Anoxic Sediments Research Articles

Methylation of mercury and tin by estuarine microbial mats

After tin and mercury salts were added to estuarine microbial mats increasing amounts of methyltin and methylmercury, respectively, were formed over a 30 to 100 hour time period. Inhibition of the methylation by molybdate, a metabolic inhibitor of sulfate reduction, stimulation by pyruvate addition and lack of methylation by sterilized mats, were evidence that sulfate reducing bacteria within the mats were responsible for the tin and mercury methylation. Methyl mercury was formed from mercuric chloride and mercuric cysteine, but not from mercuric sulfide. We suggest that mercury bound to organic complexes in anoxic sediments is likely methylated by microbial mats. Since estuarine meiofauna and macrofauna fed on microbial mats, the methylmercury and methyltin formed by microbial mats could be an important avenue for the entrance of these compounds into the marine food web.

Expanded gene and taxon sampling of diplomonads shows multiple switches to parasitic and free-living lifestyle

BackgroundDiplomonads are anaerobic flagellates classified within Metamonada. They contain both host-associated commensals and parasites that reside in the intestinal tracts of animals, including humans (e.g., Giardia intestinalis), as well as free-living representatives that inhabit freshwater and marine anoxic sediments (e.g., Hexamita inflata). The evolutionary trajectories within this group are particularly unusual as the free-living taxa appear to be nested within a clade of host-associated species, suggesting a reversal from host-dependence to a secondarily free-living lifestyle. This is thought to be an exceedingly rare event as parasites often lose genes for metabolic pathways that are essential to a free-living life strategy, as they become increasingly reliant on their host for nutrients and metabolites. To revert to a free-living lifestyle would require the reconstruction of numerous metabolic pathways. All previous studies of diplomonad evolution suffered from either low taxon sampling, low gene sampling, or both, especially among free-living diplomonads, which has weakened the phylogenetic resolution and hindered evolutionary insights into this fascinating transition.ResultsWe sequenced transcriptomes from 1 host-associated and 13 free-living diplomonad isolates; expanding the genome scale data sampling for diplomonads by roughly threefold. Phylogenomic analyses clearly show that free-living diplomonads form several branches nested within endobiotic species. Moreover, the phylogenetic distribution of genes related to an endobiotic lifestyle suggest their acquisition at the root of diplomonads, while traces of these genes have been identified in free-living diplomonads as well. Based on these results, we propose an evolutionary scenario of ancestral and derived lifestyle transitions across diplomonads.ConclusionsFree-living taxa form several clades nested within endobiotic taxa in our phylogenomic analyses, implying multiple transitions between free-living and endobiotic lifestyles. The evolutionary history of numerous virulence factors corroborates the inference of an endobiotic ancestry of diplomonads, suggesting that there have been several reversals to a free-living lifestyle. Regaining host independence may have been facilitated by a subset of laterally transferred genes. We conclude that the extant diversity of diplomonads has evolved from a non-specialized endobiont, with some taxa becoming highly specialized parasites, others becoming free-living, and some becoming capable of both free-living and endobiotic lifestyles.

Mobilization of phosphorus in sediments of eutrophic lakes induced by elevated sulfate levels

Elevated sulfate levels in eutrophic lakes have been observed to induce the release of endogenous phosphorus. While previous studies have predominantly examined its impact on iron-bound phosphorus (FeP), the influence on organic phosphorus (OP), a crucial active phosphorus component in sediments, remains poorly understood. In this study, mesocosms were established with lactate supplementation and varying sulfate concentrations to explore sulfate reduction and its impacts on phosphorus mobilization in freshwater sediments. Lactate addition induced hypoxia and provided substrates, thereby stimulating sulfate reduction with a decline of sulfate levels, an increase of sulfide concentrations, and fluctuations of sulfate-reducing bacteria. Meanwhile, concentrations of total dissolved phosphorus and phosphate were dramatically promoted during lactate decomposition, with a higher sulfate concentration associated with greater phosphorus elevation, correlating with the decrease of total phosphorus in sediment. The increase in phosphorus of the overlying water was partly attributed to FeP release from the sediment, confirmed by a decrease in its sediment content. FeP release was ascribed to dissimilatory reduction of iron oxides or chemical reduction mediated by sulfides in anoxic sediments, leading to the desorption and subsequent release of phosphorus. Evidences included the proliferation of iron-reducing bacteria, a decrease in Fe(II) concentrations in sediment pore- water, and the continuous accumulation of solid iron sulfides in surface sediments. Furthermore, OP mineralization in sediment also contributed to the increase in phosphorus in water columns, confirmed by a reduction in its content and the abundance of fermentation bacteria in surface sediment. Notably, the decrease in OP content accounted for >80 % of the total phosphorus reduction in surface sediment in the end. Thus, sulfur cycling plays a critical role in iron and phosphorus cycling, significantly stimulating not only the mobilization of FeP but also OP in sediments, with OP mineralization potentially being the primary contributor to endogenous phosphorus release.

Redox conditions influence the chemical composition of iron-associated organic carbon in boreal lake sediments: A synchrotron-based NEXAFS study

The global carbon and iron cycles are intimately linked as redox-sensitive iron oxides readily bind organic carbon in a variety of environmental settings, including marine and lacustrine sediments. While these iron-organic carbon complexes sequester vast quantities of organic carbon, the composition of the organic matter within them remains unknown for lacustrine environments. Here we present C K1s and Fe L3,2 edge Near Edge X-ray Absorption Fine Structure (NEXAFS) spectra of surface sediments and authigenic iron complexes from adjacent basins of a pristine boreal lake located in Québec, Canada, with contrasting oxygen exposure regimes. We demonstrate differences in organic carbon speciation in sediments from both basins, as well as co-localization of organic carbon and iron on a sub-micron scale in 100 nm thick samples. Differences in redox cycling across these two basins allow for a direct comparison of the effect of oscillating redox conditions on the composition of organic carbon sequestered by iron. Our results suggest that reactive organic molecules, which may be polysaccharides, were found preferentially associated with iron in the perennially oxic sediments compared to more phenol rich organics in the seasonally anoxic sediments, highlighting the importance of iron oxides in the protection and preservation of labile organic compounds. Traces of aliphatic carbon were observed in sediments from the anoxic basin, alongside carboxyl and aromatic functionalities. This carboxyl-rich aliphatic material could possibly interact with the sediment mineral matrix either through a ligand exchange mechanism between the mineral phases and the carboxyl functionalities, or via non-specific hydrophobic interactions involving the aliphatic moieties. Finally, our work also shows that OC:Fe ratios should be used with caution when inferring a binding mechanism between OC and iron oxides.

Bottom water quality plasticity in the northern gulf of Mexico hypoxic zone

The growth of the now ubiquitous hypoxic zones found throughout the global coastal ocean are primarily a consequence of nutrient enrichment in surface waters increasing organic production that sinks into bottom waters where oxygen is depleted faster than it is replenished. Hypoxic zones may increase or decline in number because of future climate changes. Here we summarize the summertime variations of dissolved inorganic silicate (DSi), phosphate (DIP), nitrogen (DIN; nitrate + nitrite and ammonium) and ammonium concentrations in the bottom waters of the northern Gulf of Mexico continental shelf from 1985 to 2022. The concentrations of all three are strongly correlated to oxygen concentrations, but not in the same way. At zero oxygen concentration, the annual concentrations of DSi, DIP, and ammonium changed over 38 years at a rate of 1.6 % y−1, 2.0 % y−1 and -1.7 % y−1, respectively. However, the nitrate + nitrite concentrations at zero oxygen concentrations did not change over the same interval. The silicate efflux from anoxic sediments is directly related to warming temperatures and is co-related to phosphate concentrations. The bottom water DSi:DIN molar ratios increased over three decades as DIN:DIP molar ratios decreased, suggesting strong nitrogen limitation compared to silicate and phosphate, and reveal significant plasticity in regeneration rates in the bottom waters that may be dependent on changes in the surface waters. Hypoxia and food web models based on a stationary equipoise of these amounts and ratios in surface and bottom waters will likely be deficient as coastal waters warm, acidification increases, and river water quality changes. Data refreshment and improved understanding of food web changes and warming futures are recommended.

Microbial hydrogenation of cholesterol to coprostanol by anaerobic bacteria: evidence from Antarctic lacustrine sediment

Fecal sterols are traditionally ascribed as important biomarkers for animal excrement, and have been widely used to identify the source of organic matter and to reconstruct paleoecological changes in Antarctic terrestrial, aquatic, and marine ecosystems. However, the in situ microbial hydrogenation of cholesterol to coprostanol could have significance as a proxy to infer paleoenvironmental studies in Antarctica, particularly in anoxic sediment. Here, we report that abundant coprostanol, which was traditionally deemed as a biomarker for human sewage contamination, was found in three anoxic sediment profiles (AC2, BI, and CH1), which were strongly influenced by animal excrement at North Victoria Land, western Ross Sea, Antarctica. Our results suggest that the high concentrations of coprostanol in these three sediment profiles were not due to animal excrement, since coprostanol is not present in penguin guano and is a minor component in seal excrement. Coprostanol/cholesterol and coprostanol/(coprostanol + cholestanol) ratios suggest that coprostanol in the sediment cores of AC2 and BI was primarily derived from bacterial hydrogenation of cholesterol introduced by penguin guano. Coprostanol in CH1 sediments is related to human sewage due to intensive research activities from 1968 to 2006 in this region. However, the low abundance of coprostanol and the ratios of coprostanol/cholesterol and coprostanol/(coprostanol + cholestanol) in a relatively oxidizing sediment core (IIL1) infer that coprostanol was likely contributed by seal settlement. Together with high-throughput sequencing of the 16S rRNA gene, the conversion of cholesterol to coprostanol by anaerobic bacteria (e.g., Eubacterium coprostanoligenes) could occur in anoxic aquatic systems. Our results suggest that the presence of coprostanol in Antarctic lacustrine sediment with anoxic conditions does not necessarily indicate seal activity and human waste as the microbial hydrogenation of cholesterol to coprostanol should also be considered.

Tracing Sediment‐Affected Water Masses From Coastal Areas to Offshore Oceans Using In Situ Sensing of Fluorescent Organic Matter

AbstractThe lateral transport of nutrient‐rich water masses from coastal areas to offshore areas is an important factor controlling the primary production of phytoplankton in offshore regions. If the coastal low‐salinity waters have high nutrient levels, lateral transport can be traced via salinity observations. However, if high level of nutrients in the waters are not coupled with low salinity, for example, input from coastal sediments, water transport cannot be traced via salinity observations. In this study, visible fluorescent organic matter (FOMvis) was monitored by an in situ sensor as a tracer for sediment‐affected water masses from coastal areas. The FOMvis distribution in the upper 500 m water layer in offshore Japan along the 143°E transect was generally controlled by the distributions of subtropical water (i.e., Kuroshio water and Tsugaru warm current water) and subarctic water (i.e., Oyashio water). However, anomalously high levels of FOMvis were observed at depths of 20–60 m at an observational station, which could not be explained by physical mixing. This likely originated from the lateral transport of water masses from coastal areas. In and around Sendai Bay, where observations were carried out as an example of the Japanese coast, high levels of FOMvis were observed, accompanied by negative N*, an indicator of denitrification, and phosphate and silicic acid inputs from anoxic sediments. These observational results imply that FOMvis observation via in situ sensors can be useful for tracing the input of nutrient‐rich sediment‐affected water masses from coastal areas to offshore oceans.

Spatial distribution of cable bacteria in nationwide organic-matter-polluted urban rivers in China

An overload of labile organic matter triggers the water blackening and odorization in urban rivers, leading to a unique microbiome driving biogeochemical cycles in these anoxic habitats. Among the key players in these environments, cable bacteria interfere directly with C/N/S/O cycling, and are closely associated with phylogenetically diverse microorganisms in anoxic sediment as an electron conduit to mediate long-distance electron transport from deep-anoxic-layer sulfide to oxic-layer oxygen. Despite their hypothesized importance in black-odorous urban rivers, the spatial distribution patterns and roles of cable bacteria in large-scale polluted urban rivers remain inadequately understood. This study examined the diversity and spatial distribution pattern of cable bacteria in sediment samples from 186 black-odorous urban rivers across China. Results revealed the co-existence of two well-characterized cable bacteria (i.e., Candidatus Electrothrix and Candidatus Electronema), with Candidatus Electrothrix exhibiting a comparatively wider distribution in the polluted urban rivers. Concentrations of DOC, SS, sulfate, nitrate, and heavy metals (e.g., Ni and Cr) were correlated with the cable bacteria diversity, indicating their essential role in biogeochemical cycles. The activation energy of cable bacteria was 0.624 eV, close to the canonical 0.65 eV. Furthermore, cable bacteria were identified as key connectors and module hubs, closely associated with denitrifiers, sulfate-reducing bacteria, methanogens and alkane degraders, highlighting their role as keystone functional lineages in the contaminated urban rivers. Our study provided the first large-scale and comprehensive insight into the cable bacteria diversity, spatial distribution, and their essential function as keystone species in organic-matter-polluted urban rivers.

Estimation of net accumulation and removal of fluorescent dissolved organic matter in different Baltic Sea water masses

This study aimed to detect non-conservative processes that affect the distribution of fluorescent dissolved organic matter (FDOM) in the Baltic Sea. An extensive data set comprised of 408 FDOM data, optical and physical profiles, and the development of a water masses balance model allowed us to ascertain the sources of mixing anomalies. These were seen as second-order deviations in the FDOM distribution as a function of salinity in three layers: surface water, Baltic Sea Winter Water, and deep water. The difference between modeled and measured FDOM values at three different excitation/emission wavelengths allowed to show the strength of non-conservative processes, such as photochemical and microbial decomposition (negative residual values) or extracellular release of dissolved organic matter from phytoplankton, heterotrophic uptake and release from anoxic sediments (positive residual values). Humic-like FDOM fractions displayed positive residuals in all seasons for intermediate and deep layers and negative residuals in surface waters. Largest accumulation rates of humic-like fractions were reached in the Gulf of Gdańsk during summer in intermediate and deep layers, while the greatest removal in surface waters was observed during spring in the Bornholm and Gotland Basins and during summer in the Gulf of Gdańsk, probably due to photodegradation. Positive residuals of the protein-like fraction were observed at the surface in summer and autumn in the Gulf of Gdańsk, probably linked to the abundance of phytoplankton and also due to the low molecular weight by-products of photodegradation of humic-like components. Spatial transects revealed an increase in humic-like residuals with depth and a strong correlation with apparent oxygen utilization, increasing with higher fluorescence and exhibiting an asymptotic trend. A relationship was found between the protein-like fractions and phytoplankton biomass proxies. A generalized concept for FDOM cycling in the Baltic Sea was proposed, highlighting photobleaching as the dominant non-linear process determining the efficiency of humic-like FDOM removal. The protein-like component was found to be more efficiently taken up by aerobic prokaryotes at the surface. Microbial utilization and reworking of organic matter, release from sediments, and a decade-long stagnation of bottom water masses, all contribute to the observed accumulation of FDOM in mesohaline deep waters below the permanent pycnocline in the Baltic Sea.

Microbial community structure and metabolic profile of anthropized freshwater tributary channels from La Plata River, Argentina, to develop sustainable remediation strategies.

Microbial communities from freshwater sediments are involved in biogeochemical cycles and they can be modified by physical and chemical changes in the environment. Linking the microbial community structure (MCS) with physicochemistry of freshwater courses allows a better understanding of its ecology and can be useful to assess the ecological impact generated by human activity. The MCS of tributary channels from La Plata River affected by oil refinery (C, D, and E) and one also by urban discharges (C) was studied. For this purpose, 16S rRNA metabarcoding analysis, in silico metagenome functional prediction, and the hydrocarbon degradation potential (in silico predictions of hydrocarbon-degrading genes and their quantification by qPCR) of the MCS were studied. Principal coordinate analysis revealed that the MCS was different between sites, and it was not structured by the hydrocarbon content. Site C showed physicochemical characteristics, bacterial taxa, and an in silico functional prediction related to fermentative/heterotrophic metabolism. Site D, despite having higher concentration of hydrocarbon, presented autotrophic, syntrophic, and methanogenic pathways commonly involved in natural processes in anoxic sediments. Site E showed and intermediate autotrophic/heterotrophic behavior. The hydrocarbon degradation potential showed no positive correlation between the hydrocarbon-degrading genes quantified and predicted. The results suggest that the hydrocarbon concentration in the sites was not enough selection pressure to structure the bacterial community composition. Understanding which is the variable that structures the bacterial community composition is essential for monitoring and designing of sustainable management strategies for contaminated freshwater ecosystems.

Middle Ordovician climatic and oceanic destabilization in a slope-setting of the Yangtze platform, South China, and its role as a regional brake on the Ordovician radiations

During the Middle Ordovician, the Great Ordovician Biodiversification Event (GOBE) saw an accelerated diversification pulse in the marine metazoan richness, which has been linked to the oceanic and climatic changes. Here we have examined a deep-water slope succession, Xijinhe section, in Lower Yangtze region by integrating sedimentological and geochemical methods. This study highlights that the climatic and oceanic destabilization might have substantially impacted the marine biodiversity during the Middle Ordovician in South China. Three phases are identified based on lithological and geochemical variations. During Phase I across the Early–Middle Ordovician transition (Floian–Dapingian), the TOC and abundances of redox sensitive elements (RSE) are relatively depleted, suggesting a suboxic-oxic environment in the slope area of Yangtze Sea. The continental chemical weathering intensity transits from stable to unstable in Phase I indicated by CIA (chemical index of alteration) that gradually fluctuate to lower values, potentially caused by the secular cooling. The slowly ameliorating climate and redox conditions advanced the biodiversification across the Early–Middle Ordovician transition. During the Phase II in the Darriwilian, the continental chemical weathering intensity continues to decrease and the concentrations of RSE start to rise. The values of Mn(%)*Co(ppm) become consistently lower than 0.4, and the bio-limited elements such as P, Ba, and Ni are substantially enriched correspondingly. This phenomenon implicates that a secular cooling climate would have resulted in oceanic destabilization by improving upwelling of deeper anoxic/euxinic and eutrophic water into epicontinental sea, potentially causing a deceleration in the biodiversification during the Darriwilian in South China. The Phase III across the Middle–Late Ordovician transition, witnesses the continuous decrease of CIA values and highest abundances of TOC and RSE though some minor fluctuations, indicating a possibly even more drastic oceanic destabilization relative to Phase II. Deeper anoxic/euxinic water continuously intruded and shoaled into the shelf area during the Phase III due to the enhanced upwelling. Consequently, the habitat of marine organisms in shallow water was contracted, and becoming harsher. Additionally, bio-limited elements such as P were released from anoxic sediments and recycle into the seawater during the Middle Ordovician, boosting primary productivity level and may further deplete oxygen in seawater. This unstable oceanic state during the Middle Ordovician, particularly Darriwilian, represented by high nutrients content in epi-continental sea and expanding anoxic/euxinic water, could be attributable for the deceleration of biodiversification in South China and potentially the spatially variable paces of biodiversification in different paleo-continents during the main phase of the GOBE.

Sulfur cycling likely obscures dynamic biologically-driven iron redox cycling in contemporary methane seep environments.

Deep-sea methane seeps are amongst the most biologically productive environments on Earth and are often characterised by stable, low oxygen concentrations and microbial communities that couple the anaerobic oxidation of methane to sulfate reduction or iron reduction in the underlying sediment. At these sites, ferrous iron (Fe2+) can be produced by organoclastic iron reduction, methanotrophic-coupled iron reduction, or through the abiotic reduction by sulfide produced by the abundant sulfate-reducing bacteria at these sites. The prevalence of Fe2+in the anoxic sediments, as well as the availability of oxygen in the overlying water, suggests that seeps could also harbour communities of iron-oxidising microbes. However, it is unclear to what extent Fe2+ remains bioavailable and in solution given that the abiotic reaction between sulfide and ferrous iron is often assumed to scavenge all ferrous iron as insoluble iron sulfides and pyrite. Accordingly, we searched the sea floor at methane seeps along the Cascadia Margin for microaerobic, neutrophilic iron-oxidising bacteria, operating under the reasoning that if iron-oxidising bacteria could be isolated from these environments, it could indicate that porewater Fe2+ can persist is long enough for biology to outcompete pyritisation. We found that the presence of sulfate in our enrichment media muted any obvious microbially-driven iron oxidation with most iron being precipitated as iron sulfides. Transfer of enrichment cultures to sulfate-depleted media led to dynamic iron redox cycling relative to abiotic controls and sulfate-containing cultures, and demonstrated the capacity for biogenic iron (oxyhydr)oxides from a methane seep-derived community. 16S rRNA analyses revealed that removing sulfate drastically reduced the diversity of enrichment cultures and caused a general shift from a Gammaproteobacteria-domainated ecosystem to one dominated by Rhodobacteraceae (Alphaproteobacteria). Our data suggest that, in most cases, sulfur cycling may restrict the biological "ferrous wheel" in contemporary environments through a combination of the sulfur-adapted sediment-dwelling ecosystems and the abiotic reactions they influence.

Microcosm study reveals the microbial and environmental effects on tributyltin degradation in an estuarine sediment

Tributyltin (TBT) is one of the most harmful contaminants ever released into the aquatic environment. Despite being banned, it is still present at many locations throughout the world. Its degradation in sediment mainly occurs through microbial biodegradation, a process that remains unclear. This study therefore aimed at better understanding TBT biodegradation in estuarine sediment and the microbial community associated with it. Microcosm experiments were set up, embracing a range of environmental control parameters. Major community shifts were recorded, mainly attributed to the change in oxygen status. The highest percentage of degradation (36,8%) occurred at 4 °C in anaerobic conditions. These results are encouraging for the in-situ bioremediation of TBT contaminated muddy sediment in temperate ports worldwide. However, with TBT able to persist in the coastal environment for decades when undisturbed in anoxic sediment, further research is needed to fully understand the mechanisms that triggered this biodegradation observed in the microcosms.

Enhanced phenanthrene biodegradation in river sediments by harnessing calcium peroxide nanoparticles and minerals in Sphingomonas sp. DSM 7526 cultivation

ABSTRACT Coupling chemical oxidation and biodegradation to remediate polycyclic aromatic hydrocarbon (PAH)-contaminated sediment has recently gained significant attention. In this study, calcium peroxide nanoparticles (nCaO2) were utilized as an innovative oxygen-releasing compound for in-situ chemical oxidation. The study investigates the bioremediation of phenanthrene (PHE)-contaminated sediment inoculated with Sphingomonas sp. DSM 7526 bacteria and treated with either aeration or nCaO2. Using three different culture media, the biodegradation efficiencies of PHE-contaminated anoxic sediment, aerobic sediment, and sediment treated with 0.2% w/w nCaO2 ranged from 57.45% to 63.52%, 69.87% to 71.00%, and 92.80% to 94.67%, respectively. These values were significantly higher compared to those observed in non-inoculated sediments. Additionally, the type of culture medium had a prominent effect on the amount of PHE removal. The presence of minerals in the culture medium increased the percentage of PHE removal compared to distilled water by about 2–10%. On the other hand, although the application of CaO2 nanoparticles negatively impacted the abundance of sediment bacteria, resulting in a 30–42% decrease in colony-forming units after 30 days of treatment, the highest PHE removal was obtained when coupling biodegradation and chemical oxidation. These findings demonstrate the successful application of bioaugmentation and chemical oxidation processes for treating PAH-contaminated sediment.

An abundant bacterial phylum with nitrite-oxidizing potential in oligotrophic marine sediments

Nitrite-oxidizing bacteria (NOB) are important nitrifiers whose activity regulates the availability of nitrite and dictates the magnitude of nitrogen loss in ecosystems. In oxic marine sediments, ammonia-oxidizing archaea (AOA) and NOB together catalyze the oxidation of ammonium to nitrate, but the abundance ratios of AOA to canonical NOB in some cores are significantly higher than the theoretical ratio range predicted from physiological traits of AOA and NOB characterized under realistic ocean conditions, indicating that some NOBs are yet to be discovered. Here we report a bacterial phylum Candidatus Nitrosediminicolota, members of which are more abundant than canonical NOBs and are widespread across global oligotrophic sediments. Ca. Nitrosediminicolota members have the functional potential to oxidize nitrite, in addition to other accessory functions such as urea hydrolysis and thiosulfate reduction. While one recovered species (Ca. Nitrosediminicola aerophilus) is generally confined within the oxic zone, another (Ca. Nitrosediminicola anaerotolerans) additionally appears in anoxic sediments. Counting Ca. Nitrosediminicolota as a nitrite-oxidizer helps to resolve the apparent abundance imbalance between AOA and NOB in oxic marine sediments, and thus its activity may exert controls on the nitrite budget.

Distribution of eukaryotic environmental DNA in global subseafloor sediments

The analysis of eukaryotic environmental DNA (eDNA) in sediment has the potential for understanding past ecosystems, even for taxa lacking skeletons or preserved only as a part of necromass. Despite the paleoenvironmental and ecological importance of eukaryotic eDNA in marine sediment, the duration of remaining eDNA and the species of eDNA present in marine sediment has not been well investigated. Here, we analyzed eDNA extracted from 299 sediment samples down to 678 m below the seafloor at 40 geologically distinct sites. The results showed that eukaryotic eDNA was amplified from more than 80% of the sediments with a depositional age of less than 100,000 years. The eDNA was well conserved in anoxic sediments than in oxic sediments, with PCR success rates of 48% and 18%, respectively. The eukaryotic communities include non-benthic organisms such as marine plankton, including diatoms, dinoflagellates, and coccolithophores. A freshwater diatom genus Aulacoseira was detected in the Baltic Sea sediments from the last glacial lacustrine environment. These results provide new insights into the global-scale distribution of the past eukaryotic eDNA preserved in marine sediment.

Resting cells of Skeletonema marinoi assimilate organic compounds and respire by dissimilatory nitrate reduction to ammonium in dark, anoxic conditions.

Diatoms can survive long periods in dark, anoxic sediments by forming resting spores or resting cells. These have been considered dormant until recently when resting cells of Skeletonema marinoi were shown to assimilate nitrate and ammonium from the ambient environment in dark, anoxic conditions. Here, we show that resting cells of S. marinoi can also perform dissimilatory nitrate reduction to ammonium (DNRA), in dark, anoxic conditions. Transmission electron microscope analyses showed that chloroplasts were compacted, and few large mitochondria had visible cristae within resting cells. Using secondary ion mass spectrometry and isotope ratio mass spectrometry combined with stable isotopic tracers, we measured assimilatory and dissimilatory processes carried out by resting cells of S. marinoi under dark, anoxic conditions. Nitrate was both respired by DNRA and assimilated into biomass by resting cells. Cells assimilated nitrogen from urea and carbon from acetate, both of which are sources of dissolved organic matter produced in sediments. Carbon and nitrogen assimilation rates corresponded to turnover rates of cellular carbon and nitrogen content ranging between 469 and 10,000 years. Hence, diatom resting cells can sustain their cells in dark, anoxic sediments by slowly assimilating and respiring substrates from the ambient environment.

Internal phosphorus loading alters nutrient limitation and contributes to cyanobacterial blooms in a polymictic lake

Clear Lake, a medium-sized hypereutrophic, polymictic lake in northern California, has had recurring harmful cyanobacteria blooms (HCBs) for over a century despite reductions in external phosphorus (P) loadings. Internal P loading can alter nutrient availability and limitation supporting HCBs but is rarely quantified or compared with external loads. We have quantified external P loads from 2019 to 2021 for the three main tributaries (accounting for 46% of the flow) and internal loadings using two methods: a P mass balance and modeled release rates of soluble reactive phosphorus from oxic and anoxic sediments. In addition, we combined high-frequency in situ measurements of water temperature and dissolved oxygen, discrete grab sampling for nutrient chemistry, and remote sensing to explore the potential drivers of the observed variability and provide a comprehensive view of the spatiotemporal dynamics of HCBs. By understanding the relative contribution of external and internal nutrient loadings and the relationship between environmental parameters and HCBs, interannual bloom variability can be better predicted. Comparative estimates of external and internal phosphorus loading indicate that internal sources accounted for 70–95% of the total P input into the system during the study period. Contrary to other lakes, the intensity of the summer bloom season was correlated to the timing and duration of anoxia rather than the magnitude of spring runoff. Internally released P shifted the system from phosphorus to nitrogen limitation during the summer, potentially favoring the proliferation of nitrogen-fixing cyanobacteria.

Impact of Chondrites on trace metal distribution in the sapropel S7 (ODP Site 966): Implications for paleoenvironmental and paleoceanographic reconstructions

Organic-rich deposits are valuable paleo-archives, recording significant paleoceanographic changes linked to past climate variations and marine deoxygenation events. The deposition of organic-rich sediments stops when bottom-water reventilation/oxygenation occurs. This impedes organic matter preservation, enabling macro and micro burrowing-organisms to recover and bioturbate the seafloor. In this sense, highly bioturbated sediments require particular attention when sampling is done for geochemical analyses, as sediments can be considerably mixed. While avoiding trace fossils during sampling for geochemical analyses is easy for large traces (e.g. Planolites, Thallasinoides, and Zoophycos), it becomes challenging for smaller and complex traces (< 0.5 cm), as is the case with Chondrites. Chondrites-producers have an opportunistic behavior, being one of the first organisms to colonize the seafloor after an anoxic event. As a result, Chondrites are commonly and sometimes abundantly found in the upper layers of organic-rich sediments, including sapropels and black shales.This study focuses on sapropel S7, which was deposited between ∼198.5 and 191.9 ka at the top of Eratosthenes Seamount and exhibits abundant Chondrites. For this sapropel, we demonstrated that Chondrites-producers can bioturbate significant volumes of organic-rich sediments (over 35%), introducing oxic/dysoxic material downward into anoxic sediments enriched in redox-sensitive trace metals and organic matter. This process can dilute up to 18% the original concentration of redox-sensitive trace metals (e.g. Mo, U and V). This dilution is especially important to consider when calculating trace metals and organic matter burial flux from bulk sediment data. Therefore, Chondrites-producers can play a crucial role in altering the sediment texture and distribution of minerals and organic matter at sub-cm scale, and may thus impact paleoenvironmental and paleoceanographic reconstructions based on geochemical signals. Furthermore, the subsequent redistribution of organic matter and redox-sensitive trace metals (including oligoelements) within the sediment can affect carbon and nutrient cycling, microbial activity, organic matter degradation in deep-marine sediments, and the overall sedimentary biogeochemistry.

Interactions of Perrhenate (Re(VII)O4−) with Fe(II)-Bearing Minerals

Rhenium (Re) is an extremely rare element, with a crustal abundance of approximately 0.4 parts per billion (ppb) and a sea water concentration of 8.3 parts per trillion (ppt). However, Re concentrations in anoxic marine sediments range from 2 to 184 ppb, which is attributed to reduction of the highly soluble perrhenate ion (Re(VII)O4−) to insoluble Re(IV) species. Anoxic sediments typically contain Fe(II) and sulfide species, which could potentially reduce Re(VII) to Re(IV). In this study, we examined the interactions of KReO4 with magnetite (Fe3O4), siderite (FeCO3), vivianite (Fe3(PO4)2•8H2O), green rust (mixed Fe(II)/Fe(III) layered double hydroxide), mackinawite (FeS), and chemically reduced nontronite (NAu-1) using X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) spectroscopy to determine the valence state and speciation of Re. Uptake of Re by green rust was rapid, with ~50% associated with the solids within 2 days. In contrast, there was &lt;10% uptake by the other Fe(II) phases over 48 days. Reduction of Re(VII) to Re(IV) was only observed in the presence of green rust, producing clusters of bidentate-coordinated Re(IV)O6 octahedra.. These results suggest that except for green rust, the potential for other Fe(II)-bearing minerals to act as reductants for ReO4− in sedimentary environments requires further investigation.