Towards a consistent classification scheme for geochemical environments, or, why we wish the term 'suboxic' would go away

Trace metals in coastal marine sediments: Natural and anthropogenic sources, correlation matrices, and proxy potentials

Rapidly spreading industrialization since the 19th century has led to a drastic increase in trace metal deposition in coastal sediments. Provided that these trace metals have remained relatively immobile after deposition, their sedimentary enrichments can serve as records of local-regional pollution histories. Factors controlling this proxy potential include trace metal geochemistry (carrier-, and host phase affinity), and depositional environmental factors (redox variability, particulate shuttling, organic matter loading, bathymetry). Yet, the relative importance and interactions between these controls are still poorly understood, hampering the reliable use of trace metal-based environmental proxies. By summarizing nine site-specific correlation matrices of 16 metal (loid) s (Pb, Cd, Cu, Zn, Sb, Sn, Ni, As, Tl, V, Mo, U, Re, Fe, Mn, Al), total organic C, and S contents in short sediment cores into a single meta-matrix, we test a novel approach for quickly detecting common and contrasting trace metal enrichment patterns across different study locations. Our meta-matrix shows two trace metal groups, within which positive correlations of e.g., Pb, Cd, Zn, Cu, Sb suggest a primary "anthropogenically sourced" (group I) control, whereas known "redox-sensitive" (group II) trace metals (Mo, U, Re) are characterized by fewer positive correlations. However, some group I metals (Cd, Zn, Cu, Sb) also covary with group II metals, inferring that redox variability may obscure primary anthropogenic signals; Sb even shows advantages over Mo and U under oxic conditions. As a more robust pollution indicator we identified Pb; yet for reconstructing historical Pb atmospheric pollution signals (1970s Pb peak), it is crucial to consider the distance from shore. In near-shore environments, local (fluvial) pollution signals may overprint large-scale (atmospheric) signals. Our findings demonstrate that combining site-specific sedimentary correlation and distribution patterns with a meta-matrix considerably aids the understanding of trace metal sequestration in different coastal sedimentary environments, which thereby improves trace metal proxy reliability.

Cycling and persistence of iron-bound organic carbon in subseafloor sediments

Reactive iron (FeR) serves as an important sink of organic carbon (OC) in marine surface sediments, which preserves approximately 20% of total OC (TOC) as reactive iron-bound OC (FeR-OC). However, the fate of FeR-OC in subseafloor sediments and its availability to microorganisms, remain undetermined. Here, we reconstructed continuous FeR-OC records in two sediment cores of the northern South China Sea encompassing the suboxic to methanic biogeochemical zones and reaching a maximum age of ~100 kyr. The downcore FeR-OC contributes a relatively stable proportion of 13.3 ± 3.2% to TOC. However, distinctly lower values of less than 5% of TOC, accompanied by notable 13C depletion of FeR-OC, are observed in the sulfate-methane transition zone (SMTZ). FeR-OC is suggested to be remobilized by microbially mediated reductive dissolution of FeR and subsequently remineralized, the flux of which is 18-30% of the methane consumption in the SMTZ. The global reservoir of FeR-OC in microbially active Quaternary marine sediments could be 19-46 times the size of the atmospheric carbon pool. Thus, the FeR-OC pool may support subseafloor microorganisms and contribute to regulating Earth's carbon cycle.

Elemental Geochemical Characteristics of Shales from Wufeng-Longmaxi Formations in the Southern Margin of the Qinling Orogenic Belt, China: Implications for Depositional Controls on Organic Matter

The tectonic background and sedimentary environment during the transition period from the Ordovician to Silurian have been widely studied by many scholars. This study focuses on the Upper Ordovician Wufeng Formation and Lower Silurian Longmaxi Formation in the Bajiaokou profile at the southern margin of the Qinling Orogenic Belt in southern China. In order to study the aggregation mechanism of organic matter, geochemical proxies were proposed, including redox proxies (V, V/Al, U, U/Al, Mo, and Mo/Al), paleoproductivity proxies (P, P/Ti, Ba, Ba/Al, and SiXS), paleoclimate proxies (CIA), and terrigenous flux proxies (Al, Zr, and Zr/Al). In addition, Al-Co[EF] × Mn[EF] is used to provide information on paleoenvironmental parameters such as watermass restriction conditions. The redox proxies show that the Wufeng-Longmaxi shale is mainly accumulated under oxic-dysoxic conditions. During the shale deposition period of Wufeng-Longmaxi formations, the marine surface primary productivity in the southern Qinling area is generally low to moderate. The paleoclimate proxies show that from the Late Ordovician to the Early Silurian the southern Qinling area generally had a warm and humid climate. The upwelling current is widely developed in the northern margin of the Sichuan Basin and the southern margin of the Qinling area. Although the upwelling current was highly developed during the deposition of the Wufeng Formation in the Bajiaokou profile, the concentrated accumulation of a large amount of volcanic ash resulted in the low primary productivity of the ocean. During the sedimentary period of the Longmaxi Formation in the Bajiaokou profile, the development of seasonal upwelling currents and a small amount of volcanic ash supply increased the primary productivity to moderate, which provided a good material basis for the enrichment of organic matter, but the high detritus flux and the water body condition of oxic-dysoxic resulted in the slight enrichment of organic matter.

Sulfide Toxicity as Key Control on Anaerobic Oxidation of Methane in Eutrophic Coastal Sediments

Coastal zones account for 75% of marine methane emissions, despite covering only 15% of the ocean surface area. In these ecosystems, the tight balance between methane production and oxidation in sediments prevents most methane from escaping into seawater. However, anthropogenic activities could disrupt this balance, leading to an increased methane escape from coastal sediments. To quantify and unravel potential mechanisms underlying this disruption, we used a suite of biogeochemical and microbiological analyses to investigate the impact of anthropogenically induced redox shifts on methane cycling in sediments from three sites with contrasting bottom water redox conditions (oxic-hypoxic-euxinic) in the eutrophic Stockholm Archipelago. Our results indicate that the methane production potential increased under hypoxia and euxinia, while anaerobic oxidation of methane was disrupted under euxinia. Experimental, genomic, and biogeochemical data suggest that the virtual disappearance of methane-oxidizing archaea at the euxinic site occurred due to sulfide toxicity. This could explain a near 7-fold increase in the extent of escape of benthic methane at the euxinic site relative to the hypoxic one. In conclusion, these insights reveal how the development of euxinia could disrupt the coastal methane biofilter, potentially leading to increased methane emissions from coastal zones.

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.

High hydrostatic pressure stimulates microbial nitrate reduction in hadal trench sediments under oxic conditions

Hadal trenches are extreme environments situated over 6000 m below sea surface, where enormous hydrostatic pressure affects the biochemical cycling of elements. Recent studies have indicated that hadal trenches may represent a previously overlooked source of fixed nitrogen loss; however, the mechanisms and role of hydrostatic pressure in this process are still being debated. To this end, we investigate the effects of hydrostatic pressure (0.1 to 115 MPa) on the chemical profile, microbial community structure and functions of surface sediments from the Mariana Trench using a Deep Ocean Experimental Simulator supplied with nitrate and oxygen. We observe enhanced denitrification activity at high hydrostatic pressure under oxic conditions, while the anaerobic ammonium oxidation - a previously recognized dominant nitrogen loss pathway - is not detected. Additionally, we further confirm the simultaneous occurrence of nitrate reduction and aerobic respiration using a metatranscriptomic dataset from in situ RNA-fixed sediments in the Mariana Trench. Taken together, our findings demonstrate that hydrostatic pressure can influence microbial contributions to nitrogen cycling and that the hadal trenches are a potential nitrogen loss hotspot. Knowledge of the influence of hydrostatic pressure on anaerobic processes in oxygenated surface sediments can greatly broaden our understanding of element cycling in hadal trenches.

Metagenome-assembled genomes of deep-sea sediments: changes in microbial functional potential lag behind redox transitions

Hadal sediments are hotspots of microbial activity in the deep sea and exhibit strong biogeochemical gradients. But although these gradients are widely assumed to exert selective forces on hadal microbial communities, the actual relationship between biogeochemistry, functional traits, and microbial community structure remains poorly understood. We tested whether the biogeochemical conditions in hadal sediments select for microbes based on their genomic capacity for respiration and carbohydrate utilization via a metagenomic analysis of over 153 samples from the Atacama Trench region (max. depth = 8085 m). The obtained 1357 non-redundant microbial genomes were affiliated with about one-third of all known microbial phyla, with more than half belonging to unknown genera. This indicated that the capability to withstand extreme hydrostatic pressure is a phylogenetically widespread trait and that hadal sediments are inhabited by diverse microbial lineages. Although community composition changed gradually over sediment depth, these changes were not driven by selection for respiratory or carbohydrate degradation capability in the oxic and nitrogenous zones, except in the case of anammox bacteria and nitrifying archaea. However, selection based on respiration and carbohydrate degradation capacity did structure the communities of the ferruginous zone, where aerobic and nitrogen respiring microbes declined exponentially (half-life = 125-419 years) and were replaced by subsurface communities. These results highlight a delayed response of microbial community composition to selective pressure imposed by redox zonation and indicated that gradual changes in microbial composition are shaped by the high-resilience and slow growth of microbes in the seafloor.

Cell-specific rates of sulfate reduction and fermentation in the sub-seafloor biosphere

Microorganisms in subsurface sediments live from recalcitrant organic matter deposited thousands or millions of years ago. Their catabolic activities are low, but the deep biosphere is of global importance due to its volume. The stability of deeply buried sediments provides a natural laboratory where prokaryotic communities that live in steady state with their environments can be studied over long time scales. We tested if a balance is established between the flow of energy, the microbial community size, and the basal power requirement needed to maintain cells in sediments buried meters below the sea floor. We measured rates of carbon oxidation by sulfate reduction and counted the microbial cells throughout ten carefully selected sediment cores with ages from years to millions of years. The rates of carbon oxidation were converted to power (J s-1 i.e., Watt) using the Gibbs free energy of the anaerobic oxidation of complex organic carbon. We separated energy dissipation by fermentation from sulfate reduction. Similarly, we separated the community into sulfate reducers and non-sulfate reducers based on the dsrB gene, so that sulfate reduction could be related to sulfate reducers. We found that the per-cell sulfate reduction rate was stable near 10-2 fmol C cell-1 day-1 right below the zone of bioturbation and did not decrease with increasing depth and sediment age. The corresponding power dissipation rate was 10-17 W sulfate-reducing cell-1. The cell-specific power dissipation of sulfate reducers in old sediments was similar to the slowest growing anaerobic cultures. The energy from mineralization of organic matter that was not dissipated by sulfate reduction was distributed evenly to all cells that did not possess the dsrB gene, i.e., cells operationally defined as fermenting. In contrast to sulfate reducers, the fermenting cells had decreasing catabolism as the sediment aged. A vast difference in power requirement between fermenters and sulfate reducers caused the microbial community in old sediments to consist of a minute fraction of sulfate reducers and a vast majority of fermenters.

Deterministic processes dominate archaeal community assembly from the Pearl River to the northern South China Sea

Archaea play a significant role in the biogeochemical cycling of nutrients in estuaries. However, comprehensive researches about their assembly processes remain notably insufficient. In this study, we systematically examined archaeal community dynamics distinguished between low-salinity and high-salinity groups in water and surface sediments over a 600-kilometer range from the upper Pearl River (PR) to the northern South China Sea (NSCS). Neutral community model analysis together with null model analysis showed that their C-score values were greater than 2, suggesting that deterministic processes could dominate the assembly of those planktonic or benthic archaeal communities at both the low-salinity and high-salinity sites. And deterministic processes contributed more in the low-salinity than high-salinity environments from the PR to the NSCS. Furthermore, through the co-occurrence network analysis, we found that the archaeal communities in the low-salinity groups possessed closer interactions and higher proportions of negative interactions than those in the high-salinity groups, which might be due to the larger environmental heterogeneities reflected by the nutrient concentrations of those low-salinity samples. Collectively, our work systematically investigated the composition and co-occurrence networks of archaeal communities in water as well as sediments from the PR to the NSCS, yielding new insights into the estuary's archaeal community assembly mechanisms.

The Impact of Sea Ice Cover on Microbial Communities in Antarctic Shelf Sediments

The area around the Antarctic Peninsula (AP) is facing rapid climatic and environmental changes, with so far unknown impacts on the benthic microbial communities of the continental shelves. In this study, we investigated the impact of contrasting sea ice cover on microbial community compositions in surface sediments from five stations along the eastern shelf of the AP using 16S ribosomal RNA (rRNA) gene sequencing. Redox conditions in sediments with long ice-free periods are characterized by a prevailing ferruginous zone, whereas a comparatively broad upper oxic zone is present at the heavily ice-covered station. Low ice cover stations were highly dominated by microbial communities of Desulfobacterota (mostly Sva1033, Desulfobacteria, and Desulfobulbia), Myxococcota, and Sva0485, whereas Gammaproteobacteria, Alphaproteobacteria, Bacteroidota, and NB1-j prevail at the heavy ice cover station. In the ferruginous zone, Sva1033 was the dominant member of Desulfuromonadales for all stations and, along with eleven other taxa, showed significant positive correlations with dissolved Fe concentrations, suggesting a significant role in iron reduction or an ecological relationship with iron reducers. Our results indicate that sea ice cover and its effect on organic carbon fluxes are the major drivers for changes in benthic microbial communities, favoring potential iron reducers at stations with increased organic matter fluxes.

The influence of the taphonomically active zone on peat formation: Establishing modern peat analogs to decipher mangrove sub-habitats from historical peats

Mangroves create unique and highly productive wetland communities in intertidal zones of tropical and subtropical coastlines. Despite their many ecosystem services, such as carbon sequestration, mangroves remain threatened by climate change, sea-level rise, and human development. The inclusion of conservation paleobiology and long-term perspectives on how these ecosystems have responded to past environmental change can inform current policy and lead to more effective conservation and restoration management strategies for modern mangrove communities. In South Florida, humified plant debris, or peat, in mangroves provides this historical record. Our research takes a novel paleobiological approach by using plant organ- and taxon-based measures to describe the influence of the taphonomically active zone (TAZ: the zone near the surface of the substrate where taphonomic processes actively formation and degrade accumulated detritus) on the decomposition of mangrove peat with depth. This allows us to understand the taphonomic biases imposed on mangrove peat as it is sequestered into the sedimentological record and provides us with the paleoecological context to better interpret preserved peats and reconstruct past mangrove sub-habitats from peat cores. Accordingly, we collected modern surficial peat cores from two contrasting mangrove sub-habitats in Barnes Sound, FL. These surficial cores were characterized and compared to historical, deep cores from other South Florida mangrove peat deposits. By comparing the proportional abundance of mangrove peat constituents in these samples, we established modern analogs needed to interpret changes in the depositional environment of historical mangrove peats found in sediment cores, which is critical for understanding shoreline responses of mangroves to sea-level rise and anthropogenic change. We demonstrate that (1) leaf mat thickness may be a relative indicator of surficial peat decomposition rates because it correlates with the degree of tidal activity and detritivore access to the leaf litter layer; (2) root percentages are valid tools to differentiate between peats at depth, and can be used as relative indicators for the distance of in situ peat from shorelines; and (3) organismal signals, such as foraminifera and insect parts, provide a means for deciphering precursor mangrove sub-habitats from sequestered peats.

Transport-limited reactions in microbial systems

Predicting microbial metabolic rates and emergent biogeochemical fluxes remains challenging due to the many unknown population dynamical, physiological and reaction-kinetic parameters and uncertainties in species composition. Here, we show that the need for these parameters can be eliminated when population dynamics and reaction kinetics operate at much shorter time scales than physical mixing processes. Such scenarios are widespread in poorly mixed water columns and sediments. In this 'fast-reaction-transport' (FRT) limit, all that is required for predictions are chemical boundary conditions, the physical mixing processes and reaction stoichiometries, while no knowledge of species composition, physiology or population/reaction kinetic parameters is needed. Using time-series data spanning years 2001-2014 and depths 180-900 m across the permanently anoxic Cariaco Basin, we demonstrate that the FRT approach can accurately predict the dynamics of major electron donors and acceptors (Pearson r ≥ 0.9 in all cases). Hence, many microbial processes in this system are largely transport limited and thus predictable regardless of species composition, population dynamics and kinetics. Our approach enables predictions for many systems in which microbial community dynamics and kinetics are unknown. Our findings also reveal a mechanism for the frequently observed decoupling between function and taxonomy in microbial systems.

Geochemistry and release risk for nutrients in lake sediments based on diffusive gradients in thin films

A comprehensive understanding of the mobility of both nitrogen (N) and phosphorus (P) and the inter-relationships between P, N, and iron (Fe) in sediments is important for controlling the "internal loadings" of nutrients in lakes. In this research, diffusive gradients in thin film (DGT) assemblies with binding layers (ZrO-AT, chelex, and ZrO) were designed for PO₄-P, Fe, ammonium (NH₄-N), and nitrate (NO₃-N) at sediment/water interface (SWI) in Western Lake Taihu (China). The biogeochemical processes of N and P related to the physicochemical properties, the dynamic P transfer, the distribution characteristics of P microniches, and the estimation of the release risks in sediments in Western Lake Taihu were simultaneously revealed by the passive sampling technique-DGT with the high spatial resolutions (millimeter and sub-millimeter). Based on DGT concentration (C_DGT) related to physicochemical properties in sediments, (1) P biogeochemical reactions included P release from Fe-bound P during Fe reduction, algae biomass decomposition, and phosphatase enzyme activity increased by NH₄-N; (2) denitrification and dissimilatory nitrate reduction to ammonium (DNRA) led to exchangeable ammonium (NH₄ex) enrichment and NH₄-N release; anammox depleted NH₄-N transfer; organic matter (OM) mineralization favored NH₄-N release; and (3) aerobic nitrification led to NO₃-N remobilization; denitrification and DNRA reduced NO₃-N release. Redox status, OM, Fe, aluminum, or calcium influenced mobilization of nutrients. The numerical model of DGT-induced fluxes in sediments was used for dynamic P transfers with resupply types ("slow" ~ "fast") controlled by labile P pool, resupply constant, response time, and Dspt rate. The formation of P microniches in two dimensions was revealed. Sediment P release risk index (0.49 ~ 36.85 [lg (nmol cm^-3 d^-1)]) with "light" ~ "high" risks and diffusive fluxes across SWI (µg m^-2 d^-1) of 15.0 ~ 639 (PO₄-P), - 1403 ~ 5010 (NH₄-N), and - 1395 ~ 149 (NO₃-N) were derived and lake management strategies were provided. The DGT technique provides the characterization of the mobilization of nutrients and evidence for biogeochemical processes at the fine spatial scales for control of internal loadings in sediments.

Eukaryogenesis and oxygen in Earth history

The endosymbiotic origin of mitochondria during eukaryogenesis has long been viewed as an adaptive response to the oxygenation of Earth's surface environment, presuming a fundamentally aerobic lifestyle for the free-living bacterial ancestors of mitochondria. This oxygen-centric view has been robustly challenged by recent advances in the Earth and life sciences. While the permanent oxygenation of the atmosphere above trace concentrations is now thought to have occurred 2.2 billion years ago, large parts of the deep ocean remained anoxic until less than 0.5 billion years ago. Neither fossils nor molecular clocks correlate the origin of mitochondria, or eukaryogenesis more broadly, to either of these planetary redox transitions. Instead, mitochondria-bearing eukaryotes are consistently dated to between these two oxygenation events, during an interval of pervasive deep-sea anoxia and variable surface-water oxygenation. The discovery and cultivation of the Asgard archaea has reinforced metabolic evidence that eukaryogenesis was initially mediated by syntrophic H₂ exchange between an archaeal host and an α-proteobacterial symbiont living under anoxia. Together, these results temporally, spatially and metabolically decouple the earliest stages of eukaryogenesis from the oxygen content of the surface ocean and atmosphere. Rather than reflecting the ancestral metabolic state, obligate aerobiosis in eukaryotes is most probably derived, having only become globally widespread over the past 1 billion years as atmospheric oxygen approached modern levels.

Methanogen Productivity and Microbial Community Composition Varies With Iron Oxide Mineralogy

Quantifying the flux of methane from terrestrial environments remains challenging, owing to considerable spatial and temporal variability in emissions. Amongst a myriad of factors, variation in the composition of electron acceptors, including metal (oxyhydr)oxides, may impart controls on methane emission. The purpose of this research is to understand how iron (oxyhydr)oxide minerals with varied physicochemical properties influence microbial methane production and subsequent microbial community development. Incubation experiments, using lake sediment as an inoculum and acetate as a carbon source, were used to understand the influence of one poorly crystalline iron oxide mineral, ferrihydrite, and two well-crystalline minerals, hematite and goethite, on methane production. Iron speciation, headspace methane, and 16S-rRNA sequencing microbial community data were measured over time. Substantial iron reduction only occurred in the presence of ferrihydrite while hematite and goethite had little effect on methane production throughout the incubations. In ferrihydrite experiments the time taken to reach the maximum methane production rate was slower than under other conditions, but methane production, eventually occurred in the presence of ferrihydrite. We suggest that this is due to ferrihydrite transformation into more stable minerals like magnetite and goethite or surface passivation by Fe(II). While all experimental conditions enriched for Methanosarcina, only the presence of ferrihydrite enriched for iron reducing bacteria Geobacter. Additionally, the presence of ferrihydrite continued to influence microbial community development after the onset of methanogenesis, with the dissimilarity between communities growing in ferrihydrite compared to no-Fe-added controls increasing over time. This work improves our understanding of how the presence of different iron oxides influences microbial community composition and methane production in soils and sediments.

Cadmium isotopes in Bahamas platform carbonates: A base for reconstruction of past surface water bioproductivity and their link with chromium isotopes

The distribution of cadmium (Cd) within the oceans strongly suggests that it is used as a nutrient by marine phytoplankton. Biologically induced removal of Cd from modern surface waters is accompanied by an isotopic fractionation leaving surface-waters enriched in isotopically heavy Cd. This first study focusses on tying the Cd isotopic record preserved in modern shallow platform carbonates of the Great Bahama Bank (GBB) to conditions in the upper water column, and provides a base for future studies aiming at reconstructing past bioproductivity levels in ancient ocean/basin surface waters. In addition, we compare δ¹¹⁴Cd values with previously published chromium (Cr) isotope values and link signals of bioproductivity with redox conditions in the surface waters. The GBB core samples yield [Cd] (21-188 μg/kg), which increases with depth alongside changes in carbonate mineralogy related to sediment supply and diagenesis. The δ¹¹⁴Cd values of these carbonates are mainly positively fractionated with an average of 0.11‰ ± 0.17 (2σ; n = 17) relative to the NIST 3108 reference standard. Unlike previously observed for Cr isotopes, there is no control of δ¹¹⁴Cd values by relative abundances of the carbonate polymorphs aragonite and calcite in the studied profile. Likewise, δ¹¹⁴Cd values are not correlated to major and trace element (e.g. Ca, Mg, Mn and Sr) contents. We postulate that the burial and diagenetic processes of carbonate cannot modify the Cd isotope signals. Using the experimental fractionation factor for Cd into calcite (-0.45‰), calculated seawater δ¹¹⁴Cd of +0.56 ± 0.17‰ is in agreement with values for modern North Atlantic Surface Seawater. This study's results suggest that δ¹¹⁴Cd values in carbonates are a reliable tool for reconstruction of bioproductivity levels in past surface seawaters, and open new possibilities in combination with Cr isotopes to link these with past ocean redox.

Microbial community structure in hadal sediments: high similarity along trench axes and strong changes along redox gradients

Hadal trench sediments are hotspots of biogeochemical activity in the deep sea, but the biogeochemical and ecological factors that shape benthic hadal microbial communities remain unknown. Here, we sampled ten hadal sites from two trench regions with a vertical resolution of down to 1 cm. We sequenced 16S rRNA gene amplicons using universal and archaea-specific primer sets and compared the results to biogeochemical parameters. Despite bathymetric and depositional heterogeneity we found a high similarity of microbial communities within each of the two trench axes, while composition at the phylum level varied strongly with sediment depth in conjunction with the redox stratification into oxic, nitrogenous, and ferruginous zones. As a result, communities of a given sediment horizon were more similar to each other across a distance of hundreds of kilometers within each trench, than to those of adjacent horizons from the same sites separated only by centimeters. Total organic carbon content statistically only explained a small part of the variation within and between trenches, and did not explain the community differences observed between the hadal and adjacent shallower sites. Anaerobic taxa increased in abundance at the top of the ferruginous zone, seeded by organisms deposited at the sediment surface and surviving burial through the upper redox zones. While an influence of other potential factors such as geographic isolation, hydrostatic pressure, and non-steady state depositional regimes could not be discerned, redox stratification and diagenesis appear to be the main selective forces that structure community composition in hadal sediments.

Anammox bacteria drive fixed nitrogen loss in hadal trench sediments

Benthic N₂ production by microbial denitrification and anammox is the largest sink for fixed nitrogen in the oceans. Most N₂ production occurs on the continental shelves, where a high flux of reactive organic matter fuels the depletion of nitrate close to the sediment surface. By contrast, N₂ production rates in abyssal sediments are low due to low inputs of reactive organics, and nitrogen transformations are dominated by aerobic nitrification and the release of nitrate to the bottom water. Here, we demonstrate that this trend is reversed in the deepest parts of the oceans, the hadal trenches, where focusing of reactive organic matter enhances benthic microbial activity. Thus, at ∼8-km depth in the Atacama Trench, underlying productive surface waters, nitrate is depleted within a few centimeters of the sediment surface, N₂ production rates reach those reported from some continental margin sites, and fixed nitrogen loss is mainly conveyed by anammox bacteria. These bacteria are closely related to those known from shallow oxygen minimum zone waters, and comparison of activities measured in the laboratory and in situ suggest they are piezotolerant. Even the Kermadec Trench, underlying oligotrophic surface waters, exhibits substantial fixed N removal. Our results underline the role of hadal sediments as hot spots of deep-sea biological activity, revealing a fully functional benthic nitrogen cycle at high hydrostatic pressure and pointing to hadal sediments as a previously unexplored niche for anaerobic microbial ecology and diagenesis.

Assessing the impacts of differential depositional settings and/or anthropogenic perturbations on sulfur and iron diagenesis in sediments of the Bohai Sea and North Yellow Sea

Natural processes and human activities exert important impacts on elemental cycling in coastal sediments, which has not been well documented. Sediments in the Bohai Sea and North Yellow Sea were investigated to assess the impacts of the Yellow River inputs and/or anthropogenic perturbations on diagenesis of iron and sulfur. Labile iron (0.5 M HCl-extractable iron) in the sediments is low due to iron-poor nature of source materials. Dynamic regimes and low availability of labile organic carbon (OC) result in relatively low sulfide contents in deltaic sediments. However, low but continuous supply of labile OC exported from an anthropogenically impacted bay could substantially elevate sulfide burial in sediments near the bay. Neither offshore oil exploitations nor frequent algal blooms in the seas have detectable influences on iron and sulfur diagenesis in the sediments. The sediments are capable of quickly consuming porewater sulfide by reaction with reactive iron under the current conditions.

Depth profiles of geochemical features, geochemical activities and biodiversity of microbial communities in marine sediments from the Shenhu area, the northern South China Sea

The biogeochemical processes, anaerobic oxidation of methane (AOM) and methanogenesis, control methane emission and create distinct geochemical profiles with depth in marine sediments. Correlating the capacities and biodiversity of the microbial communities in marine sediments remains challenging. We therefore investigated the geochemical constituents and the capabilities and diversity of microbial communities in sediments at different depths in two cores from the Shenhu area in the northern South China Sea, which is characterized by underlying gas hydrates. The geochemical features, sulfate concentration decreased linearly and the acid volatile sulfur accumulated from 4 m below the seafloor (mbsf) to the bottom, indicating significant sulfate reduction. However, the methane concentration was relatively low and showed irregular trends, indicating that our study cores did not reach the sulfate-methane transition zone (SMTZ). Nevertheless, incubation experiments showed that the microbial groups in sediments performed AOM and methanogenesis in the region where sulfate decreased linearly above the SMTZ. We mapped the diversity and abundance of microbial communities in sediments with depth using high-throughput sequencing. A small proportion of known methanogens (<0.3%) may have been responsible for the methanogenesis during incubation. No classical archaeal anaerobic methanotroph (ANME) sequences were detected across all samples; only a small amount of SEEP-SRB1 were detected, and their abundance did not increase with increasing depth. Thus, unknown or unconventional phylotypes may have participated in AOM during the incubation, and the dominant phylum Bathyarchaeota or the small number of detected methanogens are the most likely performers of AOM.

Anaerobic Sulfur Oxidation Underlies Adaptation of a Chemosynthetic Symbiont to Oxic-Anoxic Interfaces

Chemosynthetic symbioses occur worldwide in marine habitats, but comprehensive physiological studies of chemoautotrophic bacteria thriving on animals are scarce. Stilbonematinae are coated by thiotrophic Gammaproteobacteria. As these nematodes migrate through the redox zone, their ectosymbionts experience varying oxygen concentrations. However, nothing is known about how these variations affect their physiology. Here, by applying omics, Raman microspectroscopy, and stable isotope labeling, we investigated the effect of oxygen on "Candidatus Thiosymbion oneisti." Unexpectedly, sulfur oxidation genes were upregulated in anoxic relative to oxic conditions, but carbon fixation genes and incorporation of 13C-labeled bicarbonate were not. Instead, several genes involved in carbon fixation were upregulated under oxic conditions, together with genes involved in organic carbon assimilation, polyhydroxyalkanoate (PHA) biosynthesis, nitrogen fixation, and urea utilization. Furthermore, in the presence of oxygen, stress-related genes were upregulated together with vitamin biosynthesis genes likely necessary to withstand oxidative stress, and the symbiont appeared to proliferate less. Based on its physiological response to oxygen, we propose that "Ca. T. oneisti" may exploit anaerobic sulfur oxidation coupled to denitrification to proliferate in anoxic sand. However, the ectosymbiont would still profit from the oxygen available in superficial sand, as the energy-efficient aerobic respiration would facilitate carbon and nitrogen assimilation. IMPORTANCE Chemoautotrophic endosymbionts are famous for exploiting sulfur oxidization to feed marine organisms with fixed carbon. However, the physiology of thiotrophic bacteria thriving on the surface of animals (ectosymbionts) is less understood. One longstanding hypothesis posits that attachment to animals that migrate between reduced and oxic environments would boost sulfur oxidation, as the ectosymbionts would alternatively access sulfide and oxygen, the most favorable electron acceptor. Here, we investigated the effect of oxygen on the physiology of "Candidatus Thiosymbion oneisti," a gammaproteobacterium which lives attached to marine nematodes inhabiting shallow-water sand. Surprisingly, sulfur oxidation genes were upregulated under anoxic relative to oxic conditions. Furthermore, under anoxia, the ectosymbiont appeared to be less stressed and to proliferate more. We propose that animal-mediated access to oxygen, rather than enhancing sulfur oxidation, would facilitate assimilation of carbon and nitrogen by the ectosymbiont.

Active methanogenesis during the melting of Marinoan snowball Earth

Geological evidence indicates that the deglaciation of Marinoan snowball Earth ice age (~635 Myr ago) was associated with intense continental weathering, recovery of primary productivity, transient marine euxinia, and potentially extensive CH₄ emission. It is proposed that the deglacial CH₄ emissions may have provided positive feedbacks for ice melting and global warming. However, the origin of CH₄ remains unclear. Here we report Ni isotopes (δ⁶⁰Ni) and Yttrium-rare earth element (YREE) compositions of syndepositional pyrites from the upper most Nantuo Formation (equivalent deposits of the Marinoan glaciation), South China. The Nantuo pyrite displays anti-correlations between Ni concentration and δ⁶⁰Ni, and between Ni concentration and Sm/Yb ratio, suggesting mixing between Ni in seawater and Ni from methanogens. Our study indicates active methanogenesis during the termination of Marinoan snowball Earth. This suggests that methanogenesis was fueled by methyl sulfides produced in sulfidic seawater during the deglacial recovery of marine primary productivity.

The deglaciation of Marinoan snowball Earth (~635 Myr ago) has been associated with potentially extensive CH₄ emissions in relation to transient marine euxinia. Here, the authors find that active methanogenesis occurred during the termination of Marinoan snowball Earth, fueled by methyl sulfide production in sulfidic seawater.

The microbial dimension of submarine groundwater discharge: current challenges and future directions

Despite the relevance of submarine groundwater discharge (SGD) for ocean biogeochemistry, the microbial dimension of SGD remains poorly understood. SGD can influence marine microbial communities through supplying chemical compounds and microorganisms, and in turn, microbes at the land–ocean transition zone determine the chemistry of the groundwater reaching the ocean. However, compared with inland groundwater, little is known about microbial communities in coastal aquifers. Here, we review the state of the art of the microbial dimension of SGD, with emphasis on prokaryotes, and identify current challenges and future directions. Main challenges include improving the diversity description of groundwater microbiota, characterized by ultrasmall, inactive and novel taxa, and by high ratios of sediment-attached versus free-living cells. Studies should explore microbial dynamics and their role in chemical cycles in coastal aquifers, the bidirectional dispersal of groundwater and seawater microorganisms, and marine bacterioplankton responses to SGD. This will require not only combining sequencing methods, visualization and linking taxonomy to activity but also considering the entire groundwater–marine continuum. Interactions between traditionally independent disciplines (e.g. hydrogeology, microbial ecology) are needed to frame the study of terrestrial and aquatic microorganisms beyond the limits of their presumed habitats, and to foster our understanding of SGD processes and their influence in coastal biogeochemical cycles.

Seasonal dynamics modifies fate of oxygen, nitrate, and organic micropollutants during bank filtration - temperature-dependent reactive transport modeling of field data

Bank filtration is considered to improve water quality through microbially mediated degradation of pollutants and is suitable for waterworks to increase their production. In particular, aquifer temperatures and oxygen supply have a great impact on many microbial processes. To investigate the temporal and spatial behavior of selected organic micropollutants during bank filtration in dependence of relevant biogeochemical conditions, we have set up a 2D reactive transport model using MODFLOW and PHT3D under the user interface ORTI3D. The considered 160-m-long transect ranges from the surface water to a groundwater extraction well of the adjacent waterworks. For this purpose, water levels, temperatures, and chemical parameters were regularly measured in the surface water and groundwater observation wells over one and a half years. To simulate the effect of seasonal temperature variations on microbial mediated degradation, we applied an empirical temperature factor, which yields a strong reduction of the degradation rate at groundwater temperatures below 11 °C. Except for acesulfame, the considered organic micropollutants are substantially degraded along their subsurface flow paths with maximum degradation rates in the range of 10^-6 mol L^-1 s^-1. Preferential biodegradation of phenazone, diclofenac, and valsartan was found under oxic conditions, whereas carbamazepine and sulfamethoxazole were degraded under anoxic conditions. This study highlights the influence of seasonal variations in oxygen supply and temperature on the fate of organic micropollutants in surface water infiltrating into an aquifer.

The redox structure of Ediacaran and early Cambrian oceans and its controls

The rapid diversification of early animals during the Ediacaran (635-541 Ma) and early Cambrian (ca. 541-509 Ma) has frequently been attributed to increasing oceanic oxygenation. However, the pattern of oceanic oxygenation and its relationship to early animal evolution remain in debate. In this review, we examine the redox structure of Ediacaran and early Cambrian oceans and its controls, offering new insights into contemporaneous oceanic oxygenation patterns and their role in the coevolution of environments and early animals. We review the development of marine redox models which, in combination with independent distal deep-ocean redox proxies, supports a highly redox-stratified shelf and an anoxia-dominated deep ocean during the Ediacaran and early Cambrian. Geochemical and modeling evidence indicates that the marine redox structure was likely controlled by low atmospheric O₂ levels and low seawater vertical mixing rates on shelves at that time. Furthermore, theoretical analysis and increasing geochemical evidence, particularly from South China, show that limited sulfate availability was a primary control on the attenuation of mid-depth euxinia offshore, in contrast to the existing paradigm invoking decreased organic carbon fluxes distally. In light of our review, we infer that if oceanic oxygenation indeed triggered the rise of early animals, it must have done so through a shelf oxygenation which was probably driven by elevated oxidant availability. Our review calls for further studies on Ediacaran-Cambrian marine redox structure and its controls, particularly from regions outside of South China, in order to better understand the coevolutionary relationship between oceanic redox and early animals.

Effects of forced taxonomic transitions on metabolic composition and function in microbial microcosms

Surveys of microbial systems indicate that in many situations taxonomy and function may constitute largely independent ('decoupled') axes of variation. However, this decoupling is rarely explicitly tested experimentally, partly because it is hard to directly induce taxonomic variation without affecting functional composition. Here we experimentally evaluate this paradigm using microcosms resembling lake sediments and subjected to two different levels of salinity (0 and 19) and otherwise similar environmental conditions. We used DNA sequencing for taxonomic and functional profiling of bacteria and archaea and physicochemical measurements to monitor metabolic function, over 13 months. We found that the taxonomic composition of the saline systems gradually but strongly diverged from the fresh systems. In contrast, the metabolic composition (in terms of proportions of various genes) remained nearly identical across treatments and over time. Oxygen consumption rates and methane concentrations were substantially lower in the saline treatment, however, their similarity either increased (for oxygen) or did not change significantly (for methane) between the first and last sampling time, indicating that the lower metabolic activity in the saline treatments was directly and immediately caused by salinity rather than the gradual taxonomic divergence. Our experiment demonstrates that strong taxonomic shifts need not directly affect metabolic rates.

Selenium Enrichment in Pore Water of Estuarine Sediments Subject to Salt Marsh Vegetation Bioirrigation (Patos Estuary, Southern Brazil)

Selenium (Se), iron (Fe), and free sulfides contents in pore waters were measured to study the liberation of soluble Se in suboxic conditions. The sediment core was collected in a salt marsh in Patos Lagoon estuary (southern Brazil), and it was obtained during a brackish water period, in a low intertidal stand vegetated by Spartina alterniflora. The redox potential (Eh), pH, andacid volatile sulfides (AVS) content were also investigated. Pore water results sustained the idea that S. alterniflora roots promote oxygen penetration to depths of ca. 10 cm below the salt marsh surface, increasing Eh and lowering the pH in this interval. High Se concentrations (e.g., 16.9 µg L^-1), that are above US. EPA environmental criteria, were observed in the pore water to depths between 10 and 20 cm and are associated to low AVS contents and high concentrations of free sulfides. In the first 10 cm the lowering of Se contents probably happens due the low pH and biological volatilization of the metalloid.

Community, Distribution, and Ecological Roles of Estuarine Archaea

Archaea are diverse and ubiquitous prokaryotes present in both extreme and moderate environments. Estuaries, serving as links between the land and ocean, harbor numerous microbes that are relatively highly active because of massive terrigenous input of nutrients. Archaea account for a considerable portion of the estuarine microbial community. They are diverse and play key roles in the estuarine biogeochemical cycles. Ammonia-oxidizing archaea (AOA) are an abundant aquatic archaeal group in estuaries, greatly contributing estuarine ammonia oxidation. Bathyarchaeota are abundant in sediments, and they may involve in sedimentary organic matter degradation, acetogenesis, and, potentially, methane metabolism, based on genomics. Other archaeal groups are also commonly detected in estuaries worldwide. They include Euryarchaeota, and members of the DPANN and Asgard archaea. Based on biodiversity surveys of the 16S rRNA gene and some functional genes, the distribution and abundance of estuarine archaea are driven by physicochemical factors, such as salinity and oxygen concentration. Currently, increasing amount of genomic information for estuarine archaea is becoming available because of the advances in sequencing technologies, especially for AOA and Bathyarchaeota, leading to a better understanding of their functions and environmental adaptations. Here, we summarized the current knowledge on the community composition and major archaeal groups in estuaries, focusing on AOA and Bathyarchaeota. We also highlighted the unique genomic features and potential adaptation strategies of estuarine archaea, pointing out major unknowns in the field and scope for future research.

On the co-evolution of surface oxygen levels and animals

Few topics in geobiology have been as extensively debated as the role of Earth's oxygenation in controlling when and why animals emerged and diversified. All currently described animals require oxygen for at least a portion of their life cycle. Therefore, the transition to an oxygenated planet was a prerequisite for the emergence of animals. Yet, our understanding of Earth's oxygenation and the environmental requirements of animal habitability and ecological success is currently limited; estimates for the timing of the appearance of environments sufficiently oxygenated to support ecologically stable populations of animals span a wide range, from billions of years to only a few million years before animals appear in the fossil record. In this light, the extent to which oxygen played an important role in controlling when animals appeared remains a topic of debate. When animals originated and when they diversified are separate questions, meaning either one or both of these phenomena could have been decoupled from oxygenation. Here, we present views from across this interpretive spectrum-in a point-counterpoint format-regarding crucial aspects of the potential links between animals and surface oxygen levels. We highlight areas where the standard discourse on this topic requires a change of course and note that several traditional arguments in this "life versus environment" debate are poorly founded. We also identify a clear need for basic research across a range of fields to disentangle the relationships between oxygen availability and emergence and diversification of animal life.

Benthic trace metal fluxes in a heavily contaminated bay in China: Does the sediment become a source of metals to the water column?

Over three different seasons, seawater, porewater and sediment samples were collected from Jinzhou Bay, a previously heavily contaminated bay, to quantitatively assess the benthic flux of trace metals after a reduction in fluvial/sewage discharge for almost three decades. The spatial distribution patterns of trace metals in seawater, surface sediment, as well as the vertical distribution patterns of metals in porewater and solid phases in short sediment cores were reported. Metal concentrations in seawater and sediment all showed much higher Cd and Zn concentrations inside the Jinzhou Bay compared to the rest of Bohai Sea area. Zn, Ni, Pb and Co all had average benthic fluxes coming out of the sediments to the water column, contributing about 0.5%, 0.3%, 1.4% and 14% to their current standing stock in Jinzhou Bay. Seasonal difference was also identified in seawater and porewater, as well as in the benthic fluxes. In general, benthic fluxes and porewater concentrations all tended to be higher in summer, implying a close relationship between benthic flux and the temperature-dependent organic matter degradation process at the sediment-water interface. Currently, there are clearly still other sources, possibly fluvial/sewage discharge, as the main source of trace metals in Jinzhou Bay waters. For Cd and Cu, concentrations in the water column remain high on an annual basis indicating that sediment still acts as a sink. Conversely, for Pb, Zn, Co, and Ni, the sediment is beginning to act as a source to the water column. Although this may not yet be significant, it will become more and more important with time, and can last for hundreds to thousands of years.

Phosphorus (P) release risk in lake sediment evaluated by DIFS model and sediment properties: A new sediment P release risk index (SPRRI)

A new sediment P release risk index (SPRRI) for "in-situ" phosphorus (P) release risk in lake sediment, is developed based on diffusive gradients in thin films (DGT) technique, DGT induced flux in sediments (DIFS) model and sediment properties. SPRRI includes three sub-indexes, which contain (1) the labile P pool size, (2) resupply constant (r) and desorption rate (Dspt rate) for P transfer and (3) the molar ratio between iron (Fe) in sequential extraction for sediment P by bicarbonate-dithionite (BD) and aluminum (Al) by NaOH (at 25 °C), i.e. BD(Fe)/Al[NaOH25] in sediment solid. The first sub-index considers P release from (i) sediment with NH₄Cl-P+BD-P pool, i.e. the loosely sorbed P (NH₄Cl-P) plus iron associated P (BD-P), or (ii) sediment with NH₄Cl-P pool, respectively. The second and third sub-indexes reflect kinetic P desorption and resupply ability of solid phase, and the effect of P sequestration by Al hydroxide on P release, in turn. The inner relationship between SPRRI and sub-indexes, and their effects on P release risk are elucidated. SPRRI can be used to evaluate sediment P reactivity by five release risk ranks. For Lake Dianchi (China), P transfer dynamics, labile P pool, resupply ability and Al-P in sediment, and "external P-loading" control and affect P release risk in different regions, which is reflected by the spatial distribution map for SPRRI. The present SPRRI can be applied for lakes with (1) pH range varying from moderate acidity to weak alkalinity in waterbody and (2) NH₄Cl-P or NH₄Cl-P+BD-P pool in sediment solid.

Modeling sediment oxygen demand in a highly productive lake under various trophic scenarios

Hypolimnetic oxygen depletion in lakes is a widespread problem and is mainly controlled by the sediment oxygen uptake (SOU) and flux of reduced substances out of the sediments (Fred). Especially in eutrophic lakes, Fred may constitute a major fraction of the areal hypolimnetic mineralization rate, but its size and source is often poorly understood. Using a diagenetic reaction-transport model supported by a large data set of sediment porewater concentrations, bulk sediment core data and lake monitoring data, the behavior of Fred was simulated in eutrophic Lake Baldegg. Transient boundary conditions for the gross sedimentation of total organic carbon and for hypolimnetic O2 concentrations were applied to simulate the eutrophication and re-oligotrophication history of the lake. According to the model, Fred is dominated by methanogenesis, where up to70% to the total CH4 is produced from sediments older than 20 years deposited during the time of permanent anoxia between 1890 and 1982. An implementation of simplified seasonal variations of the upper boundary conditions showed that their consideration is not necessary for the assessment of annual average fluxes in long-term simulations. Four lake management scenarios were then implemented to investigate the future development of Fred and SOU until 2050 under different boundary conditions. A comparison of three trophic scenarios showed that further reduction of the lake productivity to at least a mesotrophic state is required to significantly decrease Fred and SOU from the present state. Conversely, a termination of artificial aeration at the present trophic state would result in high rates of organic matter deposition and a long-term increase of Fred from the sediments of Lake Baldegg.

Geomicrobiology of the carbon, nitrogen and sulphur cycles in Powell Lake: a permanently stratified water column containing ancient seawater

We present the first geomicrobiological characterization of the meromictic water column of Powell Lake (British Columbia, Canada), a former fjord, which has been stably stratified since the last glacial period. Its deepest layers (300-350 m) retain isolated, relict seawater from that period. Fine-scale vertical profiling of the water chemistry and microbial communities allowed subdivision of the water column into distinct geomicrobiological zones. These zones were further characterized by phylogenetic and functional marker genes from amplicon and shotgun metagenome sequencing. Binning of metagenomic reads allowed the linkage of function to specific taxonomic groups. Statistical analyses (analysis of similarities, Bray-Curtis similarity) confirmed that the microbial community structure followed closely the geochemical zonation. Yet, our characterization of the genetic potential relevant to carbon, nitrogen and sulphur cycling of each zone revealed unexpected features, including potential for facultative anaerobic methylotrophy, nitrogen fixation despite high ammonium concentrations and potential micro-aerobic nitrifiers within the chemocline. At the oxic-suboxic interface, facultative anaerobic potential was found in the widespread freshwater lineage acI (Actinobacteria), suggesting intriguing ecophysiological similarities to the marine SAR11. Evolutionary divergent lineages among diverse phyla were identified in the ancient seawater zone and may indicate novel adaptations to this unusual environment.

A 1-Dimensional Sympagic–Pelagic–Benthic Transport Model (SPBM): Coupled Simulation of Ice, Water Column, and Sediment Biogeochemistry, Suitable for Arctic Applications

Marine biogeochemical processes can strongly interact with processes occurring in adjacent ice and sediments. This is especially likely in areas with shallow water and frequent ice cover, both of which are common in the Arctic. Modeling tools are therefore required to simulate coupled biogeochemical systems in ice, water, and sediment domains. We developed a 1D sympagic–pelagic–benthic transport model (SPBM) which uses input from physical model simulations to describe hydrodynamics and ice growth and modules from the Framework for Aquatic Biogeochemical Models (FABM) to construct a user-defined biogeochemical model. SPBM coupled with a biogeochemical model simulates the processes of vertical diffusion, sinking/burial, and biogeochemical transformations within and between the three domains. The potential utility of SPBM is demonstrated herein with two test runs using modules from the European regional seas ecosystem model (ERSEM) and the bottom-redox model biogeochemistry (BROM-biogeochemistry). The first run simulates multiple phytoplankton functional groups inhabiting the ice and water domains, while the second simulates detailed redox biogeochemistry in the ice, water, and sediments. SPBM is a flexible tool for integrated simulation of ice, water, and sediment biogeochemistry, and as such may help in producing well-parameterized biogeochemical models for regions with strong sympagic–pelagic–benthic interactions.

Circumventing kinetics in biogeochemical modeling

Microbial metabolism drives biogeochemical fluxes in virtually every ecosystem. Modeling these fluxes is challenged by the incredible diversity of microorganisms, whose kinetic parameters are largely unknown. In poorly mixed systems, such as stagnant water columns or sediments, however, long-term bulk microbial metabolism may become limited by physical transport rates of substrates across space. Here we mathematically show that under these conditions, biogeochemical fluxes are largely predictable based on the system's transport properties, chemical boundary conditions, and the stoichiometry of metabolic pathways, regardless of the precise kinetics of the resident microorganisms. We formalize these considerations into a predictive modeling framework and demonstrate its use for the Cariaco Basin subeuphotic zone, one of the largest anoxic marine basins worldwide. Using chemical concentration data solely from the upper boundary (depth 180 m) and lower boundary (depth 900 m), but without a priori knowledge of metabolite fluxes, chemical depth profiles, kinetic parameters, or microbial species composition, we predict the concentrations and vertical fluxes of biologically important substances, including oxygen, nitrate, hydrogen sulfide, and ammonium, across the entire considered depth range (180-900 m). Our predictions largely agree with concentration measurements over a period of 14 years ([Formula: see text] = 0.78-0.92) and become particularly accurate during a period where the system was near biogeochemical steady state (years 2007-2009, [Formula: see text] = 0.86-0.95). Our work enables geobiological predictions for a large class of ecosystems without knowledge of kinetic parameters or geochemical depth profiles. Conceptually, our work provides a possible explanation for the decoupling between microbial species composition and bulk metabolic function, observed in various ecosystems.

Rates and pathways of CH4 oxidation in ferruginous Lake Matano, Indonesia

This study evaluates rates and pathways of methane (CH₄ ) oxidation and uptake using ¹⁴ C-based tracer experiments throughout the oxic and anoxic waters of ferruginous Lake Matano. Methane oxidation rates in Lake Matano are moderate (0.36 nmol L^-1  day^-1 to 117 μmol L^-1  day^-1 ) compared to other lakes, but are sufficiently high to preclude strong CH₄ fluxes to the atmosphere. In addition to aerobic CH₄ oxidation, which takes place in Lake Matano's oxic mixolimnion, we also detected CH₄ oxidation in Lake Matano's anoxic ferruginous waters. Here, CH₄ oxidation proceeds in the apparent absence of oxygen (O₂ ) and instead appears to be coupled to some as yet uncertain combination of nitrate ( NO 3 - ), nitrite ( NO 2 - ), iron (Fe) or manganese (Mn), or sulfate ( SO 4 2 - ) reduction. Throughout the lake, the fraction of CH₄ carbon that is assimilated vs. oxidized to carbon dioxide (CO₂ ) is high (up to 93%), indicating extensive CH₄ conversion to biomass and underscoring the importance of CH₄ as a carbon and energy source in Lake Matano and potentially other ferruginous or low productivity environments.

Environmental filtering determines family-level structure of sulfate-reducing microbial communities in subsurface marine sediments

Recent work has shown that subsurface microbial communities assemble by selective survival of surface community members during sediment burial, but it remains unclear to what extent the compositions of the subsurface communities are a product of their founding population at the sediment surface or of the changing geochemical conditions during burial. Here we investigate this question for communities of sulfate-reducing microorganisms (SRMs). We collected marine sediment samples from the upper 3-5 m at four geochemically contrasting sites in the Skagerrak and Baltic Sea and measured SRM abundance (quantitative PCR of dsrB), metabolic activity (radiotracer rate measurements), and community composition (Illumina sequencing of dsrB amplicons). These data showed that SRM abundance, richness, and phylogenetic clustering as determined by the nearest taxon index peaked below the bioturbation zone and above the depth of sulfate depletion. Minimum cell-specific rates of sulfate reduction did not vary substantially between sites. SRM communities at different sites were best distinguished based on their composition of amplicon sequence variants (ASVs), while communities in different geochemical zones were best distinguished based on their composition of SRM families. This demonstrates environmental filtering of SRM communities in sediment while a site-specific fingerprint of the founding community is retained.

Formation of Large Native Sulfur Deposits Does Not Require Molecular Oxygen

Large native (i.e., elemental) sulfur deposits can be part of caprock assemblages found on top of or in lateral position to salt diapirs and as stratabound mineralization in gypsum and anhydrite lithologies. Native sulfur is formed when hydrocarbons come in contact with sulfate minerals in presence of liquid water. The prevailing model for native sulfur formation in such settings is that sulfide produced by sulfate-reducing bacteria is oxidized to zero-valent sulfur in presence of molecular oxygen (O2). Although possible, such a scenario is problematic because: (1) exposure to oxygen would drastically decrease growth of microbial sulfate-reducing organisms, thereby slowing down sulfide production; (2) on geologic timescales, excess supply with oxygen would convert sulfide into sulfate rather than native sulfur; and (3) to produce large native sulfur deposits, enormous amounts of oxygenated water would need to be brought in close proximity to environments in which ample hydrocarbon supply sustains sulfate reduction. However, sulfur stable isotope data from native sulfur deposits emplaced at a stage after the formation of the host rocks indicate that the sulfur was formed in a setting with little solute exchange with the ambient environment and little supply of dissolved oxygen. We deduce that there must be a process for the formation of native sulfur in absence of an external oxidant for sulfide. We hypothesize that in systems with little solute exchange, sulfate-reducing organisms, possibly in cooperation with other anaerobic microbial partners, drive the formation of native sulfur deposits. In order to cope with sulfide stress, microbes may shift from harmful sulfide production to non-hazardous native sulfur production. We propose four possible mechanisms as a means to form native sulfur: (1) a modified sulfate reduction process that produces sulfur compounds with an intermediate oxidation state, (2) coupling of sulfide oxidation to methanogenesis that utilizes methylated compounds, acetate or carbon dioxide, (3) ammonium oxidation coupled to sulfate reduction, and (4) sulfur comproportionation of sulfate and sulfide. We show these reactions are thermodynamically favorable and especially useful in environments with multiple stressors, such as salt and dissolved sulfide, and provide evidence that microbial species functioning in such environments produce native sulfur. Integrating these insights, we argue that microbes may form large native sulfur deposits in absence of light and external oxidants such as O2, nitrate, and metal oxides. The existence of such a process would not only explain enigmatic occurrences of native sulfur in the geologic record, but also provide an explanation for cryptic sulfur and carbon cycling beneath the seabed.

Diversity and distribution of Archaea in global estuarine ecosystems

Estuarine ecosystem is a unique geographical transitional zone between freshwater and seawater, harboring a wide range of microbial communities including Archaea. Although a large number of Archaea have been detected in such ecosystem, the global patterns in archaeal diversity and distribution are extremely scarce. To bridge this gap, we carried out a comprehensive survey of archaeal communities using ca. 4000 publicly available archaeal 16S rRNA gene sequences (>300 bp) collected from 24 estuaries in different latitude regions. These sequences were divided into 1450 operational taxonomic units (OTUs) at 97% identity, suggesting a high biodiversity that increased gradually from the high- to low-latitude estuaries. Phylogenetic analysis showed that estuarine ecosystem was a large biodiversity pool of Archaea that was mainly composed of 12 phyla. Among them, the predominant groups were Bathyarchaeota, Euryarchaeota and Thaumarchaeota. Interestingly, archaeal distribution demonstrated a geographical differentiation in that Thaumarchaeota was dominated in the low-latitude estuaries, Bathyarchaeota in the mid-latitude estuaries, and Euryarchaeota in the high-latitude estuaries, respectively. Furthermore, the majority of the most abundant 20 OTUs demonstrated an overrepresented or underrepresented distribution pattern in some specific estuaries or latitude regions while a few were evenly distributed throughout the estuaries. This pattern indicates a potential selectivity of geographical distribution. In addition, the analysis of environmental parameters suggested that latitude would be one of the major factors driving the distribution of archaeal communities in estuarine ecosystem. This study profiles a clear framework on the diversity and distribution of Archaea in the global estuarine ecosystem and explores the general environmental factors that influence these patterns. Our findings constitute an important part of the exploration of the global ecology of Archaea.

Methylation and dealkykation of tin compounds by sulfate- and nitrate-reducing bacteria

In this study, axenic cultures of sulfate-reducing (SRB) and nitrate-reducing (NRB) bacteria were examined for their ability to methylate inorganic tin and to methylate or dealkylate butyltin compounds. Environmentally relevant concentrations of natural abundance tributyltin (TBT) and ¹¹⁶Sn-enriched inorganic tin were added to bacterial cultures to identify bacterial-mediated methylation and dealkylation reactions. The results show that none of the Desulfovibrio strains tested was able to induce any transformation process. In contrast, Desulfobulbus propionicus strain DSM-6523 degraded TBT either under sulfidogenic or non-sulfidogenic conditions. In addition, it was able to alkykate ¹¹⁶Sn-enriched inorganic tin leading to the formation of more toxic dimethyltin and trimethyltin. A similar capacity was observed for incubations of Pseudomonas but with a much greater dealkykation of TBT. As such, Pseudomonas sp. ADR42 degraded 61% of the initial TBT under aerobic conditions and 35% under nitrate-reducing conditions. This is the first work reporting a simultaneous TBT degradation and a methylation of both inorganic tin species and TBT dealkykation products by SRB and NRB under anoxic conditions. These reactions are environmentally relevant as they can control the mobility of these compounds in aquatic ecosystems; as well as their toxicity toward resident organisms.

Single-Cell Genomics Reveals a Diverse Metabolic Potential of Uncultivated Desulfatiglans-Related Deltaproteobacteria Widely Distributed in Marine Sediment

Desulfatiglans-related organisms comprise one of the most abundant deltaproteobacterial lineages in marine sediments where they occur throughout the sediment column in a gradient of increasing sulfate and organic carbon limitation with depth. Characterized Desulfatiglans isolates are dissimilatory sulfate reducers able to grow by degrading aromatic hydrocarbons. The ecophysiology of environmental Desulfatiglans-populations is poorly understood, however, possibly utilization of aromatic compounds may explain their predominance in marine subsurface sediments. We sequenced and analyzed seven Desulfatiglans-related single-cell genomes (SAGs) from Aarhus Bay sediments to characterize their metabolic potential with regard to aromatic compound degradation and energy metabolism. The average genome assembly size was 1.3 Mbp and completeness estimates ranged between 20 and 50%. Five of the SAGs (group 1) originated from the sulfate-rich surface part of the sediment while two (group 2) originated from sulfate-depleted subsurface sediment. Based on 16S rRNA gene amplicon sequencing group 2 SAGs represent the more frequent types of Desulfatiglans-populations in Aarhus Bay sediments. Genes indicative of aromatic compound degradation could be identified in both groups, but the two groups were metabolically distinct with regard to energy conservation. Group 1 SAGs carry a full set of genes for dissimilatory sulfate reduction, whereas the group 2 SAGs lacked any genetic evidence for sulfate reduction. The latter may be due to incompleteness of the SAGs, but as alternative energy metabolisms group 2 SAGs carry the genetic potential for growth by acetogenesis and fermentation. Group 1 SAGs encoded reductive dehalogenase genes, allowing them to access organohalides and possibly conserve energy by their reduction. Both groups possess sulfatases unlike their cultured relatives allowing them to utilize sulfate esters as source of organic carbon and sulfate. In conclusion, the uncultivated marine Desulfatiglans populations are metabolically diverse, likely reflecting different strategies for coping with energy and sulfate limitation in the subsurface seabed.

Function and functional redundancy in microbial systems

Microbial communities often exhibit incredible taxonomic diversity, raising questions regarding the mechanisms enabling species coexistence and the role of this diversity in community functioning. On the one hand, many coexisting but taxonomically distinct microorganisms can encode the same energy-yielding metabolic functions, and this functional redundancy contrasts with the expectation that species should occupy distinct metabolic niches. On the other hand, the identity of taxa encoding each function can vary substantially across space or time with little effect on the function, and this taxonomic variability is frequently thought to result from ecological drift between equivalent organisms. Here, we synthesize the powerful paradigm emerging from these two patterns, connecting the roles of function, functional redundancy and taxonomy in microbial systems. We conclude that both patterns are unlikely to be the result of ecological drift, but are inevitable emergent properties of open microbial systems resulting mainly from biotic interactions and environmental and spatial processes.

Arsenic mobility and characterization in lakes impacted by gold ore roasting, Yellowknife, NWT, Canada

The controls on the mobility and fate of arsenic in lakes impacted by historical gold ore roasting in northern Canada have been examined. A detailed characterization of arsenic solid and aqueous phases in lake waters, lake sediments and sediment porewaters as well as surrounding soils was conducted in three small lakes (<200ha) downwind and within 5 km of the historic mining and roasting operations of Giant Mine (Northwest Territories). These lakes are marked by differing limnological characteristics such as area, depth and organic content. Radiometric age-dating shows that the occurrence of arsenic trioxide in lake sediments coincides with the regional onset of roasting activities. Quantification by advanced electron microscopy shows that arsenic trioxide accounts for up to 6 wt% of the total arsenic in sediments. The bulk (>80 wt%) of arsenic is contained in the form of secondary sulphide precipitates, with iron oxy-hydroxides hosting a minimal amount of arsenic (<1 wt%). Soluble arsenic trioxide particles act as the primary source of arsenic into sediment porewaters. Dissolved arsenic in reducing porewaters both precipitates in-situ as secondary sulphides, and diffuses upwards into the overlying lake waters. Geogenic arsenic phases are present in sediments in low concentrations and are not considered a significant source of arsenic to porewaters or lake waters. Sediment-water interface diffusive flux calculations suggest that the diffusion of dissolved arsenic from porewaters, combined with lake water residence time, are the predominant mechanisms controlling arsenic concentrations in lake waters.

Stratified Bacterial and Archaeal Community in Mangrove and Intertidal Wetland Mudflats Revealed by High Throughput 16S rRNA Gene Sequencing

The stratified distribution of bacterial and archaeal communities has been detected in many sediment profiles from various natural environments. A better understanding of microbial composition and diversity pattern in coastal mangrove wetlands in relation to physicochemical and spatial-temporal influences could provide more insights into the ecological functions of microbes in coastal wetlands. In this study, seasonal variations of microbial communities within sediment profiles from two sediment types (mangrove forest and intertidal mudflats) at three sampling locations in coastal Mai Po wetland were characterized using MiSeq high throughput sequencing and 16S rRNA quantitative PCR methods. Bacterial 16S rRNA gene abundance showed clear decreasing trends with increasing depth for all sites, seasonality and sediment types. There is a weak seasonal dynamic of bacterial and archaeal community abundance in both seasons. Seasonality imposed more influence on the beta diversity pattern of bacterial community than archaeal community. The five most abundant phyla within bacterial and archaeal community remain stable between two distinctive seasons. Sediment depth and seasonality are the most influential factors affecting bacterial community composition and diversity. The pH is the most influential factor on shaping the archaeal community. Stratified distribution of bacterial community including aerobic and anaerobic bacterial taxa is largely represented in the surface layers and the subsurface layers, respectively. For archaeal stratification, Thaumarchaeota Marine Group I is the dominant member in surface sediments while Bathyarchaeota and MBG-B dominate in subsurface sediments. Such stratified distribution patterns are irrespective of sediment types, sampling locations or seasonality, but significantly correlated to the sediment depth, which might be shaped by oxygen availability and the distribution of other terminal electron accepters along the depth profile.

The life sulfuric: microbial ecology of sulfur cycling in marine sediments

Almost the entire seafloor is covered with sediments that can be more than 10 000 m thick and represent a vast microbial ecosystem that is a major component of Earth's element and energy cycles. Notably, a significant proportion of microbial life in marine sediments can exploit energy conserved during transformations of sulfur compounds among different redox states. Sulfur cycling, which is primarily driven by sulfate reduction, is tightly interwoven with other important element cycles (carbon, nitrogen, iron, manganese) and therefore has profound implications for both cellular- and ecosystem-level processes. Sulfur-transforming microorganisms have evolved diverse genetic, metabolic, and in some cases, peculiar phenotypic features to fill an array of ecological niches in marine sediments. Here, we review recent and selected findings on the microbial guilds that are involved in the transformation of different sulfur compounds in marine sediments and emphasise how these are interlinked and have a major influence on ecology and biogeochemistry in the seafloor. Extraordinary discoveries have increased our knowledge on microbial sulfur cycling, mainly in sulfate-rich surface sediments, yet many questions remain regarding how sulfur redox processes may sustain the deep-subsurface biosphere and the impact of organic sulfur compounds on the marine sulfur cycle.

Controls on the evolution of Ediacaran metazoan ecosystems: A redox perspective

A growing number of detailed geochemical studies of Ediacaran (635-541 Ma) marine successions have provided snapshots into the redox environments that played host to the earliest known metazoans. Whilst previous compilations have focused on the global evolution of Ediacaran water column redox chemistry, the inherent heterogeneity evident in palaeogeographically distinct environments demands a more dissected approach to better understand the nature, interactions and evolution of extrinsic controls on the development of early macrobenthic ecosystems. Here, we review available data of local-scale redox conditions within a palaeogeographic and sequence stratigraphic framework, to explore the mechanisms controlling water column redox conditions and their potential impact on the record of metazoans. The openly connected Laurentian margin, North America (632-540 Ma) and Nama basin, Namibia (550-538 Ma), and the variably restricted Yangtze Block, South China (635-520 Ma), show continued redox instability after the first fossil evidence for metazoans. This may support opportunistic benthic colonisation during periods of transient oxygenation amidst episodic upwelling of anoxic waters beneath a very shallow, fluctuating chemocline. The first skeletal metazoans appeared under conditions of continued redox stratification, such as those which characterise the Dengying Formation of the Yangtze Block and the Kuibis Subgroup of the Nama basin. Current data, however, suggests that successful metazoan reef-building demanded more persistent oxia. We propose that cratonic positioning and migration throughout the Ediacaran Period, in combination with gradually increasing dissolved oxygen loading, may have provided a first-order control on redox evolution through regulating circulation mechanisms in the Mirovian Ocean. Some unrestricted lower slope environments from mid-high latitudes benefited from sustained oxygenation via downwelling, whilst transit of isolated cratons towards more equatorial positions stifled pervasive ventilation either through ineffective surface ocean mixing, Ekman-induced upwelling, elevated surface ocean productivity or a combination of these processes.

Functional structure of the bromeliad tank microbiome is strongly shaped by local geochemical conditions

Phytotelmata in tank-forming Bromeliaceae plants are regarded as potential miniature models for aquatic ecology, but detailed investigations of their microbial communities are rare. Hence, the biogeochemistry in bromeliad tanks remains poorly understood. Here we investigate the structure of bacterial and archaeal communities inhabiting the detritus within the tanks of two bromeliad species, Aechmea nudicaulis and Neoregelia cruenta, from a Brazilian sand dune forest. We used metagenomic sequencing for functional community profiling and 16S sequencing for taxonomic profiling. We estimated the correlation between functional groups and various environmental variables, and compared communities between bromeliad species. In all bromeliads, microbial communities spanned a metabolic network adapted to oxygen-limited conditions, including all denitrification steps, ammonification, sulfate respiration, methanogenesis, reductive acetogenesis and anoxygenic phototrophy. Overall, CO2 reducers dominated in abundance over sulfate reducers, and anoxygenic phototrophs largely outnumbered oxygenic photoautotrophs. Functional community structure correlated strongly with environmental variables, between and within a single bromeliad species. Methanogens and reductive acetogens correlated with detrital volume and canopy coverage, and exhibited higher relative abundances in N. cruenta. A comparison of bromeliads to freshwater lake sediments and soil from around the world, revealed stark differences in terms of taxonomic as well as functional microbial community structure.