Microbial sulfate reduction and organic sulfur formation in sinking marine particles

Investigating organic sulfur in estuarine and offshore environments: A combined field and cultivation approach

Estuarine-offshore sediments accumulate substantial particulate organic matter, containing organic sulfur as a key component. However, the distribution and sources of organic sulfur in such environments remain poorly understood. This study investigated organic sulfur in the Yangtze River Estuary and adjacent East China Sea. Dissolved organic sulfur varied from 0.65 to 1.99 μmol/L (molar S:C 0.006-0.018), while particulate organic sulfur ranged from 0.42 to 2.69 μmol/L (molar S:C 0.007-0.082). Sedimentary organic sulfur exhibited a similar molar S:C ratio (0.014-0.071) to particulate organic sulfur in bottom water, implying that particulate matter deposition is a potential source. Furthermore, sediments exposed to frequent hypoxia harbored significantly higher organic sulfur and S:C values compared to non-hypoxic areas. Laboratory incubation experiments revealed the underlying mechanism: sustained activity of sulfate-reducing bacteria in hypoxic sediments led to a substantial increase in sedimentary organic sulfur (from 15 to 53 μmol/g) within 600 days. This microbially driven sulfurization rendered over 90 % of the organic sulfur resistant to acid hydrolysis. Therefore, this study demonstrates that, alongside particle deposition, microbial sulfurization significantly contributes to organic sulfur enrichment and likely promotes organic matter preservation in estuarine-offshore sediments, particularly under hypoxic conditions. This finding advances our understanding of organic sulfur sources in these vital ecosystems.

Multi-omics insights into biogeochemical responses to organic matter addition in an acidic pit lake: Implications for bioremediation

Acidic pit lakes (APLs) emerge as reservoirs of acid mine drainage in flooded open-pit mines, representing extreme ecosystems and environmental challenges worldwide. The bioremediation of these oligotrophic waters necessitates the addition of organic matter, but the biogeochemical response of APLs to exogenous organic matter remains inadequately comprehended. This study delves into the biogeochemical impacts and remediation effects of digestate-derived organic matter within an APL, employing a multi-omics approach encompassing geochemical analyses, amplicon and metagenome sequencing, and ultra-high resolution mass spectrometry. The results indicated that digestate addition first stimulated fungal proliferation, particularly Ascomycetes and Basidiomycetes, which generated organic acids through lignocellulosic hydrolysis and fermentation. These simple compounds further supported heterotrophic growth, including Acidiphilium, Acidithrix, and Clostridium, thereby facilitating nitrate, iron, and sulfate reduction linked with acidity consumption. Nutrients derived from digestate also promoted the macroscopic development of acidophilic algae. Notably, the increased sulfate reduction-related genes primarily originated from assimilatory metabolism, thus connecting sulfate decrease to organosulfur increase. Assimilatory and dissimilatory sulfate reduction collectively contributed to sulfate removal and metal fixation. These findings yield multi-omics insights into APL biogeochemical responses to organic matter addition, enhancing the understanding of carbon-centered biogeochemical cycling in extreme ecosystems and guiding organic amendment-based bioremediation in oligotrophic polluted environments.

Speciation and Possible Origins of Organosulfur Compounds in Rice Paddy Soils Affected by Acid Mine Drainage

Although sulfur cycling in acid mine drainage (AMD)-contaminated rice paddy soils is critical to understanding and mitigating the environmental consequences of AMD, potential sources and transformations of organosulfur compounds in such soils are poorly understood. We used sulfur K-edge X-ray absorption near edge structure (XANES) spectroscopy to quantify organosulfur compounds in paddy soils from five AMD-contaminated sites and one AMD-uncontaminated reference site near the Dabaoshan sulfide mining area in South China. We also determined the sulfur stable isotope compositions of water-soluble sulfate (δ34SWS), adsorbed sulfate (δ34SAS), fulvic acid sulfur (δ34SFAS), and humic acid sulfur (δ34SHAS) in these samples. Organosulfate was the dominant functional group in humic acid sulfur (HAS) in both AMD-contaminated (46%) and AMD-uncontaminated paddy soils (42%). Thiol/organic monosulfide contributed a significantly lower proportion of HAS in AMD-contaminated paddy soils (8%) compared to that in AMD-uncontaminated paddy soils (21%). Within contaminated soils, the concentration of thiol/organic monosulfide was positively correlated with cation exchange capacity (CEC), moisture content (MC), and total Fe (TFe). δ34SFAS ranged from -6.3 to 2.7‰, similar to δ34SWS (-6.9 to 8.9‰), indicating that fulvic acid sulfur (FAS) was mainly derived from biogenic S-bearing organic compounds produced by assimilatory sulfate reduction. δ34SHAS (-11.0 to -1.6‰) were more negative compared to δ34SWS, indicating that dissimilatory sulfate reduction and abiotic sulfurization of organic matter were the main processes in the formation of HAS.

Marine particle microbiomes during a spring diatom bloom contain active sulfate-reducing bacteria

Phytoplankton blooms fuel marine food webs with labile dissolved carbon and also lead to the formation of particulate organic matter composed of living and dead algal cells. These particles contribute to carbon sequestration and are sites of intense algal-bacterial interactions, providing diverse niches for microbes to thrive. We analyzed 16S and 18S ribosomal RNA gene amplicon sequences obtained from 51 time points and metaproteomes from 3 time points during a spring phytoplankton bloom in a shallow location (6-10 m depth) in the North Sea. Particulate fractions larger than 10 µm diameter were collected at near daily intervals between early March and late May in 2018. Network analysis identified two major modules representing bacteria co-occurring with diatoms and with dinoflagellates, respectively. The diatom network module included known sulfate-reducing Desulfobacterota as well as potentially sulfur-oxidizing Ectothiorhodospiraceae. Metaproteome analyses confirmed presence of key enzymes involved in dissimilatory sulfate reduction, a process known to occur in sinking particles at greater depths and in sediments. Our results indicate the presence of sufficiently anoxic niches in the particle fraction of an active phytoplankton bloom to sustain sulfate reduction, and an important role of benthic-pelagic coupling for microbiomes in shallow environments. Our findings may have implications for the understanding of algal-bacterial interactions and carbon export during blooms in shallow-water coastal areas.

Enrichment of Geogenic Organoiodine Compounds in Alluvial-Lacustrine Aquifers: Molecular Constraints by Organic Matter

Organoiodine compounds (OICs) are the dominant iodine species in groundwater systems. However, molecular mechanisms underlying the geochemical formation of geogenic OICs-contaminated groundwater remain unclear. Based upon multitarget field monitoring in combination with ultrahigh-resolution molecular characterization of organic components for alluvial-lacustrine aquifers, we identified a total of 939 OICs in groundwater under reducing and circumneutral pH conditions. In comparison to those in water-soluble organic matter (WSOM) in sediments, the OICs in dissolved organic matter (DOM) in groundwater typically contain fewer polycyclic aromatics and polyphenol compounds but more highly unsaturated compounds. Consequently, there were two major sources of geogenic OICs in groundwater: the migration of the OICs from aquifer sediments and abiotic reduction of iodate coupled with DOM iodination under reducing conditions. DOM iodination occurs primarily through the incorporation of reactive iodine that is generated by iodate reduction into highly unsaturated compounds, preferably containing hydrophilic functional groups as binding sites. It leads to elevation of the concentration of the OICs up to 183 μg/L in groundwater. This research provides new insights into the constraints of DOM molecular composition on the mobilization and enrichment of OICs in alluvial-lacustrine aquifers and thus improves our understanding of the genesis of geogenic iodine-contaminated groundwater systems.

Cross-shelf processes of terrigenous organic matter drive mercury speciation on the east siberian shelf in the Arctic Ocean

The cross-shelf distributions of total mercury (THg), methylmercury (MeHg) and organic and inorganic matter, as well as the presence of the hgcA gene were investigated on the East Siberian Shelf (ESS) to understand the processes underlying the speciation of sedimentary Hg. Samples were collected from 12 stations grouped into four zones based on water depth: inner shelf (5 stations), mid-shelf (3 stations), outer shelf (2 stations), and slope (2 stations). The THg concentration in the surface sediment increased from the inner shelf (0.25 ± 0.023 nmol g-1) toward the slope (0.52 nmol g-1), and, when normalized to total organic carbon content, the THg showed a positive correlation with the clay-to-sand ratio (r2 = 0.48, p = 0.012) and degree of chemical weathering (r2 = 0.79, p = 0.0001). The highest MeHg concentrations (3.0 ± 1.8 pmol g-1), as well as peaks in the S/C ratio (0.012 ± 0.002) of sediment-leached organic matter, were found on the mid-shelf, suggesting that the activities of sulfate reducers control the net Hg(II) methylation rates in the sediment. This was supported by results from a principal component analysis (PCA) performed with Hg species concentrations and sediment-leached organic matter compositions. The site-specific variation in MeHg showed the highest similarity with that of CHONS compounds in the PCA, where Deltaproteobacteria were projected to be putative Hg(II) methylators in the gene analysis. In summary, the hydrodynamic sorting of lithogenic particles appears to govern the cross-shelf distribution of THg, and in situ methylation is considered a major source of MeHg in the ESS sediment.

Microbial diversity and abundance vary along salinity, oxygen, and particle size gradients in the Chesapeake Bay

Marine snow and other particles are abundant in estuaries, where they drive biogeochemical transformations and elemental transport. Particles range in size, thereby providing a corresponding gradient of habitats for marine microorganisms. We used standard normalized amplicon sequencing, verified with microscopy, to characterize taxon-specific microbial abundances, (cells per litre of water and per milligrams of particles), across six particle size classes, ranging from 0.2 to 500 μm, along the main stem of the Chesapeake Bay estuary. Microbial communities varied in salinity, oxygen concentrations, and particle size. Many taxonomic groups were most densely packed on large particles (in cells/mg particles), yet were primarily associated with the smallest particle size class, because small particles made up a substantially larger portion of total particle mass. However, organisms potentially involved in methanotrophy, nitrite oxidation, and sulphate reduction were found primarily on intermediately sized (5-180 μm) particles, where species richness was also highest. All abundant ostensibly free-living organisms, including SAR11 and Synecococcus, appeared on particles, albeit at lower abundance than in the free-living fraction, suggesting that aggregation processes may incorporate them into particles. Our approach opens the door to a more quantitative understanding of the microscale and macroscale biogeography of marine microorganisms.

Microbial regulation of feedbacks to ecosystem change

Microbes are key biodiversity components of all ecosystems and control vital ecosystem functions. Although we have just begun to unravel the scales and factors that regulate microbial communities, their role in mediating ecosystem stability in response to disturbances remains underexplored. Here, we review evidence of how, when, and where microbes regulate or drive disturbance feedbacks. Negative feedbacks dampen the impacts of disturbance, which maintain ecosystem stability, whereas positive feedbacks instead erode stability by amplifying the disturbance. Here we describe the processes underlying the responses to disturbance using a hierarchy of functional traits, and we exemplify how these may drive biogeochemical feedbacks. We suggest that the feedback potential of functional traits at different hierarchical levels is contingent on the complexity and heterogeneity of the environment.

Hypoxia diversifies molecular composition of dissolved organic matter and enhances preservation of terrestrial organic carbon in the Yangtze River Estuary

Dissolved organic matter (DOM) is an essential component of the global carbon cycle, and estuaries link the rivers and the oceans, thus playing important roles in land-ocean DOM transformation and transport. However, the effects of hypoxia on DOM transport and fate in estuaries and coastal oceans remains poorly understood. To address this gap, we characterized the molecular composition of DOM in bottom water (BW) and sediment porewater (PW) at hypoxic and non-hypoxic sites in the Yangtze River Estuary (YRE) using ultra-high-resolution Fourier transform ion cyclotron resonance mass spectrometry. Our results showed significant differences in DOM molecular composition between hypoxic and non-hypoxic areas for both BW and PW. Specifically, DOM in hypoxic sites was more recalcitrant than that in non-hypoxic areas for both BW and PW, with lower H/C, and higher O/C, double bond equivalent, and modified aromaticity index. The presence of higher polyphenols, and black carbon in hypoxic areas suggested that hypoxic conditions could facilitate the preservation of terrestrial organic matter. Furthermore, we identified a much higher number of hypoxia-unique formulas than ocean-non-hypoxia-unique formulas, indicating that hypoxia could diversify the DOM pool. Within hypoxia-unique formulas for PW, both biologically labile (unsaturated aliphatic compounds and peptides) and recalcitrant formulas (carboxyl-rich alicyclic molecules) were found, suggesting that hypoxia could facilitate the preservation of labile formulas and the production of recalcitrant formulas. In addition, we formulated that the sulfurization is more important in PW than BW in hypoxic areas based on the higher dissolved organic sulfur (DOS) abundance and larger number of hypoxia-only formulas in hypoxic PW, and also the precursor analysis results. Overall, our study provides insights into the effect of hypoxia on the molecular characteristics and preservation of DOM in estuaries and coastal oceans, highlighting the importance of considering hypoxia in understanding the biogeochemical processes of these ecosystems.

Fungi increases kelp (Ecklonia radiata) remineralisation and dissolved organic carbon, alkalinity, and dimethylsulfoniopropionate (DMSP) production

Fungi are key players in terrestrial organic matter (OM) degradation, but little is known about their role in marine environments. Here we compared the degradation of kelp (Ecklonia radiata) in mesocosms with and without fungicides over 45 days. The aim was to improve our understanding of the vital role of fungal OM degradation and remineralisation and its relevance to marine biogeochemical cycles (e.g., carbon, nitrogen, sulfur, or volatile sulfur). In the presence of fungi, 68 % of the kelp detritus degraded over 45 days, resulting in the production of 0.6 mol of dissolved organic carbon (DOC), 0.16 mol of dissolved inorganic carbon (DIC), 0.23 mol of total alkalinity (TA), and 0.076 mol of CO2, which was subsequently emitted to the atmosphere. Conversely, when fungi were inhibited, the bacterial community diversity was reduced, and only 25 % of the kelp detritus degraded over 45 days. The application of fungicides resulted in the generation of an excess amount of 1.5 mol of DOC, but we observed only 0.02 mol of DIC, and 0.04 mol of TA per one mole of kelp detritus, accompanied by a CO2 emission of 0.081 mol. In contrast, without fungi, remineralisation of kelp detritus to DIC, TA, dimethyl sulfide (DMS), dimethylsulfoniopropionate (DMSP) and methanethiol (MeSH) was significantly reduced. Fungal kelp remineralisation led to a remarkable 100,000 % increase in DMSP production. The observed substantial changes in sediment chemistry when fungi are inhibited highlight the important biogeochemical role of fungal remineralisation, which likely plays a crucial role in defining coastal biogeochemical cycling, blue carbon sequestration, and thus climate regulation.

Sulfurization alters phenol-formaldehyde resin microplastics redox property and their efficiency in mediating arsenite oxidation

Microplastics weathering by various types of oxidants in the oxic environment and their interaction with environmental contaminants have drawn numerous scientific attention. However, the environmental fate of microplastics under a reducing environment has been largely unresolved. Herein, the change of physicochemical and redox properties of microplastics during the weathering under a sulfate-reducing environment and the interaction with arsenite were addressed. The sulfurization of phenol-formaldehyde resin microplastics under a sulfate-reducing environment generated smooth and porous particles with the induction of organic S species. Multiple spectroscopic results demonstrated thioether and thiophene groups formed by the substitute removal of O-containing functional groups. Moreover, the sulfurization process induced the reduction of carbonyl groups and oxidation of phenolic hydroxyl groups and resulted in the formation of semiquinone radicals. The O-containing functional groups contributed to microplastics redox property and As(III) oxidation while S-containing functional groups showed no obvious effect. The sulfurized microplastics had lower efficiency in mediating arsenite oxidation than the unsulfurized counterparts due to the decreased electron donating capacity. Producing hydrogen peroxides by electron-donating phenol groups and semiquinone radicals and the direct semiquinone radicals oxidation could mediate arsenite oxidation. The findings of this study help us understand the fate of microplastics in redox fluctuation interfaces.

Substrate Specificity of Biofilms Proximate to Historic Shipwrecks

The number of built structures on the seabed, such as shipwrecks, energy platforms, and pipelines, is increasing in coastal and offshore regions. These structures, typically composed of steel or wood, are substrates for microbial attachment and biofilm formation. The success of biofilm growth depends on substrate characteristics and local environmental conditions, though it is unclear which feature is dominant in shaping biofilm microbiomes. The goal of this study was to understand the substrate- and site-specific impacts of built structures on short-term biofilm composition and functional potential. Seafloor experiments were conducted wherein steel and wood surfaces were deployed for four months at distances extending up to 115 m away from three historic (>50 years old) shipwrecks in the Gulf of Mexico. DNA from biofilms on the steel and wood was extracted, and metagenomes were sequenced on an Illumina NextSeq. A bioinformatics analysis revealed that the taxonomic composition was significantly different between substrates and sites, with substrate being the primary determining factor. Regardless of site, the steel biofilms had a higher abundance of genes related to biofilm formation, and sulfur, iron, and nitrogen cycling, while the wood biofilms showed a higher abundance of manganese cycling and methanol oxidation genes. This study demonstrates how substrate composition shapes biofilm microbiomes and suggests that marine biofilms may contribute to nutrient cycling at depth. Analyzing the marine biofilm microbiome provides insight into the ecological impact of anthropogenic structures on the seabed.

Selective Photochemical Oxidation of Reduced Dissolved Organic Sulfur to Inorganic Sulfate

The chemical nature and stability of reduced dissolved organic sulfur (DOS_Red) have implications on the biogeochemical cycling of trace and major elements across fresh and marine aquatic environments, but the underlying processes governing DOS_Red stability remain obscure. Here, dissolved organic matter (DOM) was isolated from a sulfidic wetland, and laboratory experiments quantified dark and photochemical oxidation of DOS_Red using atomic-level measurement of sulfur X-ray absorption near-edge structure (XANES) spectroscopy. DOS_Red was completely resistant to oxidation by molecular oxygen in the dark and underwent rapid and quantitative oxidation to inorganic sulfate (SO₄^2-) in the presence of sunlight. The rate of DOS_Red oxidation to SO₄^2- greatly exceeded that of DOM photomineralization, resulting in a 50% loss of total DOS and 78% loss of DOS_Red over 192 h of irradiance. Sulfonates (DOS_SO3) and other minor oxidized DOS functionalities were not susceptible to photochemical oxidation. The observed susceptibility of DOS_Red to photodesulfurization, which has implications on carbon, sulfur, and mercury cycling, should be comprehensively evaluated across diverse aquatic environments of differing DOM composition.

Bacteria are driving the ocean's organosulfur cycle

Bacteria are key players in the marine sulfur cycle, from the sunlit ocean surface to the dark abyssal depths. Here, we provide a brief overview of the interlinked metabolic processes of organosulfur compounds, an elusive sulfur cycling process that exists in the dark ocean, and the current challenges that limit our understanding of this key nutrient cycle.

SiC@FeZnZiF as a Bifunctional Catalyst with Catalytic Activating PMS and Photoreducing Carbon Dioxide

Herein, we encapsulated modified silicon carbide nanoparticles utilizing a metal-organic backbone. E-SiC-FeZnZIF composites were successfully prepared via Fe doping. The catalysis activity of this bifunctional composite material was evaluated by the degradation of tetracycline (THC) and carbamazepine (CBZ) and the reduction of carbon dioxide (CO₂). Nano SiC has received widespread attention in advanced oxidation applications, especially in the catalytic activation of peroxymonosulfate (PMS). However, the inferior activity of SiC has severely restricted its practical use. In this study of dual functional composite materials, nano SiC was firstly etched under aqueous alkali. Then, zeolite imidazolate frame-8 (ZIF-8) was used for immobilization. The filling of the etched nano SiC with FeZnZiF was confirmed by SEM, XRD, FTIR, BET, and XPS analyses. In addition, E-SiC-FeZnZIF exhibited excellent catalytic activation of peroxymonosulfate (PMS) to oxidize water pollutants, which can degrade tetracycline hydrochloride (THC), achieving a removal rate of 72% within 60 min. Moreover, E-SiC-FeZnZIF exhibited a relatively high CO₂ reduction rate with H₂O. The yields of CO and CH₄ were 0.085 and 0.509 μmol g^-1, respectively, after 2 h, which are higher than that of 50 nm of commercial SiC (CO: 0.084 μmol g^-1; CH₄: 0.209 μmol g^-1). This work provides a relatively convenient synthesis path for constructing metal skeleton composites for advanced oxidation and photocatalytic applications. This will have practical significance in protecting water bodies and reducing CO₂, which are vital not only for maintaining the natural ecological balance and negative feedback regulation, but also for creating a new application carrier based on nano silicon carbide.

Organic preservation of vase-shaped microfossils from the late Tonian Chuar Group, Grand Canyon, Arizona, USA

Vase-shaped microfossils (VSMs) are found globally in middle Neoproterozoic (800-730 Ma) marine strata and represent the earliest evidence for testate (shell-forming) amoebozoans. VSM tests are hypothesized to have been originally organic in life but are most commonly preserved as secondary mineralized casts and molds. A few reports, however, suggest possible organic preservation. Here, we test the hypothesis that VSMs from shales of the lower Walcott Member of the Chuar Group, Grand Canyon, Arizona, contain original organic material, as reported by B. Bloeser in her pioneering studies of Chuar VSMs. We identified VSMs from two thin section samples of Walcott Member black shales in transmitted light microscopy and used scanning electron microscopy to image VSMs. Carbonaceous material is found within the internal cavity of all VSM tests from both samples and is interpreted as bitumen mobilized from Walcott shales likely during the Cretaceous. Energy dispersive X-ray spectroscopy (EDS) and wavelength dispersive X-ray spectroscopy (WDS) reveal that VSM test walls contain mostly carbon, iron, and sulfur, while silica is present only in the surrounding matrix. Raman spectroscopy was used to compare the thermal maturity of carbonaceous material within the samples and indicated the presence of pyrite and jarosite within fossil material. X-ray absorption spectroscopy revealed the presence of reduced organic sulfur species within the carbonaceous test walls, the carbonaceous material found within test cavities, and in the sedimentary matrix, suggesting that organic matter sulfurization occurred within the Walcott shales. Our suite of spectroscopic analyses reveals that Walcott VSM test walls are organic and sometimes secondarily pyritized (with the pyrite variably oxidized to jarosite). Both preservation modes can occur at a millimeter spatial scale within sample material, and at times even within a single specimen. We propose that sulfurization within the Walcott Shales promoted organic preservation, and furthermore, the ratio of iron to labile VSM organic material controlled the extent of pyrite replacement. Based on our evidence, we conclude that the VSMs are preserved with original organic test material, and speculate that organic VSMs may often go unrecognized, given their light-colored, translucent appearance in transmitted light.

Molecular evidence for the production of labile, sulfur-bearing dissolved organic matter in the seep sediments of the South China Sea

Cold seeps with methane-rich fluids leaking out of the seafloor usually support massive biomass of chemosynthetic organisms and associated fauna. A substantial amount of methane is converted to dissolved inorganic carbon by microbial metabolism, and this process also releases dissolved organic matter (DOM) into pore water. Here, pore water samples from "Haima cold seeps" sediments and the non-seep reference sediments in the northern South China Sea were analyzed for optical properties and molecular compositions of pore water DOM. Our results showed that the relative abundance of protein-like DOM, H/C_wa and molecular lability boundary percentage (MLB_L%) in the seep sediments were significantly higher than those in the reference sediments, indicating that more labile DOM related to unsaturated aliphatic compounds is produced in the seep sediments. Spearman's correlation of the fluoresce and molecular data suggested that the humic-like components (C1 and C2) mainly constituted the refractory compounds (CRAM, highly unsaturated and aromatics compounds). In contrast, the protein-like component (C3) had high H/C ratios featuring high degree of DOM lability. The amount of S-containing formulas (CHOS and CHONS) was greatly elevated in the seep sediments, likely caused by abiotic and biotic sulfurization of DOM in the sulfidic environment. Although the abiotic sulfurization was proposed to have a stabilizing effect on organic matter, our results implied that the biotic sulfurization in the cold seep sediments would increase DOM lability. Overall, the labile DOM accumulated in the seep sediments is closely linked to methane oxidation, which not only support heterotrophic communities and but also likely have an impact on carbon and sulfur cycling in the sediments and the ocean.

Morphology and Size of Bacterial Colonies Control Anoxic Microenvironment Formation in Porous Media

Bacterial metabolisms using electron acceptors other than oxygen (e.g., methanogenesis and fermentation) largely contribute to element cycling and natural contaminant attenuation/mobilization, even in well-oxygenated porous environments, such as shallow aquifers. This paradox is commonly explained by the occurrence of small-scale anoxic microenvironments generated by the coupling of bacterial respiration and dissolved oxygen (O₂) transport by pore water. Such microenvironments allow facultative anaerobic bacteria to proliferate in oxic environments. Microenvironment dynamics are still poorly understood due to the challenge of directly observing biomass and O₂ distributions at the microscale within an opaque sediment matrix. To overcome these limitations, we integrated a microfluidic device with transparent O₂ planar optical sensors to measure the temporal behavior of dissolved O₂ concentrations and biomass distributions with time-lapse videomicroscopy. Our results reveal that bacterial colony morphology, which is highly variable in flowing porous systems, controls the formation of anoxic microenvironments. We rationalize our observations through a colony-scale Damköhler number comparing dissolved O₂ diffusion and a bacterial O₂ uptake rate. Our Damköhler number enables us to predict the pore space fraction occupied by anoxic microenvironments in our system for a given bacterial organization.

Novel sulfur isotope analyses constrain sulfurized porewater fluxes as a minor component of marine dissolved organic matter

Marine dissolved organic matter (DOM) is a major reservoir that links global carbon, nitrogen, and phosphorus. DOM is also important for marine sulfur biogeochemistry as the largest water column reservoir of organic sulfur. Dissolved organic sulfur (DOS) can originate from phytoplankton-derived biomolecules in the surface ocean or from abiotically "sulfurized" organic matter diffusing from sulfidic sediments. These sources differ in ³⁴S/³²S isotope ratios (δ³⁴S values), with phytoplankton-produced DOS tracking marine sulfate (21‰) and sulfurized DOS mirroring sedimentary porewater sulfide (∼0 to -10‰). We measured the δ³⁴S values of solid-phase extracted (SPE) DOM from marine water columns and porewater from sulfidic sediments. Marine DOM_SPE δ³⁴S values ranged from 14.9‰ to 19.9‰ and C:S ratios from 153 to 303, with lower δ³⁴S values corresponding to higher C:S ratios. Marine DOM_SPE samples showed consistent trends with depth: δ³⁴S values decreased, C:S ratios increased, and δ¹³C values were constant. Porewater DOM_SPE was ³⁴S-depleted (∼-0.6‰) and sulfur-rich (C:S ∼37) compared with water column samples. We interpret these trends as reflecting at most 20% (and on average ∼8%) contribution of abiotic sulfurized sources to marine DOS_SPE and conclude that sulfurized porewater is not a main component of oceanic DOS and DOM. We hypothesize that heterogeneity in δ³⁴S values and C:S ratios reflects the combination of sulfurized porewater inputs and preferential microbial scavenging of sulfur relative to carbon without isotope fractionation. Our findings strengthen links between oceanic sulfur and carbon cycling, supporting a realization that organic sulfur, not just sulfate, is important to marine biogeochemistry.

Secondary Mineral Formation and Carbon Dynamics during FeS Oxidation in the Presence of Dissolved Organic Matter

Iron (Fe) minerals constitute a major control on organic carbon (OC) storage in soils and sediments. While previous research has mainly targeted Fe (oxyhydr)oxides, the impact of Fe sulfides and their subsequent oxidation on OC dynamics remains unresolved in redox-fluctuating environments. Here, we investigated the impact of dissolved organic matter (DOM) on FeS oxidation and how FeS and its oxidation may alter the retention and nature of DOM. After the anoxic reaction of DOM with FeS, FeS preferentially removed high-molecular-weight and nitrogen-rich compounds and promoted the formation of aqueous sulfurized organic molecules, according to Fourier transform-ion cyclotron resonance-mass spectrometry (FT-ICR-MS) analysis. When exposed to O₂, FeS oxidized to nanocrystalline lepidocrocite and additional aqueous sulfurized organic compounds were generated. The presence of DOM decreased the particle size of the resulting nano-lepidocrocite based on Mössbauer spectroscopy. Following FeS oxidation, most solid-phase OC remained associated with the newly formed lepidocrocite via a monodentate chelating mechanism (based on FTIR analysis), and FeS oxidation caused only a slight increase in the solubilization of solid-phase OC. Collectively, this work highlights the under-appreciated role of Fe sulfides and their oxidation in driving OC transformation and preservation.

Diffusion of H2 S from anaerobic thiolated ligand biodegradation rapidly generated bioavailable mercury

Methylmercury (MeHg) is a potent neurotoxin that biomagnifies through food webs and which production depends on anaerobic microbial uptake of inorganic mercury (Hg) species. One outstanding knowledge gap in understanding Hg methylation is the nature of bioavailable Hg species. It has become increasingly obvious that Hg bioavailability is spatially diverse and temporally dynamic but current models are built on single thiolated ligand systems, mostly omitting ligand exchanges and interactions, or the inclusion of dissolved gaseous phases. In this study, we used a whole-cell anaerobic biosensor to determine the role of a mixture of thiolated ligands on Hg bioavailability. Serendipitously, we discovered how the diffusion of trace amounts of exogenous biogenic H₂ S, originating from anaerobic microbial ligand degradation, can alter Hg speciation - away from H₂ S production site - to form bioavailable species. Regardless of its origins, H₂ S stands as a mobile mediator of microbial Hg metabolism, connecting spatially separated microbial communities. At a larger scale, global planetary changes are expected to accelerate the production and mobilization of H₂ S and Hg, possibly leading to increased production of the potent neurotoxin; this work provides mechanistic insights into the importance of co-managing biogeochemical cycle disruptions. This article is protected by copyright. All rights reserved.

Quantification of Organic Carbon Sequestered by Biogenic Iron Sulfide Minerals in Long-Term Anoxic Laboratory Incubations

Organic carbon sequestration in sedimentary environments controls oxygen and carbon dioxide concentrations in the atmosphere. While minerals play an important role in the preservation of organic carbon, there is a lack of understanding about the formation and stability of organo-mineral interactions in anoxic environments, especially those involving authigenic iron sulfide minerals. In this study, we quantified organic carbon and nitrogen sequestered in biogenic iron sulfide minerals co-precipitated with sulfate-reducing bacteria (SRB) in freshwater and marine conditions in long-term laboratory experiments. The amounts of C and N associated with biogenic iron sulfide minerals increased with increasing cell biomass concentrations available in the media. C and N levels stabilized over the first 2 months of incubation and remained stable for up to 1 year. Crystalline mackinawite (FeS) formed in all experimental conditions and transformed to greigite only in some experimental conditions. We did not find evidence that this mineral transformation affected C and N levels, neither could we identify the factors that controlled greigite formation. Pyrite did not form in our experimental conditions. While C concentrations in minerals correlated with concentrations of reduced sulfate in both the freshwater and marine media, removal of OC by iron sulfide minerals was more efficient in freshwater than marine conditions. Removal of OC by iron sulfide minerals was also more efficient when cells were present (SRB biomass) in comparison with abiotic incubations with organic mixtures (e.g., tryptone, yeast extract, and casamino acids). Our study highlights the potential for biogenic iron sulfide minerals to quantitatively contribute to organic carbon preservation in anoxic environments.

Insights into Prokaryotic Community and Its Potential Functions in Nitrogen Metabolism in the Bay of Bengal, a Pronounced Oxygen Minimum Zone

Ocean oxygen minimum zones (OMZs) around the global ocean are expanding both horizontally and vertically. Multiple studies have identified the significant influence of anoxic conditions (≤1 μM O₂) on marine prokaryotic communities and biogeochemical cycling of elements. However, little attention has been paid to the expanding low-oxygen zones where the oxygen level is still above the anoxic level. Here, we studied the abundance and taxonomic and functional profiles of prokaryotic communities in the Bay of Bengal (BoB), where the oxygen concentration is barely above suboxic level (5 μM O₂). We found the sinking of Trichodesmium into deep water was far more efficient than that of Prochlorococcus, suggesting Trichodesmium blooms might be an essential carbon and nitrogen source for the maintenance of the BoB OMZ. In addition to the shift in the prokaryotic community composition, the abundance of some functional genes also changed with the change of oxygen concentration. Compared to oxic (>60 μM O₂) Tara Ocean and high-hypoxic (>20 to ≤60 μM O₂) BoB samples, we found more SAR11-nar sequences (responsible for reducing nitrate to nitrite) in low-hypoxic (>5 to ≤20 μM O₂) BoB waters. This suggested SAR11-nar genes would be more widespread due to the expansion of OMZs. It seems that the nitrite-N was not further reduced to nitrogen through denitrification but likely oxidized to nitrate by Nitrospinae in the BoB OMZ and then accumulated in the form of nitrate-N. However, the lack of N₂ production in the BoB would change if the BoB OMZ became anoxic. Together, these results suggested that reduction of oxygen concentration and OMZ expansion may increase the use of nitrate by SAR11 and N₂ production in the BoB.

IMPORTANCE Recognizing the prokaryotic community and its functions in hypoxic (>5 to ≤60 μM O₂) environments before further expansion of OMZs is critical. We demonstrate the prokaryotic community and its potential functions in nitrogen metabolism in the Bay of Bengal (BoB), where oxygen concentration is barely above suboxic level. This study highlighted that Trichodesmium might be an essential carbon and nitrogen source in the maintenance of the BoB OMZ. Additionally, we suggest that the lack of N₂ production in the BoB would change if the BoB OMZ became anoxic, and the expansion of OMZs in the global ocean may potentially increase the use of nitrate by SAR11.

Microbial Activities and Selection from Surface Ocean to Subseafloor on the Namibian Continental Shelf

Oxygen minimum zones (OMZs) are hot spots for redox-sensitive nitrogen transformations fueled by sinking organic matter. In comparison, the regulating role of sulfur-cycling microbes in marine OMZs, their impact on carbon cycling in pelagic and benthic habitats, and activities below the seafloor remain poorly understood. Using ¹³C DNA stable isotope probing (SIP) and metatranscriptomics, we explored microbial guilds involved in sulfur and carbon cycling from the ocean surface to the subseafloor on the Namibian shelf. There was a clear separation in microbial community structure across the seawater-seafloor boundary, which coincided with a 100-fold-increased concentration of microbial biomass and unique gene expression profiles of the benthic communities. ¹³C-labeled 16S rRNA genes in SIP experiments revealed carbon-assimilating taxa and their distribution across the sediment-water interface. Most of the transcriptionally active taxa among water column communities that assimilated ¹³C from diatom exopolysaccharides (mostly Bacteroidetes, Actinobacteria, Alphaproteobacteria, and Planctomycetes) also assimilated ¹³C-bicarbonate under anoxic conditions in sediment incubations. Moreover, many transcriptionally active taxa from the seafloor community (mostly sulfate-reducing Deltaproteobacteria and sulfide-oxidizing Gammaproteobacteria) that assimilated ¹³C-bicarbonate under sediment anoxic conditions also assimilated ¹³C from diatom exopolysaccharides in the surface ocean and OMZ waters. Despite strong selection at the sediment-water interface, many taxa related to either planktonic or benthic communities were found to be present at low abundance and actively assimilating carbon under both sediment and water column conditions. In austral winter, mixing of shelf waters reduces stratification and suspends sediments from the seafloor into the water column, potentially spreading metabolically versatile microbes across niches.

IMPORTANCE Microbial activities in oxygen minimum zones (OMZs) transform inorganic fixed nitrogen into greenhouse gases, impacting the Earth’s climate and nutrient equilibrium. Coastal OMZs are predicted to expand with global change and increase carbon sedimentation to the seafloor. However, the role of sulfur-cycling microbes in assimilating carbon in marine OMZs and related seabed habitats remain poorly understood. Using ¹³C DNA stable isotope probing and metatranscriptomics, we explore microbial guilds involved in sulfur and carbon cycling from ocean surface to subseafloor on the Namibian shelf. Despite strong selection and differential activities across the sediment-water interface, many active taxa were identified in both planktonic and benthic communities, either fixing inorganic carbon or assimilating organic carbon from algal biomass. Our data show that many planktonic and benthic microbes linked to the sulfur cycle can cross redox boundaries when mixing of the shelf waters reduces stratification and suspends seafloor sediment particles into the water column.

An analysis of protists in Pacific oxygen deficient zones: implications for Prochlorococcus and N2 -producing bacteria

Ocean oxygen deficient zones (ODZs) host 30%-50% of marine N₂ production. Cyanobacteria photosynthesizing in the ODZ create a secondary chlorophyll maximum and provide organic matter to N₂ -producing bacteria. This chlorophyll maximum is thought to occur due to reduced grazing in anoxic waters. We first examine ODZ protists with long amplicon reads. We then use non-primer-based methods to examine the composition and relative abundance of protists in metagenomes from the Eastern Tropical North and South Pacific ODZs and compare these data to the oxic Hawaii Ocean Time-series (HOT) in the North Pacific. We identify and quantify protists in proportion to the total microbial community. From metagenomic data, we see a large drop in abundance of fungi and protists such as choanoflagellates, radiolarians, cercozoa and ciliates in the ODZs but not in the oxic mesopelagic at HOT. Diplonemid euglenozoa were the only protists that increased in the ODZ. Dinoflagellates and foraminifera reads were also present in the ODZ though less abundant compared to oxic waters. Denitrification has been found in foraminifera but not yet in dinoflagellates. DNA techniques cannot separate dinoflagellate cells and cysts. Metagenomic analysis found taxonomic groups missed by amplicon sequencing and identified trends in abundance.

Heterogeneity of the sediment oxygen demand and its contribution to the hypoxia off the Changjiang estuary and its adjacent waters

The severe hypoxia off the Changjiang estuary (CE) has a dual-core structure, and the two hypoxic zones exhibit behavioural, physical and biochemical differences. Currently, few studies have revealed straightforward differences regarding the key biochemical processes between these two hypoxic zones. In this study, the phytoplankton sinking rate (PSR) and sediment oxygen demand (SOD) were measured by field experiments and compared between the two hypoxic regions. PSR and SOD ranged from 0.75-3.34 m day^-1 and 5.67-16.19 mmol m^-2 day^-1, respectively. Interestingly, PSR and SOD were higher in the southern region than in the northern region, implying stronger pelagic-benthic biogeochemical coupling in the southern region. SOD accounted for approximately 44% and 51% of DO net consumption in the northern and southern regions, respectively, from July to August. The southern hypoxic region appeared to exhibit intense DO consumption and fast DO supplementation, while the northern hypoxic region seemed to exhibit slow DO consumption and supplementation.

Rapid, concurrent formation of organic sulfur and iron sulfides during experimental sulfurization of sinking marine particles

Organic matter (OM) sulfurization can enhance the preservation and sequestration of carbon in anoxic sediments, and it has been observed in sinking marine particles from marine O₂-deficient zones. The magnitude of this effect on carbon burial remains unclear, however, because the transformations that occur when sinking particles encounter sulfidic conditions remain undescribed. Here, we briefly expose sinking marine particles from the eastern tropical North Pacific O₂-deficient zone to environmentally relevant sulfidic conditions (20°C, 0.5 mM [poly]sulfide, two days) and then characterize the resulting solid-phase organic and inorganic products in detail. During these experiments, the abundance of organic sulfur in both hydrolyzable and hydrolysis-resistant solids roughly triples, indicating extensive OM sulfurization. Lipids also sulfurize on this timescale, albeit less extensively. In all three pools, OM sulfurization produces organic monosulfides, thiols, and disulfides. Hydrolyzable sulfurization products appear within ≤ 200-μm regions of relatively homogenous composition that are suggestive of sulfurized extracellular polymeric substances (EPS). Concurrently, reactions with particulate iron oxyhydroxides generate low and fairly uniform concentrations of iron sulfide (FeS) within these same EPS-like materials. Iron oxyhydroxides were not fully consumed during the experiment, which demonstrates that organic materials can be competitive with reactive iron for sulfide. These experiments support the hypothesis that sinking, OM- and EPS-rich particles in a sulfidic water mass can sulfurize within days, potentially contributing to enhanced sedimentary carbon sequestration. Additionally, sulfur-isotope and chemical records of organic S and iron sulfides in sediments have the potential to incorporate signals from water column processes.

Microbial Roles in Dissolved Organic Matter Transformation in Full-Scale Wastewater Treatment Processes Revealed by Reactomics and Comparative Genomics

Understanding the degradation of dissolved organic matter (DOM) is vital for optimizing DOM control. However, the microbe-mediated DOM transformation during wastewater treatment remains poorly characterized. Here, microbes and DOM along full-scale biotreatment processes were simultaneously characterized using comparative genomics and high-resolution mass spectrometry-based reactomics. Biotreatments significantly increased DOM's aromaticity and unsaturation due to the overproduced lignin and polyphenol analogs. DOM was diversified by over five times in richness, with thousands of nitrogenous and sulfur-containing compounds generated through microbe-mediated oxidoreduction, functional group transfer, and C-N and C-S bond formation. Network analysis demonstrated microbial division of labor in DOM transformation. However, their roles were determined by their functional traits rather than taxa. Specifically, network and module hubs exhibited rapid growth potentials and broad substrate affinities but were deficient in xenobiotics-metabolism-associated genes. They were mainly correlated to liable DOM consumption and its transformation to recalcitrant compounds. In contrast, connectors and peripherals were potential degraders of recalcitrant DOM but slow in growth. They showed specialized associations with fewer DOM molecules and probably fed on metabolites of hub microbes. Thus, developing technologies (e.g., carriers) to selectively enrich peripheral degraders and consequently decouple the liable and recalcitrant DOM transformation processes may advance DOM removal.

Ecophysiology of the Cosmopolitan OM252 Bacterioplankton (Gammaproteobacteria)

Among the thousands of species that comprise marine bacterioplankton communities, most remain functionally obscure. One key cosmopolitan group in this understudied majority is the OM252 clade of Gammaproteobacteria. Although frequently found in sequence data and even previously cultured, the diversity, metabolic potential, physiology, and distribution of this clade has not been thoroughly investigated. Here, we examined these features of OM252 bacterioplankton using a newly isolated strain and genomes from publicly available databases. We demonstrated that this group constitutes a globally distributed novel genus ("Candidatus Halomarinus"), sister to Litoricola, comprising two subclades and multiple distinct species. OM252 organisms have small genomes (median, 2.21 Mbp) and are predicted obligate aerobes capable of alternating between chemoorganoheterotrophic and chemolithotrophic growth using reduced sulfur compounds as electron donors. Subclade I genomes encode genes for the Calvin-Benson-Bassham cycle for carbon fixation. One representative strain of subclade I, LSUCC0096, had extensive halotolerance and a mesophilic temperature range for growth, with a maximum rate of 0.36 doublings/h at 35°C. Cells were curved rod/spirillum-shaped, ∼1.5 by 0.2 μm. Growth yield on thiosulfate as the sole electron donor under autotrophic conditions was roughly one-third that of heterotrophic growth, even though calculations indicated similar Gibbs energies for both catabolisms. These phenotypic data show that some "Ca. Halomarinus" organisms can switch between serving as carbon sources or sinks and indicate the likely anabolic cost of lithoautotrophic growth. Our results thus provide new hypotheses about the roles of these organisms in global biogeochemical cycling of carbon and sulfur. IMPORTANCE Marine microbial communities are teeming with understudied taxa due to the sheer numbers of species in any given sample of seawater. One group, the OM252 clade of Gammaproteobacteria, has been identified in gene surveys from myriad locations, and one isolated organism has even been genome sequenced (HIMB30). However, further study of these organisms has not occurred. Using another isolated representative (strain LSUCC0096) and publicly available genome sequences from metagenomic and single-cell genomic data sets, we examined the diversity within the OM252 clade and the distribution of these taxa in the world's oceans, reconstructed the predicted metabolism of the group, and quantified growth dynamics in LSUCC0096. Our results generate new knowledge about the previously enigmatic OM252 clade and point toward the importance of facultative chemolithoautotrophy for supporting some clades of ostensibly "heterotrophic" taxa.

Sulfurization of dissolved organic matter in the anoxic water column of the Black Sea

Today's oceans store as much dissolved organic carbon (DOC) in the water column as there is CO₂ in the atmosphere, and as such dissolved organic matter (DOM) is an important component of the global carbon cycle. It was shown that in anoxic marine sediments, reduced sulfur species (e.g., H₂S) abiotically react with organic matter, contributing to carbon preservation. It is not known whether such processes also contribute to preserving DOM in ocean waters. Here, we show DOM sulfurization within the sulfidic waters of the Black Sea, by combining elemental, isotopic, and molecular analyses. Dissolved organic sulfur (DOS) is formed largely in the water column and not derived from sediments or allochthonous nonmarine sources. Our findings suggest that during large-scale anoxic events, DOM may accumulate through abiotic reactions with reduced sulfur species, having long-lasting effects on global climate by enhancing organic carbon sequestration.