadmium and Ionizing Radiation on Zooplankton Carbon Incorporation, Growth and Mobility.

The risk of exposure to radioactive elements is seldom assessed considering mixture toxicity, potentially over- or underestimating biological and ecological effects on ecosystems. This study investigated how three end points, carbon transfer between phytoplankton and Daphnia magna, D. magna mobility and growth, responded to exposure to γ-radiation in combination with the heavy metal cadmium (Cd), using the MIXTOX approach. Observed effects were compared with mixture effects predicted by concentration addition (CA) and independent action (IA) models and with deviations for synergistic/antagonistic (S/A), dose-level (DL), and dose-ratio (DR) dependency interactions. Several patterns of response were observed depending on the end point tested. DL-dependent deviation from the IA model was observed for carbon incorporation with antagonism switching to synergism at higher doses, while the CA model indicated synergism, mainly driven by effects at high doses of γ-radiation. CA detected antagonism regarding acute immobilization, while IA predicted DR-dependency. Both CA and IA also identified antagonism for daphnid growth. In general, effects of combinations of γ-radiation and Cd seem to be antagonistic at lower doses, but synergistic at the higher range of the doses tested. Our results highlight the importance of investigating the effects of exposure to γ-radiation in a multistressor context.

Combined Effects from γ Radiation and Fluoranthene Exposure on Carbon Transfer from Phytoplankton to Zooplankton.

Risk assessment does not usually take into account mixtures of contaminants, thus potentially under- or overestimating environmental effects. We investigated how the transfer of carbon between a primary producer, Pseudokirchneriella subcapitata, and a consumer, Daphnia magna, is affected by acute exposure of γ radiation (GR) in combination with the polycyclic aromatic hydrocarbon fluoranthene (FA). We exposed D. magna to five concentrations of FA and five acute doses of GR as single contaminants and in nine binary combinations. We compared the observed data for three end points (incorporation of carbon by D. magna, D. magna ingestion rates, and growth) to the predicted joint effects of the mixed stressors based on the independent action (IA) concept. There were deviations from the IA predictions, especially for ingestion rates and carbon incorporation by D. magna, where antagonistic effects were observed at the lower doses, while synergism was seen at the highest doses. Our results highlight the importance of investigating the effects of exposure to GR in a multistressor context. In mixtures of GR and FA, the IA-predicted effects seem to be conservative as antagonism between the two stressors was the dominant pattern, possibly due to stimulation of cellular antioxidative stress mechanisms.

Thin-layer capping with granular activated carbon and calcium-silicate to remediate organic and metal polluted harbor sediment - A mesocosm study.

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.

Biotic interactions between benthic infauna and aerobic methanotrophs mediate methane fluxes from coastal sediments.

Coastal ecosystems dominate oceanic methane (CH4) emissions. However, there is limited knowledge about how biotic interactions between infauna and aerobic methanotrophs (i.e. CH4 oxidizing bacteria) drive the spatial-temporal dynamics of these emissions. Here, we investigated the role of meio- and macrofauna in mediating CH4 sediment-water fluxes and aerobic methanotrophic activity that can oxidize significant portions of CH4. We show that macrofauna increases CH4 fluxes by enhancing vertical solute transport through bioturbation, but this effect is somewhat offset by high meiofauna abundance. The increase in CH4 flux reduces CH4 pore-water availability, resulting in lower abundance and activity of aerobic methanotrophs, an effect that counterbalances the potential stimulation of these bacteria by higher oxygen flux to the sediment via bioturbation. These findings indicate that a larger than previously thought portion of CH4 emissions from coastal ecosystems is due to faunal activity and multiple complex interactions with methanotrophs.

Effects of bottom trawling and environmental factors on benthic bacteria, meiofauna and macrofauna communities and benthic ecosystem processes.

Soft sediment marine benthic ecosystems comprise a diverse community of bacteria, meiofauna and macrofauna, which together support a range of ecosystem processes such as biogeochemical cycling. These ecosystems are also fishing grounds for demersal species that are often caught using bottom trawling. This fishing method can have deleterious effects on benthic communities by causing injury or mortality, and through alteration of sediment properties that in turn influence community structure. Although the impacts of bottom trawling on macrofauna are relatively well studied, less is known about the responses of meiofauna and bacteria to such disturbances, or how bottom trawling impacts benthic ecosystem processes. Quantifying trawling impacts against a background of natural environmental variability is also a challenge. To address these questions, we examined effects of bottom trawling and a range of environmental variables (e.g. water chemistry and physical and biochemical surface sediment properties) on a) bacterial, meiofaunal and macrofaunal community structure and b) benthic ecosystem processes (nutrient fluxes, extracellular enzyme activities and carbon turnover and degradation rates). We also investigated the link between the benthic macrofauna community and the same ecosystem processes. While there was a significant effect of bottom trawling intensity on macrofaunal community structure, the same was not seen for bacterial or meiofaunal community composition, which were more affected by environmental factors, such as surface sediment properties. The labile component of the surface sediment carbon pool was higher at highly trawled sites. Carbon degradation rates, extracellular enzyme activities, oxygen fluxes and some nutrient fluxes were significantly affected by trawling, but ecosystem processes were also strongly linked to the abundance of key bioturbators (Macoma balthica, Halicryptus spinulosus, Scoloplos armiger and Pontoporeia femorata). Although benthic ecosystems were affected by a combination of trawling and natural variability, disentangling these showed that the anthropogenic effects were clearest on the larger component of the community, i.e. macrofauna composition, and on ecosystem processes related to sedimentary carbon.

Ebullition dominates methane emissions in stratified coastal waters.

Coastal areas are an important source of methane (CH4). However, the exact origins of CH4 in the surface waters of coastal regions, which in turn drive sea-air emissions, remain uncertain. To gain a comprehensive understanding of the current and future climate change feedbacks, it is crucial to identify these CH4 sources and processes that regulate its formation and oxidation. This study investigated coastal CH4 dynamics by comparing water column data from six stations located in the brackish Tvärminne Archipelago, Baltic Sea. The sediment biogeochemistry and microbiology were further investigated at two stations (i.e., nearshore and offshore). These stations differed in terms of stratification, bottom water redox conditions, and organic matter loading. At the nearshore station, CH4 diffusion from the sediment into the water column was negligible, because nearly all CH4 was oxidized within the upper sediment column before reaching the sediment surface. On the other hand, at the offshore station, there was significant benthic diffusion of CH4, albeit the majority underwent oxidation before reaching the sediment-water interface, due to shoaling of the sulfate methane transition zone (SMTZ). The potential contribution of CH4 production in the water column was evaluated and was found to be negligible. After examining the isotopic signatures of δ13C-CH4 across the sediment and water column, it became apparent that the surface water δ13C-CH4 values observed in areas with thermal stratification could not be explained by diffusion, advective fluxes, nor production in the water column. In fact, these values bore a remarkable resemblance to those detected below the SMTZ. This supports the hypothesis that the source of CH4 in surface waters is more likely to originate from ebullition than diffusion in stratified brackish coastal systems.

Linking prokaryotic genome size variation to metabolic potential and environment.

While theories and models have appeared to explain genome size as a result of evolutionary processes, little work has shown that genome sizes carry ecological signatures. Our work delves into the ecological implications of microbial genome size variation in benthic and pelagic habitats across environmental gradients of the brackish Baltic Sea. While depth is significantly associated with genome size in benthic and pelagic brackish metagenomes, salinity is only correlated to genome size in benthic metagenomes. Overall, we confirm that prokaryotic genome sizes in Baltic sediments (3.47 Mbp) are significantly bigger than in the water column (2.96 Mbp). While benthic genomes have a higher number of functions than pelagic genomes, the smallest genomes coded for a higher number of module steps per Mbp for most of the functions irrespective of their environment. Some examples of this functions are amino acid metabolism and central carbohydrate metabolism. However, we observed that nitrogen metabolism was almost absent in pelagic genomes and was mostly present in benthic genomes. Finally, we also show that Bacteria inhabiting Baltic sediments and water column not only differ in taxonomy, but also in their metabolic potential, such as the Wood-Ljungdahl pathway or the presence of different hydrogenases. Our work shows how microbial genome size is linked to abiotic factors in the environment, metabolic potential and taxonomic identity of Bacteria and Archaea within aquatic ecosystems.

Molecular diet analysis enables detection of diatom and cyanobacteria DNA in the gut of Macoma balthica.

Detritivores are essential to nutrient cycling, but are often neglected in trophic networks, due to difficulties with determining their diet. DNA analysis of gut contents shows promise of trophic link discrimination, but many unknown factors limit its usefulness. For example, DNA can be rapidly broken down, especially by digestion processes, and DNA provides only a snapshot of the gut contents at a specific time. Few studies have been performed on the length of time that prey DNA can be detected in consumer guts, and none so far using benthic detritivores. Eutrophication, along with climate change, is altering the phytoplankton communities in aquatic ecosystems, on which benthic detritivores in aphotic soft sediments depend. Nutrient-poor cyanobacteria blooms are increasing in frequency, duration, and magnitude in many water bodies, while nutrient-rich diatom spring blooms are shrinking in duration and magnitude, creating potential changes in diet of benthic detritivores. We performed an experiment to identify the taxonomy and quantify the abundance of phytoplankton DNA fragments on bivalve gut contents, and how long these fragments can be detected after consumption in the Baltic Sea clam Macoma balthica. Two common species of phytoplankton (the cyanobacteria Nodularia spumigena or the diatom Skeletonema marinoi) were fed to M. balthica from two regions (from the northern and southern Stockholm archipelago). After removing the food source, M. balthica gut contents were sampled every 24 hours for seven days to determine the number of 23S rRNA phytoplankton DNA copies and when the phytoplankton DNA could no longer be detected by quantitative PCR. We found no differences in diatom 18S rRNA gene fragments of the clams by region, but the southern clams showed significantly more cyanobacteria 16S rRNA gene fragments in their guts than the northern clams. Interestingly, the cyanobacteria and diatom DNA fragments were still detectable by qPCR in the guts of M. balthica one week after removal from its food source. However, DNA metabarcoding of the 23S rRNA phytoplankton gene found in the clam guts showed that added food (i.e. N. spumigena and S. marinoi) did not make up a majority of the detected diet. Our results suggest that these detritivorous clams therefore do not react as quickly as previously thought to fresh organic matter inputs, with other phytoplankton than large diatoms and cyanobacteria constituting the majority of their diet. This experiment demonstrates the viability of using molecular methods to determine feeding of detritivores, but further studies investigating how prey DNA signals can change over time in benthic detritivores will be needed before this method can be widely applicable to both models of ecological functions and conservation policy.

Temporal and spatial changes in benthic invertebrate trophic networks along a taxonomic richness gradient.

Species interactions underlie most ecosystem functions and are important for understanding ecosystem changes. Representing one type of species interaction, trophic networks were constructed from biodiversity monitoring data and known trophic links to assess how ecosystems have changed over time. The Baltic Sea is subject to many anthropogenic pressures, and low species diversity makes it an ideal candidate for determining how pressures change food webs. In this study, we used benthic monitoring data for 20 years (1980-1989 and 2010-2019) from the Swedish coast of the Baltic Sea and Skagerrak to investigate changes in benthic invertebrate trophic interactions. We constructed food webs and calculated fundamental food web metrics evaluating network horizontal and vertical diversity, as well as stability that were compared over space and time. Our results show that the west coast of Sweden (Skagerrak) suffered a reduction in benthic invertebrate biodiversity by 32% between the 1980s and 2010s, and that the number of links, generality of predators, and vulnerability of prey have been significantly reduced. The other basins (Bothnian Sea, Baltic Proper, and Bornholm Basin) do not show any significant changes in species richness or consistent significant trends in any food web metrics investigated, demonstrating resilience at a lower species diversity. The decreased complexity of the Skagerrak food webs indicates vulnerability to further perturbations and pressures should be limited as much as possible to ensure continued ecosystem functions.

Microbial functional genes are driven by gradients in sediment stoichiometry, oxygen, and salinity across the Baltic benthic ecosystem.

BACKGROUND: Microorganisms in the seafloor use a wide range of metabolic processes, which are coupled to the presence of functional genes within their genomes. Aquatic environments are heterogenous and often characterized by natural physiochemical gradients that structure these microbial communities potentially changing the diversity of functional genes and its associated metabolic processes. In this study, we investigated spatial variability and how environmental variables structure the diversity and composition of benthic functional genes and metabolic pathways across various fundamental environmental gradients. We analyzed metagenomic data from sediment samples, measured related abiotic data (e.g., salinity, oxygen and carbon content), covering 59 stations spanning 1,145 km across the Baltic Sea. RESULTS: The composition of genes and microbial communities were mainly structured by salinity plus oxygen, and the carbon to nitrogen (C:N) ratio for specific metabolic pathways related to nutrient transport and carbon metabolism. Multivariate analyses indicated that the compositional change in functional genes was more prominent across environmental gradients compared to changes in microbial taxonomy even at genus level, and indicate functional diversity adaptation to local environments. Oxygen deficient areas (i.e., dead zones) were more different in gene composition when compared to oxic sediments. CONCLUSIONS: This study highlights how benthic functional genes are structured over spatial distances and by environmental gradients and resource availability, and suggests that changes in, e.g., oxygenation, salinity, and carbon plus nitrogen content will influence functional metabolic pathways in benthic habitats. Video Abstract.

Diversity of larger consumers enhances interference competition effects on smaller competitors.

Competition between large and small species for the same food is common in a number of ecosystems including aquatic ones. How diversity of larger consumers affects the access of smaller competitors to a limiting resource is not well understood. We tested experimentally how species richness (0-3 spp.) of benthic deposit-feeding macrofauna changes meiofaunal ostracods' incorporation of fresh organic matter from a stable-isotope-labeled cyanobacterial bloom, using fauna from the species-poor Baltic Sea. Presence of macrofauna mostly decreased meiofaunal incorporation of bloom material, depending on the macrofauna species present. As expected, the species identity of macrofauna influenced the incorporation of organic matter by meiofauna. Interestingly, our results show that, in addition, species richness of the macrofauna significantly reduced meiofauna incorporation of freshly settled nitrogen and carbon. With more than one macrofauna species, the reduction was always greater than expected from the single-species treatments. Field data from the Baltic Sea showed a negative correlation between macrofauna diversity and meiofaunal ostracod abundance, as expected from the experimental results. We argue that this is caused by interference competition, due to spatial niche differentiation between macrofauna species reducing the sediment volume in which ostracods can feed undisturbed by larger competitors. Interference from macrofauna significantly reduces organic matter incorporation by meiofauna, indicating that diversity of larger consumers is an important factor controlling the access of smaller competitors to a limiting food resource.

Cyanophage Diversity and Community Structure in Dead Zone Sediments.

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.IMPORTANCE Cyanophages are viruses that target cyanobacteria and directly control their abundance via viral lysis. Cyanobacteria are known to cause large blooms in water bodies, substantially contributing to oxygen depletion in bottom waters resulting in areas called dead zones. Our knowledge of cyanophages in dead zones is very scarce, and so far, no studies have assembled partial cyanophage genomes and investigated their associated cyanobacteria in these dark and anoxic sediments. Here, we present the first study using DNA and RNA sequencing to investigate in situ diversity of cyanophages and cyanobacteria in dead zones. Our study shows that dead zone sediments contain different cyanophages compared to oxic sediments and suggest that these viruses are able to affect cyanobacterial photosystem and phosphate regulation. Furthermore, cyanophage-controlled lysis of cyanobacteria might also increase the turnover of carbon, phosphorus, and nitrogen in these oxygen-free environments at the bottom of the sea.

Phytoplankton settling quality has a subtle but significant effect on sediment microeukaryotic and bacterial communities.

In coastal aphotic sediments, organic matter (OM) input from phytoplankton is the primary food resource for benthic organisms. Current observations from temperate ecosystems like the Baltic Sea report a decline in spring bloom diatoms, while summer cyanobacteria blooms are becoming more frequent and intense. These climate-driven changes in phytoplankton communities may in turn have important consequences for benthic biodiversity and ecosystem functions, but such questions are not yet sufficiently explored experimentally. Here, in a 4-week experiment, we investigated the response of microeukaryotic and bacterial communities to different types of OM inputs comprising five ratios of two common phytoplankton species in the Baltic Sea, the diatom Skeletonema marinoi and filamentous cyanobacterium Nodularia spumigena. Metabarcoding analyses on 16S and 18S ribosomal RNA (rRNA) at the experiment termination revealed subtle but significant changes in diversity and community composition of microeukaryotes in response to settling OM quality. Sediment bacteria were less affected, although we observed a clear effect on denitrification gene expression (nirS and nosZ), which was positively correlated with increasing proportions of cyanobacteria. Altogether, these results suggest that future changes in OM input to the seafloor may have important effects on both the composition and function of microbenthic communities.

Effects of Recreational Boating on Microbial and Meiofauna Diversity in Coastal Shallow Ecosystems of the Baltic Sea.

Recreational boating can impact benthic ecosystems in coastal waters. Reduced height and cover of aquatic vegetation in shallow Baltic Sea inlets with high boat traffic have raised concerns about cascading effects on benthic communities in these ecosystems. Here, we characterized the diversity and composition of sediment-associated microbial and meiofaunal communities across five bays subjected to low and high degrees of boating activity and examined the community-environment relationships and association with bay morphometry. We found that recreational boating activity altered meiofauna alpha diversity and the composition of both micro- and meiobenthic communities, and there were strong correlations between community structure and morphometric variables like topographic openness, wave exposure, water surface area, and total phosphorous concentrations. Inlets with high boat traffic showed an increase of bacterial taxa like Hydrogenophilaceae and Burkholderiaceae. Several meiofauna taxa previously reported to respond positively to high levels of suspended organic matter were found in higher relative abundances in the bays with high boat traffic. Overall, our results show that morphometric characteristics of inlets are the strongest drivers of benthic diversity in shallow coastal environments. However, while the effects were small, we found significant effects of recreational boating on benthic community structure that should be considered when evaluating the new mooring projects. IMPORTANCE With the increase of recreational boating activity and development of boating infrastructure in shallow, wave-protected areas, there is growing concern for their impact on coastal ecosystems. In order to properly assess the effects and consider the potential for recovery, it is important to investigate microbial and meiofaunal communities that underpin the functioning of these ecosystems. Here, we present the first study that uses DNA metabarcoding to assess how benthic biodiversity in shallow coastal areas is impacted by recreational boating. Our study shows a relatively small, but significant, effect of recreational boating both on meiofauna alpha diversity and meiofauna and bacterial community composition. However, both meiofauna and bacterial community composition in shallow benthic habitats is mediated to a higher degree by abiotic variables, such as topographic openness, area or size of the inlets, and wave exposure. Despite the fact that the effects were small, such impacts on benthic biodiversity should be considered in the management of coastal shallow habitats.

Active DNRA and denitrification in oxic hypereutrophic waters.

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 microniches associated with abundant organic particles, but studies on nitrate reduction in coastal pelagic environments are scarce. Here, we report on 15N 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 O2). DNRA in the bottom water corresponded to 83% of whole-ecosystem DNRA (water + sediment), while denitrification was predominant in the sediment. Microbial taxa important for DNRA according to the metagenomic data were dominated by Bacteroidetes (genus Parabacteroides) and Proteobacteria (genus Wolinella), while denitrification was mainly associated with proteobacterial genera Pseudomonas, Achromobacter, and Brucella. The metagenomic and microscopy data suggest that these anaerobic 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.