Eutrophication and Deoxygenation Drive High Methane Emissions from a Brackish Coastal System.

Coastal environments are a major source of marine methane in the atmosphere. Eutrophication and deoxygenation have the potential to amplify the coastal methane emissions. Here, we investigate methane dynamics in the eutrophic Stockholm Archipelago. We cover a range of sites with contrasting water column redox conditions and rates of organic matter degradation, with the latter reflected by the depth of the sulfate-methane transition zone (SMTZ) in the sediment. We find the highest benthic release of methane (2.2-8.6 mmol m-2 d-1) at sites where the SMTZ is located close to the sediment-water interface (2-10 cm). A large proportion of methane is removed in the water column via aerobic or anaerobic microbial pathways. At many locations, water column methane is highly depleted in 13C, pointing toward substantial bubble dissolution. Calculated and measured rates of methane release to the atmosphere range from 0.03 to 0.4 mmol m-2 d-1 and from 0.1 to 1.7 mmol m-2 d-1, respectively, with the highest fluxes at locations with a shallow SMTZ and anoxic and sulfidic bottom waters. Taken together, our results show that sites suffering most from both eutrophication and deoxygenation are hotspots of coastal marine methane emissions.

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.

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.

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.

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.

Coprecipitation of Phosphate and Silicate Affects Environmental Iron (Oxyhydr)Oxide Transformations: A Gel-Based Diffusive Sampler Approach.

Sorption of nutrients such as phosphate (P) and silicate (Si) by ferric iron (oxyhydr)oxides (FeOx) modulates nutrient mobility and alters the structure and reactivity of the FeOx. We investigated the impact of these interactions on FeOx transformations using a novel approach with samplers containing synthetic FeOx embedded in diffusive hydrogels. The FeOx were prepared by Fe(III) hydrolysis and Fe(II) oxidation, in the absence and presence of P or Si. Coprecipitation of P or Si during synthesis altered the structure of Fe precipitates and, in the case of Fe(II) oxidation, lepidocrocite was (partly) substituted by poorly ordered FeOx. The pure and P- or Si-bearing FeOx were deployed in (i) freshwater sediment rich in dissolved Fe(II) and P and (ii) marine sediment with sulfidic pore water. Iron(II)-catalyzed crystallization of poorly ordered FeOx was negligible, likely due to surface passivation by adsorption of dissolved P. Reaction with dissolved sulfide was modulated by diffusion limitations and therefore the extent of sulfidation was the lowest for poorly ordered FeOx with high reactivity toward sulfide that created temporary, local sulfide depletion (Fh < Lp). We show that coprecipitation-induced changes in the FeOx structure affect coupled iron-nutrient cycling in aquatic ecosystems. The gel-based method enriches our geochemical toolbox by enabling detailed characterization of target phases under natural conditions.

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.

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.

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.

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.