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Globally, the methane (CH4) efflux from the ocean to the atmosphere is small, despite high rates of CH4 production in continental shelf and slope environments. This low efflux results from the biological removal of CH4 through anaerobic oxidation with sulfate in marine sediments. In some settings, however, pore water CH4 is found throughout the sulfate-bearing zone, indicating an apparently inefficient oxidation barrier for CH4. Here we demonstrate that rapid sediment accumulation can explain this limited capacity for CH4 removal in coastal sediments. In a saline coastal reservoir (Lake Grevelingen, The Netherlands), we observed high diffusive CH4 effluxes from the sediment into the overlying water column (0.2-0.8 mol m-2 yr-1) during multiple years. Linear pore water CH4 profiles and the absence of an isotopic enrichment commonly associated with CH4 oxidation in a zone with high rates of sulfate reduction (50-170 nmol cm-3 d-1) both suggest that CH4 is bypassing the zone of sulfate reduction. We propose that the rapid sediment accumulation at this site (~ 13 cm yr-1) reduces the residence time of the CH4 oxidizing microorganisms in the sulfate/methane transition zone (< 5 years), thus making it difficult for these slow growing methanotrophic communities to build-up sufficient biomass to efficiently remove pore water CH4. In addition, our results indicate that the high input of organic matter (~ 91 mol C m-2 yr-1) allows for the co-occurrence of different dissimilatory respiration processes, such as (acetotrophic) methanogenesis and sulfate reduction in the surface sediments by providing abundant substrate. We conclude that anthropogenic eutrophication and rapid sediment accumulation likely increase the release of CH4 from coastal sediments.

Over the past few years, the scale of sensor networks has greatly expanded. This generates extended spatiotemporal datasets, which form a crucial information resource in numerous fields, ranging from sports and healthcare to environmental science and surveillance. Unfortunately, these datasets often contain missing values due to systematic or inadvertent sensor misoperation. This incompleteness hampers the subsequent data analysis, yet addressing these missing observations forms a challenging problem. This is especially the case when both the temporal correlation of timestamps within a single sensor and the spatial correlation between sensors are important. Here, we apply and evaluate 12 imputation methods to complete the missing values in a dataset originating from large-scale environmental monitoring. As part of a large citizen science project, IoT-based microclimate sensors were deployed for six months in 4400 gardens across the region of Flanders, generating 15-min recordings of temperature and soil moisture. Methods based on spatial recovery as well as time-based imputation were evaluated, including Spline Interpolation, MissForest, MICE, MCMC, M-RNN, BRITS, and others. The performance of these imputation methods was evaluated for different proportions of missing data (ranging from 10% to 50%), as well as a realistic missing value scenario. Techniques leveraging the spatial features of the data tend to outperform the time-based methods, with matrix completion techniques providing the best performance. Our results therefore provide a tool to maximize the benefit from costly, large-scale environmental monitoring efforts.

BackgroundThe International Maritime Organization (IMO) has set limits on sulphur content in fuels for marine transport. However, vessels continue to use these residual high-sulphur fuels in combination with exhaust gas cleaning systems (EGCS or scrubbers). Next to high sulphur, combustion of these fuels also results in higher emissions of contaminants including metals and PAHs. In scrubbers, exhaust gases are sprayed with water in order to remove SOx, resulting in acidic washwater with elevated contaminant concentrations discharged in the aquatic ecosystem. The number of vessels with scrubbers is increasing rapidly, but knowledge on washwater quality and impact are limited.ResultsThe scrubber washwater is found to be acidic with elevated concentrations of, e.g. zinc, vanadium, copper, nickel, phenanthrene, naphthalene, fluorene and fluoranthene. Model calculations on the effects of scrubber discharge under scenario HIGH (20% of vessels, 90th percentile concentrations) on the water quality in harbour docks showed a decrease in pH of 0.015 units and an increase in surface water concentrations for e.g. naphthalene (189% increase) and vanadium (46% increase).ConclusionsThe IMO established sulphur regulations to mitigate the impact of high sulphur emissions of the maritime sector. However, the use of open-loop scrubbers as an abatement technology will not reduce their contribution to ocean acidification. In addition, different types of scrubbers discharge washwater that is acutely toxic for aquatic organisms. However, washwater is diluted and the compounds for which a large increase in surface water concentrations was calculated in the Antwerp (Belgium) harbour docks (naphthalene > phenanthrene > fluorene > acenaphthene > vanadium) were not the compounds that already exceed their respective Water Quality Standards (WQS). Nevertheless, the WQS of several ‘priority hazardous substances’ (Water Framework Directive) are already exceeded in the docks and the Scheldt estuary. Since these hazardous substances are also identified in the washwater, scrubber washwater discharge should be discouraged in coastal waters and estuaries with large ecological value.

Background Cable bacteria are filamentous members of the Desulfobulbaceae family that are capable of performing centimetre‑scale electron transport in marine and freshwater sediments. This long‑distance electron transport is mediated by a network of parallel conductive fibres embedded in the cell envelope. This fibre network efficiently transports electrical currents along the entire length of the centimetre‑long filament. Recent analyses show that these fibres consist of metalloproteins that harbour a novel nickel‑containing cofactor, which indicates that cable bacteria have evolved a unique form of biological electron transport. This nickel‑dependent conduction mechanism suggests that cable bacteria are strongly dependent on nickel as a biosynthetic resource. Here, we performed a comprehensive comparative genomic analysis of the genes linked to nickel homeostasis. We compared the genome‑encoded adaptation to nickel of cable bacteria to related members of the Desulfobulbaceae family and other members of the Desulfobulbales order. Results Presently, four closed genomes are available for the monophyletic cable bacteria clade that consists of the genera Candidatus Electrothrix and Candidatus Electronema. To increase the phylogenomic coverage, we additionally generated two closed genomes of cable bacteria: Candidatus Electrothrix gigas strain HY10‑6 and Candidatus Electrothrix antwerpensis strain GW3‑4, which are the first closed genomes of their respective species. Nickel homeostasis genes were identified in a database of 38 cable bacteria genomes (including 6 closed genomes). Gene prevalence was compared to 19 genomes of related strains, residing within the Desulfobulbales order but outside of the cable bacteria clade, revealing several genome‑encoded adaptations to nickel homeostasis in cable bacteria. Phylogenetic analysis indicates that nickel importers, nickel‑binding enzymes and nickel chaperones of cable bacteria are affiliated to organisms outside the Desulfobulbaceae family, with several proteins showing affiliation to organisms outside of the Desulfobacterota phylum. Conspicuously, cable bacteria encode a unique periplasmic nickel export protein RcnA, which possesses a putative cytoplasmic histidine‑rich loop that has been largely expanded compared to RcnA homologs in other organisms. Conclusion Cable bacteria genomes show a clear genetic adaptation for nickel utilization when compared to closely related genera. This fully aligns with the nickel‑dependent conduction mechanism that is uniquely found in cable bacteria.

Seasonal oxygen depletion (hypoxia) in coastal bottom waters can lead to the release and persistence of free sulfide (euxinia), which is highly detrimental to marine life. Although coastal hypoxia is relatively common, reports of euxinia are less frequent, which suggests that certain environmental controls can delay the onset of euxinia. However, these controls and their prevalence are poorly understood. Here we present field observations from a seasonally hypoxic marine basin (Grevelingen, The Netherlands), which suggest that the activity of cable bacteria, a recently discovered group of sulfur-oxidizingmicroorganisms inducing long-distance electron transport, can delay the onset of euxinia in coastal waters. Our results reveal a remarkable seasonal succession of sulfur cycling pathways, which was observed over multiple years. Cable bacteria dominate the sediment geochemistry in winter, whereas, after the summer hypoxia,Beggiatoaceaemats colonize the sediment. The specific electrogenic metabolism of cable bacteria generates a large buffer of sedimentary iron oxides before the onset of summer hypoxia, which captures free sulfide in the surface sediment, thus likely preventing the development of bottom water euxinia. As cable bacteria are present in many seasonally hypoxic systems, this euxinia-preventing firewall mechanism could be widely active, and may explain why euxinia is relatively infrequently observed in the coastal ocean.

The quantitative mapping of food web flows based on empirical data is a crucial yet difficult task in ecology. The difficulty arises from the under-sampling of food webs, because most data sets are incomplete and uncertain. In this article, we review methods to quantify food web flows based on empirical data using linear inverse models (LIM). The food web in a LIM is described as a linear function of its flows, which are estimated from empirical data by inverse modeling. The under-sampling of food webs implies that infinitely many different solutions exist that are consistent with a given data set. The existing approaches to food web LIM select a single solution from this infinite set by invoking additional assumptions: either a specific selection criterion that has no solid ecological basis is used or the data set is artificially upgraded by assigning fixed values to, for example, physiological parameters. Here, we advance a likelihood approach (LA) that follows a different solution philosophy. Rather than singling out one particular solution, the LA generates a large set of possible solutions from which the marginal probability density function (mPDF) of each flow and correlations between flows can be derived. The LA is exemplified with an example model of a soil food web and is made available in the open-source R-software. Moreover, we show how stoichiometric data, stable isotope signatures, and fatty acid compositions can be included in the LIM to alleviate the under-sampling problem. Overall, LIM prove to be a powerful tool in food web research, which can bridge the gap between empirical data and the analysis of food web structures.

Background Cable bacteria are filamentous, sulphur-oxidizing microorganisms of the Desulfobulbaceae family that conduct electrons over centimetre-scale distances, coupling sulphide oxidation in deeper sediments to oxygen reduction near the surface. Geochemical evidence demonstrates high rates of aerobic sulphide oxidation in sediments inhabited by cable bacteria. Still, the underlying physiological and molecular basis of this electrogenic sulphur metabolism remains unresolved. Previous genomic analysis proposed that cable bacteria oxidize sulphide by reversing the canonical dissimilatory sulphite reduction (Dsr) pathway. Results We evaluated the sulphur metabolism of cable bacteria and related Desulfobulbales through comparative genomics, using an expanded set of 31 quality-filtered cable bacteria genomes, including 7 closed assemblies. We showed that cable bacteria encode a complete Dsr pathway, including the previously missing dsrD and dsrT genes, as well as a novel gene cluster with DsrOP homologues. All Dsr genes were classified as reductive-type, and phylogenetic analyses indicated a close affiliation with those of other Desulfobulbaceae (sulphate-reducing and/or sulphur-disproportionating bacteria). In addition, several other previously unrecognized sulphur-metabolism genes were identified in both cable bacteria and closely related Desulfobulbales , including a novel subtype of sulphide:quinone oxidoreductase (SQR), a putative rhodanese–persulphide dioxygenase fusion (Rho–PDO), and a YTD gene cluster (consisting of five genes) previously proposed to be characteristic of sulphur-disproportionation lineages. Structural predictions indicate that three uncharacterized YTD-encoded proteins assemble into a DsrEFH-like double heterotrimer, albeit with highly divergent, non-orthologous sequences. Finally, we integrated publicly available transcriptomic and proteomic data to confirm the in vivo expression of these genes, with expression patterns mirroring those of Desulfolithobacter dissulfuricans and Desulfurivibrio alkaliphilus . Conclusion Cable bacteria show minimal genetic divergence and little differential expression in their sulphur-metabolism genes compared to related organisms. Together, our findings challenge the idea that sulphide oxidation occurs via a reversed Dsr pathway. We propose a unique sulphur metabolism model for cable bacteria, in which a canonical reductive/disproportionating sulphur-metabolism repertoire (similar to Desulfolithobacter dissulfuricans and Desulfurivibrio alkaliphilus ) is coupled to net sulphide oxidation through long-distance electron transport. Key steps include sulphide oxidation to polysulphide by SQR, putative conversion to sulphite via Rho–PDO and/or proteins encoded in the YTD cluster, and subsequent disproportionation through the Dsr pathway, where sulphide re-enters the cycle. Net sulphide oxidation and sulphate production arise because electrons are efficiently drained via long-distance electron transport, effectively coupling the metabolism to oxygen reduction.

Recently, long filamentous bacteria have been reported conducting electrons over centimetre distances in marine sediments. These so-called cable bacteria perform an electrogenic form of sulfur oxidation, whereby long-distance electron transport links sulfide oxidation in deeper sediment horizons to oxygen reduction in the upper millimetres of the sediment. Electrogenic sulfur oxidation exerts a strong impact on the local sediment biogeochemistry, but it is currently unknown how prevalent the process is within the seafloor. Here we provide a state-of-the-art assessment of its global distribution by combining new field observations with previous reports from the literature. This synthesis demonstrates that electrogenic sulfur oxidation, and hence microbial long-distance electron transport, is a widespread phenomenon in the present-day seafloor. The process is found in coastal sediments within different climate zones (off the Netherlands, Greenland, the USA, Australia) and thrives on a range of different coastal habitats (estuaries, salt marshes, mangroves, coastal hypoxic basins, intertidal flats). The combination of a widespread occurrence and a strong local geochemical imprint suggests that electrogenic sulfur oxidation could be an important, and hitherto overlooked, component of the marine cycle of carbon, sulfur and other elements.

The geochemical cycles of iron and sulphur in marine sediments are strongly intertwined and give rise to a complex network of redox and precipitation reactions. Bioturbation refers to all modes of transport of particles and solutes induced by larger organisms, and in the present-day seafloor, bioturbation is one of the most important factors controlling the biogeochemical cycling of iron and sulphur. To better understand how bioturbation controls Fe and S cycling, we developed reactive transport model of a coastal sediment impacted by faunal activity. Subsequently, we performed a model sensitivity analysis, separately investigating the two different transport modes of bioturbation, i.e. bio-mixing (solid particle transport) and bio-irrigation (enhanced solute transport). This analysis reveals that bio-mixing and bio-irrigation have distinct—and largely opposing effects on both the iron and sulphur cycles. Bio-mixing enhances transport between the oxic and suboxic zones, thus promoting the reduction of oxidised species (e.g. iron oxyhydroxides) and the oxidation of reduced species (e.g. iron sulphides). Through the re-oxidation of iron sulphides, bio-mixing strongly enhances the recycling of Fe and S between their reduced and oxidised states. Bio-irrigation on the other hand removes reduced solutes, i.e. ferrous iron and free sulphide, from the sediment pore water. These reduced species are then reoxidised in the overlying water and not recycled within the sediment column, which leads to a decrease in Fe and S recycling. Overall, our results demonstrate that the ecology of the macrofauna (inducing bio-mixing or bio-irrigation, or both) matters when assessing their impact on sediment geochemistry. This finding seems particularly relevant for sedimentary cycling across Cambrian transition, when benthic fauna started colonizing and reworking the seafloor.

Over the last decades, hypoxia in marine coastal environments has become more and more widespread, prolonged and intense. Hypoxic events have large consequences for the functioning of benthic ecosystems. In severe cases, they may lead to complete anoxia and the presence of toxic sulfides in the sediment and bottom-water, thereby strongly affecting biological compartments of benthic marine ecosystems. Within these ecosystems, benthic foraminifera show a high diversity of ecological responses, with a wide range of adaptive life strategies. Some species are particularly resistant to hypoxia–anoxia, and consequently it is interesting to study the whole foraminiferal community as well as species-specific responses to such events. Here we investigated the temporal dynamics of living benthic foraminiferal communities (recognised by CellTracker™ Green) at two sites in the saltwater Lake Grevelingen in the Netherlands. These sites are subject to seasonal anoxia with different durations and are characterised by the presence of free sulfide (H2S) in the uppermost part of the sediment. Our results indicate that foraminiferal communities are impacted by the presence of H2S in their habitat, with a stronger response in the case of longer exposure times. At the deepest site (34 m), in summer 2012, 1 to 2 months of anoxia and free H2S in the surface sediment resulted in an almost complete disappearance of the foraminiferal community. Conversely, at the shallower site (23 m), where the duration of anoxia and free H2S was shorter (1 month or less), a dense foraminiferal community was found throughout the year except for a short period after the stressful event. Interestingly, at both sites, the foraminiferal community showed a delayed response to the onset of anoxia and free H2S, suggesting that the combination of anoxia and free H2S does not lead to increased mortality, but rather to strongly decreased reproduction rates. At the deepest site, where highly stressful conditions prevailed for 1 to 2 months, the recovery time of the community takes about half a year. In Lake Grevelingen, Elphidium selseyense and Elphidium magellanicum are much less affected by anoxia and free H2S than Ammonia sp. T6. We hypothesise that this is not due to a higher tolerance for H2S, but rather related to the seasonal availability of food sources, which could have been less suitable for Ammonia sp. T6 than for the elphidiids.