Solid phase speciation controls copper mobilisation from marine sediments by methanobactin

Although marine environments represent huge reservoirs of the potent greenhouse gas methane, they currently contribute little to global net methane emissions. Most of the methane is oxidized by methanotrophs, minimizing escape to the atmosphere. Aerobic methanotrophs oxidize methane mostly via the copper (Cu)-bearing enzyme particulate methane monooxygenase (pMMO). Therefore, aerobic methane oxidation depends on sufficient Cu acquisition by methanotrophs. Because they require both oxygen and methane, aerobic methanotrophs reside at oxic-anoxic interfaces, often close to sulphidic zones where Cu bioavailability can be limited by poorly soluble Cu sulphide mineral phases. Under Cu-limiting conditions, certain aerobic methanotrophs exude Cu-binding ligands termed chalkophores, such as methanobactin (mb) exuded by Methylosinus trichosporium OB3b. Our main objective was to establish whether chalkophores can mobilise Cu from Cu sulphide-bearing marine sediments to enhance Cu bioavailability. Through a series of kinetic batch experiments, we investigated Cu mobilisation by mb from a set of well-characterized sulphidic marine sediments differing in sediment properties, including Cu content and phase distribution. Characterization of solid-phase Cu speciation included X-ray absorption spectroscopy and a targeted sequential extraction. Furthermore, in batch experiments, we investigated to what extent adsorption of metal-free mb and Cu-mb complexes to marine sediments constrains Cu mobilisation. Our results are the first to show that both solid phase Cu speciation and chalkophore adsorption can constrain methanotrophic Cu acquisition from marine sediments. Only for certain sediments did mb addition enhance dissolved Cu concentrations. Cu mobilisation by mb was not correlated to the total Cu content of the sediment, but was controlled by solid-phase Cu speciation. Cu was only mobilised from sediments containing a mono-Cu-sulphide (CuSx) phase. We also show that mb adsorption to sediments limits Cu acquisition by mb to less compact (surface) sediments. Therefore, in sulphidic sediments, mb-mediated Cu acquisition is presumably constrained to surface-sediment interfaces containing mono-Cu-sulphide phases.

Seasonal dynamics of the microbial methane filter in the water column of a eutrophic coastal basin

In coastal waters, methane-oxidizing bacteria (MOB) can form a methane biofilter and mitigate methane emissions. The metabolism of these MOBs is versatile, and the resilience to changing oxygen concentrations is potentially high. It is still unclear how seasonal changes in oxygen availability and water column chemistry affect the functioning of the methane biofilter and MOB community composition. Here, we determined water column methane and oxygen depth profiles, the methanotrophic community structure, methane oxidation potential, and water-air methane fluxes of a eutrophic marine basin during summer stratification and in the mixed water in spring and autumn. In spring, the MOB diversity and relative abundance were low. Yet, MOB formed a methane biofilter with up to 9% relative abundance and vertical niche partitioning during summer stratification. The vertical distribution and potential methane oxidation of MOB did not follow the upward shift of the oxycline during summer, and water-air fluxes remained below 0.6 mmol m-2 d-1. Together, this suggests active methane removal by MOB in the anoxic water. Surprisingly, with a weaker stratification, and therefore potentially increased oxygen supply, methane oxidation rates decreased, and water-air methane fluxes increased. Thus, despite the potential resilience of the MOB community, seasonal water column dynamics significantly influence methane removal.

Impact of iron addition on phosphorus dynamics in sediments of a shallow peat lake 10 years after treatment

Internal phosphorus (P) loading is a key water quality challenge for shallow lakes. Addition of iron (Fe) salts has been used to enhance P retention in lake sediments. However, its effects on sediment geochemistry are poorly studied, albeit pivotal for remediation success. Here, we assess the factors controlling the retention of P and long-term effects following application of FeCl3 (0.5-1 mol Fe/m2, 2010) in the eutrophic, shallow peat lake Terra Nova (the Netherlands). Treatment reduced P levels in the lake for two years, but afterwards summer release of P intensified, resulting in higher surface water P concentrations than before treatment. Porewater and sediment analyses indicate that the majority of the added Fe is still undergoing redox cycling within the top 10 cm of sediment accounting for the binding of up to 70 % of sedimentary P. Sequential extractions further suggest that organic matter (OM) plays a key role in the resulting P and Fe dynamics: While reduction of P binding Fe(III) phases results in P release to porewaters, the produced Fe2+ remains bound to the solid phase presumably stabilized by OM. This causes P release from the sediments in excess to Fe during temporary low oxygen conditions in summer months, as confirmed by whole core flux incubation experiments. Quantitative coprecipitation of P with Fe upon reoxygenation of the water body is then impossible, leading to a gradual increase in surface water P. This first long-term study on a shallow peat lake underpins the role of OM for Fe cycling and the need to carefully consider the sediment properties and diagenetic pathways in the planning of Fe-amendments.

Anaerobic methanotrophy is stimulated by graphene oxide in a brackish urban canal sediment

Anthropogenic activities are influencing aquatic environments through increased chemical pollution and thus are greatly affecting the biogeochemical cycling of elements. This has increased greenhouse gas emissions, particularly methane, from lakes, wetlands, and canals. Most of the methane produced in anoxic sediments is converted into carbon dioxide by methanotrophs before it reaches the atmosphere. Anaerobic oxidation of methane requires an electron acceptor such as sulphate, nitrate, or metal oxides. Here, we explore the anaerobic methanotrophy in sediments of three urban canals in Amsterdam, covering a gradient from freshwater to brackish conditions. Biogeochemical analysis showed the presence of a shallow sulphate-methane transition zone in sediments of the most brackish canal, suggesting that sulphate could be a relevant electron acceptor for anaerobic methanotrophy in this setting. However, sediment incubations amended with sulphate or iron oxides (ferrihydrite) did not lead to detectable rates of methanotrophy. Despite the presence of known nitrate-dependent anaerobic methanotrophs (Methanoperedenaceae), no nitrate-driven methanotrophy was observed in any of the investigated sediments either. Interestingly, graphene oxide stimulated anaerobic methanotrophy in incubations of brackish canal sediment, possibly catalysed by anaerobic methanotrophs of the ANME-2a/b clade. We propose that natural organic matter serving as electron acceptor drives anaerobic methanotrophy in brackish sediments.

Versatile methanotrophs form an active methane biofilter in the oxycline of a seasonally stratified coastal basin

The potential and drivers of microbial methane removal in the water column of seasonally stratified coastal ecosystems and the importance of the methanotrophic community composition for ecosystem functioning are not well explored. Here, we combined depth profiles of oxygen and methane with 16S rRNA gene amplicon sequencing, metagenomics and methane oxidation rates at discrete depths in a stratified coastal marine system (Lake Grevelingen, The Netherlands). Three amplicon sequence variants (ASVs) belonging to different genera of aerobic Methylomonadaceae and the corresponding three methanotrophic metagenome-assembled genomes (MOB-MAGs) were retrieved by 16S rRNA sequencing and metagenomic analysis, respectively. The abundances of the different methanotrophic ASVs and MOB-MAGs peaked at different depths along the methane oxygen counter-gradient and the MOB-MAGs show a quite diverse genomic potential regarding oxygen metabolism, partial denitrification and sulphur metabolism. Moreover, potential aerobic methane oxidation rates indicated high methanotrophic activity throughout the methane oxygen counter-gradient, even at depths with low in situ methane or oxygen concentration. This suggests that niche-partitioning with high genomic versatility of the present Methylomonadaceae might contribute to the functional resilience of the methanotrophic community and ultimately the efficiency of methane removal in the stratified water column of a marine basin.

Gene-Based Modeling of Methane Oxidation in Coastal Sediments: Constraints on the Efficiency of the Microbial Methane Filter

Methane is a powerful greenhouse gas that is produced in large quantities in marine sediments. Microbially mediated oxidation of methane in sediments, when in balance with methane production, prevents the release of methane to the overlying water. Here, we present a gene-based reactive transport model that includes both microbial and geochemical dynamics and use it to investigate whether the rate of growth of methane oxidizers in sediments impacts the efficiency of the microbial methane filter. We focus on iron- and methane-rich coastal sediments and, with the model, show that at our site, up to 10% of all methane removed is oxidized by iron and manganese oxides, with the remainder accounted for by oxygen and sulfate. We demonstrate that the slow growth rate of anaerobic methane-oxidizing microbes limits their ability to respond to transient perturbations, resulting in periodic benthic release of methane. Eutrophication and deoxygenation decrease the efficiency of the microbial methane filter further, thereby enhancing the role of coastal environments as a source of methane to the atmosphere.

Influence of filter age on Fe, Mn and NH4+ removal in dual media rapid sand filters used for drinking water production

Rapid sand filtration is a common method for removal of iron (Fe), manganese (Mn) and ammonium (NH4+) from anoxic groundwaters used for drinking water production. In this study, we combine geochemical and microbiological data to assess how filter age influences Fe, Mn and NH4+ removal in dual media filters, consisting of anthracite overlying quartz sand, that have been in operation for between ∼2 months and ∼11 years. We show that the depth where dissolved Fe and Mn removal occurs is reflected in the filter medium coatings, with ferrihydrite forming in the anthracite in the top of the filters (< 1 m), while birnessite-type Mn oxides are mostly formed in the sand (> 1 m). Removal of NH4+ occurs through nitrification in both the anthracite and sand and is the key driver of oxygen loss. Removal of Fe is independent of filter age and is always efficient (> 97% removal). In contrast, for Mn, the removal efficiency varies with filter age, ranging from 9 to 28% at ∼2-3 months after filter replacement to 100% after 8 months. After 11 years, removal reduces to 60-80%. The lack of Mn removal in the youngest filters (at 2-3 months) is likely the result of a relatively low abundance of mineral coatings that adsorb Mn2+ and provide surfaces for the establishment of a microbial community. 16S rRNA gene amplicon sequencing shows that Gallionella, which are known Fe2+ oxidizers, are present after 2 months, yet Fe2+ removal is mostly chemical. Efficient NH4+ removal (> 90%) establishes within 3 months of operation but leakage occurs upon high NH4+loading (> 160 µM). Two-step nitrification by Nitrosomonas and Candidatus Nitrotoga is likely the most important NH4+ removal mechanism in younger filters during ripening (2 months), after which complete ammonia oxidation by Nitrospira and canonical two-step nitrification occur simultaneously in older filters. Our results highlight the strong effect of filter age on especially Mn2+but also NH4+ removal. We show that ageing of filter medium leads to the development of thick coatings, which we hypothesize leads to preferential flow, and breakthrough of Mn2+. Use of age-specific flow rates may increase the contact time with the filter medium in older filters and improve Mn2+ and NH4+ removal.

Enhanced phosphorus recycling during past oceanic anoxia amplified by low rates of apatite authigenesis

Enhanced recycling of phosphorus as ocean deoxygenation expanded under past greenhouse climates contributed to widespread organic carbon burial and drawdown of atmospheric CO2. Redox-dependent phosphorus recycling was more efficient in such ancient anoxic marine environments, compared to modern anoxic settings, for reasons that remain unclear. Here, we show that low rates of apatite authigenesis in organic-rich sediments can explain the amplified phosphorus recycling in ancient settings as reflected in highly elevated ratios of organic carbon to total phosphorus. We argue that the low rates may be partly the result of the reduced saturation state of sediment porewaters with respect to apatite linked to ocean warming and acidification and/or a decreased availability of calcium carbonate, which acts as a template for apatite formation. Future changes in temperature and ocean biogeochemistry, induced by elevated atmospheric CO2, may similarly increase phosphorus availability and accelerate ocean deoxygenation and organic carbon burial.

Eutrophication and Deoxygenation Forcing of Marginal Marine Organic Carbon Burial During the PETM

The Paleocene-Eocene Thermal Maximum (PETM) is recognized globally by a negative excursion in stable carbon isotope ratios (δ¹³C) in sedimentary records, termed the carbon isotope excursion (CIE). Based on the CIE, the cause, duration, and mechanisms of recovery of the event have been assessed. Here, we focus on the role of increased organic carbon burial on continental margins as a key driver of CO₂ drawdown and global exogenic δ¹³C during the recovery phase. Using new and previously published sediment proxy data, we show evidence for widespread enhanced primary production, low oxygen waters, and high organic carbon (C_org) burial in marginal and restricted environments throughout the δ¹³C excursion. With a new biogeochemical box model for deep and marginal environments, we show that increased phosphorus availability and water column stratification on continental margins can explain the increased C_org burial during the PETM. Deoxygenation and recycling of phosphorus relative to C_org were relatively mild, compared to modern day anoxic marine systems. Our model reproduces the conditions reconstructed by field data, resulting in a burial of 6,000 Pg across the PETM, in excess of late Paleocene burial, and ∼3,300 Pg C for the critical first 40 kyr of the recovery, primarily located on continental margins. This value is consistent with prior data and model estimates (∼2,000-3,000 Pg C). To reproduce global exogenic δ¹³C patterns, this C_org burial implies an injection of 5,000-10,000 Pg C during the first ∼100-150 kyr of the PETM, depending on the source's δ¹³C (-11‰ to -55‰).

Iron-Phosphorus Feedbacks Drive Multidecadal Oscillations in Baltic Sea Hypoxia

Hypoxia has occurred intermittently in the Baltic Sea since the establishment of brackish-water conditions at ∼8,000 years B.P., principally as recurrent hypoxic events during the Holocene Thermal Maximum (HTM) and the Medieval Climate Anomaly (MCA). Sedimentary phosphorus release has been implicated as a key driver of these events, but previous paleoenvironmental reconstructions have lacked the sampling resolution to investigate feedbacks in past iron-phosphorus cycling on short timescales. Here we employ Laser Ablation (LA)-ICP-MS scanning of sediment cores to generate ultra-high resolution geochemical records of past hypoxic events. We show that in-phase multidecadal oscillations in hypoxia intensity and iron-phosphorus cycling occurred throughout these events. Using a box model, we demonstrate that such oscillations were likely driven by instabilities in the dynamics of iron-phosphorus cycling under preindustrial phosphorus loads, and modulated by external climate forcing. Oscillatory behavior could complicate the recovery from hypoxia during future trajectories of external loading reductions.

Enrichment of novel Verrucomicrobia, Bacteroidetes, and Krumholzibacteria in an oxygen-limited methane- and iron-fed bioreactor inoculated with Bothnian Sea sediments

Microbial methane oxidation is a major biofilter preventing larger emissions of this powerful greenhouse gas from marine coastal areas into the atmosphere. In these zones, various electron acceptors such as sulfate, metal oxides, nitrate, or oxygen can be used. However, the key microbial players and mechanisms of methane oxidation are poorly understood. In this study, we inoculated a bioreactor with methane‐ and iron‐rich sediments from the Bothnian Sea to investigate microbial methane and iron cycling under low oxygen concentrations. Using metagenomics, we investigated shifts in microbial community composition after approximately 2.5 years of bioreactor operation. Marker genes for methane and iron cycling, as well as respiratory and fermentative metabolism, were identified and used to infer putative microbial metabolism. Metagenome‐assembled genomes representing novel Verrucomicrobia, Bacteroidetes, and Krumholzibacteria were recovered and revealed a potential for methane oxidation, organic matter degradation, and iron cycling, respectively. This work brings new hypotheses on the identity and metabolic versatility of microorganisms that may be members of such functional guilds in coastal marine sediments and highlights that microorganisms potentially composing the methane biofilter in these sediments may be more diverse than previously appreciated.

Coupled dynamics of iron, manganese, and phosphorus in brackish coastal sediments populated by cable bacteria

Coastal waters worldwide suffer from increased eutrophication and seasonal bottom water hypoxia. Here, we assess the dynamics of iron (Fe), manganese (Mn), and phosphorus (P) in sediments of the eutrophic, brackish Gulf of Finland populated by cable bacteria. At sites where bottom waters are oxic in spring, surface enrichments of Fe and Mn oxides and high abundances of cable bacteria were observed in sediments upon sampling in early summer. At one site, Fe and P were enriched in a thin layer (~ 3 mm) just below the sediment-water interface. X-ray absorption near edge structure and micro X-ray fluorescence analyses indicate that two-thirds of the P in this layer was associated with poorly crystalline Fe oxides, with an additional contribution of Mn(II) phosphates. The Fe enriched layer was directly overlain by a Mn oxide-rich surface layer (~ 2 mm). The Fe oxide layer was likely of diagenetic origin, formed through dissolution of Fe monosulfides and carbonates, potentially induced by cable bacteria in the preceding months when bottom waters were oxic. Most of the Mn oxides were likely deposited from the water column as part of a cycle of repeated deposition and remobilization. Further research is required to confirm whether cable bacteria activity in spring indeed promotes the formation of distinct layers enriched in Fe, Mn, and P minerals in Gulf of Finland sediments. The temporal variations in biogeochemical cycling in this seasonally hypoxic coastal system, potentially controlled by cable bacteria activity, have little impact on permanent sedimentary Fe, Mn, and P burial.

Anthropogenic and Environmental Constraints on the Microbial Methane Cycle in Coastal Sediments

Large amounts of methane, a potent greenhouse gas, are produced in anoxic sediments by methanogenic archaea. Nonetheless, over 90% of the produced methane is oxidized via sulfate-dependent anaerobic oxidation of methane (S-AOM) in the sulfate-methane transition zone (SMTZ) by consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). Coastal systems account for the majority of total marine methane emissions and typically have lower sulfate concentrations, hence S-AOM is less significant. However, alternative electron acceptors such as metal oxides or nitrate could be used for AOM instead of sulfate. The availability of electron acceptors is determined by the redox zonation in the sediment, which may vary due to changes in oxygen availability and the type and rate of organic matter inputs. Additionally, eutrophication and climate change can affect the microbiome, biogeochemical zonation, and methane cycling in coastal sediments. This review summarizes the current knowledge on the processes and microorganisms involved in methane cycling in coastal sediments and the factors influencing methane emissions from these systems. In eutrophic coastal areas, organic matter inputs are a key driver of bottom water hypoxia. Global warming can reduce the solubility of oxygen in surface waters, enhancing water column stratification, increasing primary production, and favoring methanogenesis. ANME are notoriously slow growers and may not be able to effectively oxidize methane upon rapid sedimentation and shoaling of the SMTZ. In such settings, ANME-2d (Methanoperedenaceae) and ANME-2a may couple iron- and/or manganese reduction to AOM, while ANME-2d and NC10 bacteria (Methylomirabilota) could couple AOM to nitrate or nitrite reduction. Ultimately, methane may be oxidized by aerobic methanotrophs in the upper millimeters of the sediment or in the water column. The role of these processes in mitigating methane emissions from eutrophic coastal sediments, including the exact pathways and microorganisms involved, are still underexplored, and factors controlling these processes are unclear. Further studies are needed in order to understand the factors driving methane-cycling pathways and to identify the responsible microorganisms. Integration of the knowledge on microbial pathways and geochemical processes is expected to lead to more accurate predictions of methane emissions from coastal zones in the future.

Recovery from multi-millennial natural coastal hypoxia in the Stockholm Archipelago, Baltic Sea, terminated by modern human activity

Enhanced nutrient input and warming have led to the development of low oxygen (hypoxia) in coastal waters globally. For many coastal areas, insight into redox conditions prior to human impact is lacking. Here, we reconstructed bottom water redox conditions and sea surface temperatures (SSTs) for the coastal Stockholm Archipelago over the past 3000 yr. Elevated sedimentary concentrations of molybdenum indicate (seasonal) hypoxia between 1000 b.c.e. and 1500 c.e. Biomarker-based (TEX₈₆) SST reconstructions indicate that the recovery from hypoxia after 1500 c.e. coincided with a period of significant cooling (∼ 2°C), while human activity in the study area, deduced from trends in sedimentary lead and existing paleobotanical and archeological records, had significantly increased. A strong increase in sedimentary lead and zinc, related to more intense human activity in the 18^th and 19^th century, and the onset of modern warming precede the return of hypoxia in the Stockholm Archipelago. We conclude that climatic cooling played an important role in the recovery from natural hypoxia after 1500 c.e., but that eutrophication and warming, related to modern human activity, led to the return of hypoxia in the 20^th century. Our findings imply that ongoing global warming may exacerbate hypoxia in the coastal zone of the Baltic Sea.

Abundance and Biogeochemical Impact of Cable Bacteria in Baltic Sea Sediments

Oxygen depletion in coastal waters may lead to release of toxic sulfide from sediments. Cable bacteria can limit sulfide release by promoting iron oxide formation in sediments. Currently, it is unknown how widespread this phenomenon is. Here, we assess the abundance, activity, and biogeochemical impact of cable bacteria at 12 Baltic Sea sites. Cable bacteria were mostly absent in sediments overlain by anoxic and sulfidic bottom waters, emphasizing their dependence on oxygen or nitrate as electron acceptors. At sites that were temporarily reoxygenated, cable bacterial densities were low. At seasonally hypoxic sites, cable bacterial densities correlated linearly with the supply of sulfide. The highest densities were observed at Gulf of Finland sites with high rates of sulfate reduction. Microelectrode profiles of sulfide, oxygen, and pH indicated low or no in situ cable bacteria activity at all sites. Reactivation occurred within 5 days upon incubation of an intact sediment core from the Gulf of Finland with aerated overlying water. We found no relationship between cable bacterial densities and macrofaunal abundances, salinity, or sediment organic carbon. Our geochemical data suggest that cable bacteria promote conversion of iron monosulfides to iron oxides in the Gulf of Finland in spring, possibly explaining why bottom waters in this highly eutrophic region rarely contain sulfide in summer.

The hunt for the most-wanted chemolithoautotrophic spookmicrobes

Microorganisms are the drivers of biogeochemical methane and nitrogen cycles. Essential roles of chemolithoautotrophic microorganisms in these cycles were predicted long before their identification. Dedicated enrichment procedures, metagenomics surveys and single-cell technologies have enabled the identification of several new groups of most-wanted spookmicrobes, including novel methoxydotrophic methanogens that produce methane from methylated coal compounds and acetoclastic 'Candidatus Methanothrix paradoxum', which is active in oxic soils. The resultant energy-rich methane can be oxidized via a suite of electron acceptors. Recently, 'Candidatus Methanoperedens nitroreducens' ANME-2d archaea and 'Candidatus Methylomirabilis oxyfera' bacteria were enriched on nitrate and nitrite under anoxic conditions with methane as an electron donor. Although 'Candidatus Methanoperedens nitroreducens' and other ANME archaea can use iron citrate as an electron acceptor in batch experiments, the quest for anaerobic methane oxidizers that grow via iron reduction continues. In recent years, the nitrogen cycle has been expanded by the discovery of various ammonium-oxidizing prokaryotes, including ammonium-oxidizing archaea, versatile anaerobic ammonium-oxidizing (anammox) bacteria and complete ammonium-oxidizing (comammox) Nitrospira bacteria. Several biogeochemical studies have indicated that ammonium conversion occurs under iron-reducing conditions, but thus far no microorganism has been identified. Ultimately, iron-reducing and sulfate-dependent ammonium-oxidizing microorganisms await discovery.

Anaerobic Methane-Oxidizing Microbial Community in a Coastal Marine Sediment: Anaerobic Methanotrophy Dominated by ANME-3

The microbial community inhabiting the shallow sulfate-methane transition zone in coastal sediments from marine Lake Grevelingen (The Netherlands) was characterized, and the ability of the microorganisms to carry out anaerobic oxidation of methane coupled to sulfate reduction was assessed in activity tests. In vitro activity tests of the sediment with methane and sulfate demonstrated sulfide production coupled to the simultaneous consumption of sulfate and methane at approximately equimolar ratios over a period of 150 days. The maximum sulfate reduction rate was 5 μmol sulfate per gram dry weight per day during the incubation period. Diverse archaeal and bacterial clades were retrieved from the sediment with the majority of them clustered with Euryarchaeota, Thaumarcheota, Bacteroidetes, and Proteobacteria. The 16S rRNA gene sequence analysis showed that the sediment from marine Lake Grevelingen contained anaerobic methanotrophic Archaea (ANME) and methanogens as archaeal clades with a role in the methane cycling. ANME at the studied site mainly belong to the ANME-3 clade. This study provides one of the few reports for the presence of ANME-3 in a shallow coastal sediment. Sulfate-reducing bacteria from Desulfobulbus clades were found among the sulfate reducers, however, with very low relative abundance. Desulfobulbus has previously been commonly found associated with ANME, whereas in our study, ANME-3 and Desulfobulbus were not observed simultaneously in clusters, suggesting the possibility of independent AOM by ANME-3.

Rapid Sediment Accumulation Results in High Methane Effluxes from Coastal Sediments

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.

Cable Bacteria Control Iron-Phosphorus Dynamics in Sediments of a Coastal Hypoxic Basin

Phosphorus is an essential nutrient for life. The release of phosphorus from sediments is critical in sustaining phytoplankton growth in many aquatic systems and is pivotal to eutrophication and the development of bottom water hypoxia. Conventionally, sediment phosphorus release is thought to be controlled by changes in iron oxide reduction driven by variations in external environmental factors, such as organic matter input and bottom water oxygen. Here, we show that internal shifts in microbial communities, and specifically the population dynamics of cable bacteria, can also induce strong seasonality in sedimentary iron-phosphorus dynamics. Field observations in a seasonally hypoxic coastal basin demonstrate that the long-range electrogenic metabolism of cable bacteria leads to a dissolution of iron sulfides in winter and spring. Subsequent oxidation of the mobilized ferrous iron with manganese oxides results in a large stock of iron-oxide-bound phosphorus below the oxic zone. In summer, when bottom water hypoxia develops and cable bacteria are undetectable, the phosphorus associated with these iron oxides is released, strongly increasing phosphorus availability in the water column. Future research should elucidate whether formation of iron-oxide-bound phosphorus driven by cable bacteria, as observed in this study, contributes to the seasonality in iron-phosphorus cycling in aquatic sediments worldwide.

Phylogenetic Characterization of Phosphatase-Expressing Bacterial Communities in Baltic Sea Sediments

Phosphate release from sediments hampers the remediation of aquatic systems from a eutrophic state. Microbial phosphatases in sediments release phosphorus during organic matter degradation. Despite the important role of phosphatase-expressing bacteria, the identity of these bacteria in sediments is largely unknown. We herein presented a culture-independent method to phylogenetically characterize phosphatase-expressing bacteria in sediments. We labeled whole-cell extracts of Baltic Sea sediments with an artificial phosphatase substrate and sorted phosphatase-expressing cells with a flow cytometer. Their phylogenetic affiliation was determined by Denaturing Gradient Gel Electrophoresis. The phosphatase-expressing bacterial community coarsely reflected the whole-cell bacterial community, with a similar dominance of Alphaproteobacteria.

Iron-mediated anaerobic oxidation of methane in brackish coastal sediments

Methane is a powerful greenhouse gas and its biological conversion in marine sediments, largely controlled by anaerobic oxidation of methane (AOM), is a crucial part of the global carbon cycle. However, little is known about the role of iron oxides as an oxidant for AOM. Here we provide the first field evidence for iron-dependent AOM in brackish coastal surface sediments and show that methane produced in Bothnian Sea sediments is oxidized in distinct zones of iron- and sulfate-dependent AOM. At our study site, anthropogenic eutrophication over recent decades has led to an upward migration of the sulfate/methane transition zone in the sediment. Abundant iron oxides and high dissolved ferrous iron indicate iron reduction in the methanogenic sediments below the newly established sulfate/methane transition. Laboratory incubation studies of these sediments strongly suggest that the in situ microbial community is capable of linking methane oxidation to iron oxide reduction. Eutrophication of coastal environments may therefore create geochemical conditions favorable for iron-mediated AOM and thus increase the relevance of iron-dependent methane oxidation in the future. Besides its role in mitigating methane emissions, iron-dependent AOM strongly impacts sedimentary iron cycling and related biogeochemical processes through the reduction of large quantities of iron oxides.

Are iron-phosphate minerals a sink for phosphorus in anoxic Black Sea sediments?

Phosphorus (P) is a key nutrient for marine organisms. The only long-term removal pathway for P in the marine realm is burial in sediments. Iron (Fe) bound P accounts for a significant proportion of this burial at the global scale. In sediments underlying anoxic bottom waters, burial of Fe-bound P is generally assumed to be negligible because of reductive dissolution of Fe(III) (oxyhydr)oxides and release of the associated P. However, recent work suggests that Fe-bound P is an important burial phase in euxinic (i.e. anoxic and sulfidic) basin sediments in the Baltic Sea. In this study, we investigate the role of Fe-bound P as a potential sink for P in Black Sea sediments overlain by oxic and euxinic bottom waters. Sequential P extractions performed on sediments from six multicores along two shelf-to-basin transects provide evidence for the burial of Fe-bound P at all sites, including those in the euxinic deep basin. In the latter sediments, Fe-bound P accounts for more than 20% of the total sedimentary P pool. We suggest that this P is present in the form of reduced Fe-P minerals. We hypothesize that these minerals may be formed as inclusions in sulfur-disproportionating Deltaproteobacteria. Further research is required to elucidate the exact mineral form and formation mechanism of this P burial phase, as well as its role as a sink for P in sulfide-rich marine sediments.

Rapid and extensive alteration of phosphorus speciation during oxic storage of wet sediment samples

The chemical forms of phosphorus (P) in sediments are routinely measured in studies of P in modern and ancient marine environments. However, samples for such analyses are often exposed to atmospheric oxygen during storage and handling. Recent work suggests that long-term exposure of pyrite-bearing sediments can lead to a decline in apatite P and an increase in ferric Fe-bound P. Here, we report on alterations in P speciation in reducing modern Baltic Sea sediments that we deliberately exposed to atmospheric oxygen for a period of either one week or one year. During oxidation of the sediment, extensive changes occurred in all measured P reservoirs. Exchangeable P all but disappeared during the first week of exposure, likely reflecting adsorption of porewater PO₄ by Fe(III) (oxyhydr)oxides (i.e. ferric Fe-bound P formation). Detrital and organic P were also rapidly affected: decreases in both reservoirs were already observed after the first week of exposure to atmospheric oxygen. This was likely because of acidic dissolution of detrital apatite and oxidation of organic matter, respectively. These processes produced dissolved PO₄ that was then scavenged by Fe(III) (oxyhydr)oxides. Interestingly, P in authigenic calcium phosphates (i.e. apatite: authigenic Ca-P) remained unaffected after the first week of exposure, which we attributed to the shielding effect of microfossils in which authigenic Ca-P occurs in Baltic Sea sediments. This effect was transient; a marked decrease in the authigenic Ca-P pool was observed in the sediments after one year of exposure to oxygen. In summary, we show that handling and storage of wet sediments under oxic conditions can lead to rapid and extensive alteration of the original sediment P speciation.

Effect of redox conditions on bacterial community structure in Baltic Sea sediments with contrasting phosphorus fluxes

Phosphorus release from sediments can exacerbate the effect of eutrophication in coastal marine ecosystems. The flux of phosphorus from marine sediments to the overlying water is highly dependent on the redox conditions at the sediment-water interface. Bacteria are key players in the biological processes that release or retain phosphorus in marine sediments. To gain more insight in the role of bacteria in phosphorus release from sediments, we assessed the effect of redox conditions on the structure of bacterial communities. To do so, we incubated surface sediments from four sampling sites in the Baltic Sea under oxic and anoxic conditions and analyzed the fingerprints of the bacterial community structures in these incubations and the original sediments. This paper describes the effects of redox conditions, sampling station, and sample type (DNA, RNA, or whole-cell sample) on bacterial community structure in sediments. Redox conditions explained only 5% of the variance in community structure, and bacterial communities from contrasting redox conditions showed considerable overlap. We conclude that benthic bacterial communities cannot be classified as being typical for oxic or anoxic conditions based on community structure fingerprints. Our results suggest that the overall structure of the benthic bacterial community has only a limited impact on benthic phosphate fluxes in the Baltic Sea.

Hypoxia in the Baltic Sea: biogeochemical cycles, benthic fauna, and management

Hypoxia has occurred intermittently over the Holocene in the Baltic Sea, but the recent expansion from less than 10 000 km(2) before 1950 to >60 000 km(2) since 2000 is mainly caused by enhanced nutrient inputs from land and atmosphere. With worsening hypoxia, the role of sediments changes from nitrogen removal to nitrogen release as ammonium. At present, denitrification in the water column and sediments is equally important. Phosphorus is currently buried in sediments mainly in organic form, with an additional contribution of reduced Fe-phosphate minerals in the deep anoxic basins. Upon the transition to oxic conditions, a significant proportion of the organic phosphorus will be remineralized, with the phosphorus then being bound to iron oxides. This iron-oxide bound phosphorus is readily released to the water column upon the onset of hypoxia again. Important ecosystems services carried out by the benthic fauna, including biogeochemical feedback-loops and biomass production, are also lost with hypoxia. The results provide quantitative knowledge of nutrient release and recycling processes under various environmental conditions in support of decision support tools underlying the Baltic Sea Action Plan.

Model-based integration and analysis of biogeochemical and isotopic dynamics in a nitrate-polluted pyritic aquifer

Leaching of nitrate from agricultural land to groundwater and the resulting nitrate pollution are a major environmental problem worldwide. Its impact is often mitigated in aquifers hosting sufficiently reactive reductants that can promote autotrophic denitrification. In the case of pyrite acting as reductant, however, denitrification is associated with the release of sulfate and often also with the mobilization of trace metals (e.g., arsenic). In this study, reactive transport modeling was used to reconstruct, quantify and analyze the dynamics of the dominant biogeochemical processes in a nitrate-polluted pyrite-containing aquifer and its evolution over the last 50 years in response to changing agricultural practices. Model simulations were constrained by measured concentration depth profiles. Measured (3)H/(3)He profiles were used to support the calibration of flow and conservative transport processes, while the comparison of simulated and measured sulfur isotope signatures acted as additional calibration constraint for the reactive processes affecting sulfur cycling. The model illustrates that denitrification largely prevented an elevated discharge of nitrate to surface waters, while sulfate discharges were significantly increased, peaking around 15 years after the maximum nitrogen inputs.

Global trends and uncertainties in terrestrial denitrification and N₂O emissions

Soil nitrogen (N) budgets are used in a global, distributed flow-path model with 0.5° × 0.5° resolution, representing denitrification and N2O emissions from soils, groundwater and riparian zones for the period 1900-2000 and scenarios for the period 2000-2050 based on the Millennium Ecosystem Assessment. Total agricultural and natural N inputs from N fertilizers, animal manure, biological N2 fixation and atmospheric N deposition increased from 155 to 345 Tg N yr(-1) (Tg = teragram; 1 Tg = 10(12) g) between 1900 and 2000. Depending on the scenario, inputs are estimated to further increase to 408-510 Tg N yr(-1) by 2050. In the period 1900-2000, the soil N budget surplus (inputs minus withdrawal by plants) increased from 118 to 202 Tg yr(-1), and this may remain stable or further increase to 275 Tg yr(-1) by 2050, depending on the scenario. N2 production from denitrification increased from 52 to 96 Tg yr(-1) between 1900 and 2000, and N2O-N emissions from 10 to 12 Tg N yr(-1). The scenarios foresee a further increase to 142 Tg N2-N and 16 Tg N2O-N yr(-1) by 2050. Our results indicate that riparian buffer zones are an important source of N2O contributing an estimated 0.9 Tg N2O-N yr(-1) in 2000. Soils are key sites for denitrification and are much more important than groundwater and riparian zones in controlling the N flow to rivers and the oceans.

Does microbial stoichiometry modulate eutrophication of aquatic ecosystems?

The stoichiometry of prokaryotes (Bacteria and Archaea) can control benthic phosphorus (P) fluxes relative to carbon (C) and nitrogen (N) during organic matter remineralization. This paper presents the first experimental data on benthic microbial stoichiometry. We used X-ray microanalysis to determine C : N : P ratios of individual prokaryotes from C-limited Baltic Sea sediments incubated under oxic or anoxic conditions. At approximately 400:1, C : P ratios of prokaryotes from both oxic and anoxic incubations were higher than the Redfield ratio for marine organic matter (106:1), whereas prokaryotic C : N ratios (6.4:1) were close to the Redfield ratio. We conclude that high microbial C : P ratios contribute to the enhanced remineralization of P from organic matter relative to C and N observed in many low oxygen marine settings.

Hypoxia-related processes in the Baltic Sea

Hypoxia, a growing worldwide problem, has been intermittently present in the modern Baltic Sea since its formation ca. 8000 cal. yr BP. However, both the spatial extent and intensity of hypoxia have increased with anthropogenic eutrophication due to nutrient inputs. Physical processes, which control stratification and the renewal of oxygen in bottom waters, are important constraints on the formation and maintenance of hypoxia. Climate controlled inflows of saline water from the North Sea through the Danish Straits is a critical controlling factor governing the spatial extent and duration of hypoxia. Hypoxia regulates the biogeochemical cycles of both phosphorus (P) and nitrogen (N) in the water column and sediments. Significant amounts of P are currently released from sediments, an order of magnitude larger than anthropogenic inputs. The Baltic Sea is unique for coastal marine ecosystems experiencing N losses in hypoxic waters below the halocline. Although benthic communities in the Baltic Sea are naturally constrained by salinity gradients, hypoxia has resulted in habitat loss over vast areas and the elimination of benthic fauna, and has severely disrupted benthic food webs. Nutrient load reductions are needed to reduce the extent, severity, and effects of hypoxia.

Geochemistry of trace metals in a fresh water sediment: field results and diagenetic modeling

Concentrations of Fe, Mn, Cd, Co, Ni, Pb, and Zn were determined in pore water and sediment of a coastal fresh water lake (Haringvliet Lake, The Netherlands). Elevated sediment trace metal concentrations reflect anthropogenic inputs from the Rhine and Meuse Rivers. Pore water and sediment analyses, together with thermodynamic calculations, indicate a shift in trace metal speciation from oxide-bound to sulfide-bound over the upper 20 cm of the sediment. Concentrations of reducible Fe and Mn decline with increasing depth, but do not reach zero values at 20 cm depth. The reducible phases are relatively more important for the binding of Co, Ni, and Zn than for Pb and Cd. Pore waters exhibit supersaturation with respect to Zn, Pb, Co, and Cd monosulfides, while significant fractions of Ni and Co are bound to pyrite. A multi-component, diagenetic model developed for organic matter degradation was expanded to include Zn and Ni dynamics. Pore water transport of trace metals is primarily diffusive, with a lesser contribution of bioirrigation. Reactions affecting trace metal mobility near the sediment-water interface, especially sulfide oxidation and sorption to newly formed oxides, strongly influence the modeled estimates of the diffusive effluxes to the overlying water. Model results imply less efficient sediment retention of Ni than Zn. Sensitivity analyses show that increased bioturbation and sulfate availability, which are expected upon restoration of estuarine conditions in the lake, should increase the sulfide bound fractions of Zn and Ni in the sediments.

Potential nitrate removal in a coastal freshwater sediment (Haringvliet Lake, The Netherlands) and response to salinization

Nitrogen transformations and their response to salinization were studied in bottom sediment of a coastal freshwater lake (Haringvliet Lake, The Netherlands). The lake was formed as the result of a river impoundment along the south-western coast of the Netherlands, and is currently targeted for restoration of estuarine conditions. Nitrate porewater profiles indicate complete removal of NO(3)(-) within the upper few millimeters of sediment. Rapid NO(3)(-) consumption is consistent with the high potential rates of nitrate reduction (up to 200 nmol N cm(-3) h(-1)) measured with flow-through reactors (FTRs) on intact sediment slices. Acetylene-block FTR experiments indicate that complete denitrification accounts for approximately half of the nitrate reducing activity. The remaining NO(3)(-) reduction is due to incomplete denitrification and alternative reaction pathways, most likely dissimilatory nitrate reduction to NH(4)(+) (DNRA). Results of FTR experiments further indicate that increasing bottom water salinity may lead to a transient release of NH(4)(+) and dissolved organic carbon from the sediment, and enhance the rates of nitrate reduction and nitrite production. Increased salinity may thus, at least temporarily, increase the efflux of NH(4)(+) from the sediment to the surface water. This work shows that salinity affects the relative importance of denitrification compared to alternative nitrate reduction pathways, limiting the ability of denitrification to remove bioavailable nitrogen from aquatic ecosystems.

Modelling the geochemical fate and transport of wastewater-derived phosphorus in contrasting groundwater systems

A 1D reactive transport model (RTM) is used to obtain a mechanistic understanding of the fate of phosphorus (P) in the saturated zone of two contrasting aquifer systems. We use the field data from two oxic, electron donor-poor, wastewater-impacted, sandy Canadian aquifers, (Cambridge and Muskoka sites) as an example of a calcareous and non-calcareous groundwater system, respectively, to validate our reaction network. After approximately 10 years of wastewater infiltration, P is effectively attenuated within the first 10 m down-gradient of the source mainly through fast sorption onto calcite and Fe oxides. Slow, kinetic sorption contributes further to P removal, while precipitation of phosphate minerals (strengite, hydroxyapatite) is quantitatively unimportant in the saturated zone. Nitrogen (N) dynamics are also considered, but nitrate behaves essentially as a conservative tracer in both systems. The model-predicted advancement of the P plume upon continued wastewater discharge at the calcareous site is in line with field observations. Model results suggest that, upon removal of the wastewater source, the P plume at both sites will persist for at least 20 years, owing to desorption of P from aquifer solids and the slow rate of P mineral precipitation. Sensitivity analyses for the non-calcareous scenario (Muskoka) illustrate the importance of the sorption capacity of the aquifer solids for P in modulating groundwater N:P ratios in oxic groundwater. The model simulations predict the breakthrough of groundwater with high P concentrations and low N:P ratios after 17 years at 20 m from the source for an aquifer with low sorption capacity (<0.02% w/w Fe(OH)(3)). In this type of system, denitrification plays a minor role in lowering the N:P ratios because it is limited by the availability of labile dissolved organic matter.