The Biogeochemical Sulfur Cycle of Marine Sediments

Microbial diversity and oil biodegradation potential of northern Barents Sea sediments

The Arctic, an essential ecosystem on Earth, is subject to pronounced anthropogenic pressures, most notable being the climate change and risks of crude oil pollution. As crucial elements of Arctic environments, benthic microbiomes are involved in climate-relevant biogeochemical cycles and hold the potential to remediate upcoming contamination. Yet, the Arctic benthic microbiomes are among the least explored biomes on the planet. Here we combined geochemical analyses, incubation experiments, and microbial community profiling to detail the biogeography and biodegradation potential of Arctic sedimentary microbiomes in the northern Barents Sea. The results revealed a predominance of bacterial and archaea phyla typically found in the deep marine biosphere, such as Chloroflexi, Atribacteria, and Bathyarcheaota. The topmost benthic communities were spatially structured by sedimentary organic carbon, lacking a clear distinction among geographic regions. With increasing sediment depth, the community structure exhibited stratigraphic variability that could be correlated to redox geochemistry of sediments. The benthic microbiomes harbored multiple taxa capable of oxidizing hydrocarbons using aerobic and anaerobic pathways. Incubation of surface sediments with crude oil led to proliferation of several genera from the so-called rare biosphere. These include Alkalimarinus and Halioglobus, previously unrecognized as hydrocarbon-degrading genera, both harboring the full genetic potential for aerobic alkane oxidation. These findings increase our understanding of the taxonomic inventory and functional potential of unstudied benthic microbiomes in the Arctic.

Ebullition dominates methane emissions in stratified coastal waters

Coastal areas are an important source of methane (CH4). However, the exact origins of CH4 in the surface waters of coastal regions, which in turn drive sea-air emissions, remain uncertain. To gain a comprehensive understanding of the current and future climate change feedbacks, it is crucial to identify these CH4 sources and processes that regulate its formation and oxidation. This study investigated coastal CH4 dynamics by comparing water column data from six stations located in the brackish Tvärminne Archipelago, Baltic Sea. The sediment biogeochemistry and microbiology were further investigated at two stations (i.e., nearshore and offshore). These stations differed in terms of stratification, bottom water redox conditions, and organic matter loading. At the nearshore station, CH4 diffusion from the sediment into the water column was negligible, because nearly all CH4 was oxidized within the upper sediment column before reaching the sediment surface. On the other hand, at the offshore station, there was significant benthic diffusion of CH4, albeit the majority underwent oxidation before reaching the sediment-water interface, due to shoaling of the sulfate methane transition zone (SMTZ). The potential contribution of CH4 production in the water column was evaluated and was found to be negligible. After examining the isotopic signatures of δ13C-CH4 across the sediment and water column, it became apparent that the surface water δ13C-CH4 values observed in areas with thermal stratification could not be explained by diffusion, advective fluxes, nor production in the water column. In fact, these values bore a remarkable resemblance to those detected below the SMTZ. This supports the hypothesis that the source of CH4 in surface waters is more likely to originate from ebullition than diffusion in stratified brackish coastal systems.

Biogeochemical mechanisms of iron (Fe) and manganese (Mn) in groundwater and soil profiles in the Zhongning section of the Weining Plain (northwest China)

High levels of Iron (Fe) and manganese (Mn) in soils may contribute to secondary contamination of groundwater. However, there is limited understanding of the cycling mechanisms of Fe and Mn in groundwater and soil. This study aimed to investigate the biogeochemical processes constituting the Fe and Mn cycle by combining hydrochemistry, sequential extraction and microbiological techniques. The results indicated a similar vertical distribution pattern of Fe and Mn, with lower levels of the effective form (EFC-Fe/Mn) observed at the oxygenated surface, increasing near the groundwater table and decreasing below it. Generally, there was a tendency for accumulation above the water table, with Mn exhibiting a higher release potential compared to Fe. Iron‑manganese oxides (Ox-Fe/Mn) dominated the effective forms, with Fe and Mn in the soil entering groundwater through the reduction dissolution of Ox-Fe/Mn and the oxidative degradation of organic matter or sulfide (OM-Fe/Mn). Correlation analysis revealed that Fe and Mn tend to accumulate in media with fine particles and high organic carbon (TOC) contents. 16S rRNA sequencing analysis disclosed significant variation in the abundance of microorganisms associated with Fe and Mn transformations among unsaturated zone soils, saturated zone media and groundwater, with Fe/Mn content exerting an influence on microbial communities. Furthermore, functional bacterial identification results from the FAPROTAX database show a higher abundance of iron-oxidizing bacteria (9.3 %) in groundwater, while iron and manganese-reducing bacteria are scarce in both groundwater and soil environments. Finally, a conceptual model of Fe and Mn cycling was constructed, elucidating the biogeochemical processes in groundwater and soil environments. This study provides a new perspective for a deeper understanding of the environmental fate of Fe and Mn, which is crucial for mitigating Fe and Mn pollution in groundwater.

Microbial consortium involved in ferromanganese and francolite biomineralization in an anchialine environment (Zinzulùsa Cave, Castro, Italy)

Tidally-influenced subterranean settings represent natural geomicrobiological laboratories, relatively unexplored, that facilitate the investigation of new biomineralization processes. The unusual water chemistry of Zinzulùsa Cave and its oligotrophic and aphotic conditions have allowed the development of a unique ecosystem in which complex bacterial activities induce rare biomineralization processes. A diversified microbial community develops on centimeter-thick crusts that form in the submerged part of the cave. The crusts are formed of Ca-phosphate minerals, mostly carbonate-fluoroapatite (francolite), covered by a black crust, few microns in thickness, composed of ferromanganiferous oxides (hematite and vernadite). Diffuse coccoidal and filamentous bacteria and amorphous organic matter are mixed with the minerals. The micromorphologies and comparative 16S rRNA gene-based metabarcoding analyses identify a "core microbiota" also common to other natural environments characterized by FeMn and Ca-phosphate mineralization. The microbiota is characterized by nitrifying, sulfide/sulfur/thiosulfate-oxidizing and sulfate/thiosulfate/sulfur-reducing bacteria. In addition, manganese-oxidizing bacteria include the recently described "Ca. Manganitrophus noduliformans" and an abundance of bacteria belonging to the Planctomycetes-Verrucomicrobia-Chlamydiae (PVC) superphylum, as well as Haliangiales (fruiting body-forming bacteria) and Hyphomicrobiales (stalked and budding bacteria) that are known to produce extracellular polymers that trap iron and manganese oxides. 16S rRNA gene metabarcoding analysis showed the presence of bacteria able to utilize many organic P substrates, including Ramlibacter, and SEM images revealed traces of fossilized microorganisms resembling "cable bacteria", which may play a role in Ca-phosphate biomineralization. Overall, the data indicate biomineralization processes induced by microbial metabolic activities for both ferromanganiferous oxide and francolite components of these crusts.

The mechanism of microbial sulfate reduction in high concentration sulfate wastewater enhanced by maifanite

Excessive sulfate levels in water bodies pose a dual threat to the ecological environment and human health. The microbial removal of sulfate encounters challenges, particularly in environments with high sulfate concentrations, where the gradual accumulation of sulfide hampers microbial activity. This study focuses on elucidating the mechanisms underlying the enhancement of microbial sulfate reduction in high-concentration sulfate wastewater through a comparative analysis of maifanite and zeolite biostimulants. The investigation reveals that zeolite primarily facilitates microbial growth by providing attachment sites, while maifanite augments sulfate-reducing bacteria (SRB) activity through the release of active substances such as Mo, Ca, and Cu. The addition of maifanite proves instrumental in enhancing microbial activity, manifesting as increased microbial load and protein production, augmented extracellular polymer generation, accelerated electron transfer, and facilitated microbial growth and biofilm formation. Noteworthy is the observation that the combined application of maifanite and zeolite exhibited a synergistic effect, resulting in a 167 % and 68 % increase in sulfate reduction rate compared to the utilization of maifanite (0.12 d-1) or zeolite (0.19 d-1) in isolation. Within this synergistic context, the relative abundance of Desulfobacteraceae reaches a peak of 15.4 %. The outcomes of this study corroborate the distinct promotion mechanisms of maifanite and zeolite in microbial sulfate reduction, offering novel insights into the application of maifanite in the context of high-concentration sulfate removal.

Unexpected increase of sulfate concentrations and potential impact on CH4 budgets in freshwater lakes

The continuous increase in sulfate (SO42-) concentrations discharged by anthropogenic activities lacks insights into their dynamics and potential impact on CH4 budgets in freshwater lakes. Here we conducted a field investigation in the lakes along the highly developed Yangtze River basin, China, additionally, we analyzed long-term data (1950-2020) from Lake Taihu, a typical eutrophic lake worldwide. We observed a gradual increase in SO42- concentrations up to 100 mg/L, which showed a positive correlation with the trophic state of the lakes. The annual variations indicated that eutrophication intensified the fluctuation of SO42- concentrations. A random forest model was applied to assess the impact of SO42- concentrations on CH4 emissions, revealing a significant negative effect. Synchronously, a series of microcosms with added SO42- were established to simulate cyanobacteria decomposition processes and explore the coupling mechanism between sulfate reduction and CH4 production. The results showed a strong negative correlation between CH4 concentrations and initial SO42- levels (R2 = 0.83), indicating that higher initial SO42- concentrations led to lower final CH4 concentrations. This was attributed to the competition for cyanobacteria-supplied substrates between sulfate reduction bacteria (SRB) and methane production archaea (MPA). Our study highlights the importance of considering the unexpectedly increasing SO42- concentrations in eutrophic lakes when estimating global CH4 emission budgets.

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

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

Fe/S proteins in microbial sulfur oxidation

Iron-sulfur clusters serve as indispensable cofactors within proteins across all three domains of life. Fe/S clusters emerged early during the evolution of life on our planet and the biogeochemical cycle of sulfur is one of the most ancient and important element cycles. It is therefore no surprise that Fe/S proteins have crucial roles in the multiple steps of microbial sulfur metabolism. During dissimilatory sulfur oxidation in prokaryotes, Fe/S proteins not only serve as electron carriers in several steps, but also perform catalytic roles, including unprecedented reactions. Two cytoplasmic enzyme systems that oxidize sulfane sulfur to sulfite are of particular interest in this context: The rDsr pathway employs the reverse acting dissimilatory sulfite reductase rDsrAB as its key enzyme, while the sHdr pathway utilizes polypeptides resembling the HdrA, HdrB and HdrC subunits of heterodisulfide reductase from methanogenic archaea. Both pathways involve components predicted to bind unusual noncubane Fe/S clusters acting as catalysts for the formation of disulfide or sulfite. Mapping of Fe/S cluster machineries on the sulfur-oxidizing prokaryote tree reveals that ISC, SUF, MIS and SMS are all sufficient to meet the Fe/S cluster maturation requirements for operation of the sHdr or rDsr pathways. The sHdr pathway is dependent on lipoate-binding proteins that are assembled by a novel pathway, involving two Radical SAM proteins, namely LipS1 and LipS2. These proteins coordinate sulfur-donating auxiliary Fe/S clusters in atypical patterns by three cysteines and one histidine and act as lipoyl synthases by jointly inserting two sulfur atoms to an octanoyl residue. This article is part of a Special Issue entitled: Biogenesis and Function of Fe/S proteins.

Enriching electroactive microorganisms from ferruginous lake waters - Mind the sulfate reducers!

Electroactive microorganisms are pivotal players in mineral transformation within redox interfaces characterized by pronounced oxygen and dissolved metal gradients. Yet, their systematic cultivation from such environments remains elusive. Here, we conducted an anodic enrichment using anoxic ferruginous waters from a post-mining lake as inoculum. Weak electrogenicity (j = ∼5 µA cm-2) depended on electroactive planktonic cells rather than anodic biofilms, with a preference for formate as electron donor. Addition of yeast extract decreased the lag phase but did not increase current densities. The enriched bacterial community varied depending on the substrate composition but mainly comprised of sulfate- and nitrate-reducing bacteria (e.g., Desulfatomaculum spp. and Stenotrophomonas spp.). A secondary enrichment strategy resulted in different bacterial communities composed of iron-reducing (e.g., Klebsiella spp.) and fermentative bacteria (e.g., Paeniclostridium spp.). Secondary electron microscopy and energy-dispersive X-ray spectroscopy results indicate the precipitation of sulfur- and iron-rich organomineral aggregates at the anode surface, presumably impeding current production. Our findings indicate that (i) anoxic waters containing geogenically derived metals can be used to enrich weak electricigens, and (ii) it is necessary to specifically inhibit sulfate reducers. Otherwise, sulfate reducers tend to dominate over EAM during cultivation, which can lead to anode passivation due to biomineralization.

Co-evolution of early Earth environments and microbial life

Two records of Earth history capture the evolution of life and its co-evolving ecosystems with interpretable fidelity: the geobiological and geochemical traces preserved in rocks and the evolutionary histories captured within genomes. The earliest vestiges of life are recognized mostly in isotopic fingerprints of specific microbial metabolisms, whereas fossils and organic biomarkers become important later. Molecular biology provides lineages that can be overlayed on geologic and geochemical records of evolving life. All these data lie within a framework of biospheric evolution that is primarily characterized by the transition from an oxygen-poor to an oxygen-rich world. In this Review, we explore the history of microbial life on Earth and the degree to which it shaped, and was shaped by, fundamental transitions in the chemical properties of the oceans, continents and atmosphere. We examine the diversity and evolution of early metabolic processes, their couplings with biogeochemical cycles and their links to the oxygenation of the early biosphere. We discuss the distinction between the beginnings of metabolisms and their subsequent proliferation and their capacity to shape surface environments on a planetary scale. The evolution of microbial life and its ecological impacts directly mirror the Earth's chemical and physical evolution through cause-and-effect relationships.

Microbial Detoxification of Sediments Underpins Persistence of Zostera marina Meadows

Eelgrass meadows have attracted much attention not only for their ability to maintain marine ecosystems as feeding grounds for marine organisms but also for their potential to store atmospheric and dissolved CO2 as blue carbon. This study comprehensively evaluated the bacterial and chemical data obtained from eelgrass sediments of different scales along the Japanese coast to investigate the effect on the acclimatization of eelgrass. Regardless of the eelgrass habitat, approximately 1% Anaerolineales, Babeliales, Cytophagales, and Phycisphaerales was present in the bottom sediment. Sulfate-reducing bacteria (SRB) were present at 3.69% in eelgrass sediment compared to 1.70% in bare sediment. Sulfur-oxidizing bacteria (SOB) were present at 2.81% and 1.10% in the eelgrass and bare sediment, respectively. Bacterial composition analysis and linear discriminant analysis revealed that SOB detoxified H2S in the eelgrass meadows and that the larger-scale eelgrass meadows had a higher diversity of SOB. Our result indicated that there were regional differences in the system that detoxifies H2S in eelgrass meadows, either microbial oxidation mediated by SOB or O2 permeation via the physical diffusion of benthos. However, since bacterial flora and phylogenetic analyses cannot show bias and/or causality due to PCR, future kinetic studies on microbial metabolism are expected.

Microbial mechanisms of C/N/S geochemical cycling during low-water-level sediment remediation in urban rivers

Low-water-level regulation has been effectively implemented in the restoration of urban river sediments in Guangzhou City, China. Further investigation is needed to understand the microbial mechanisms involved in pollutant degradation in low-water-level environments. This study examined sediment samples from nine rivers, including low-water-level rivers (LW), tidal waterways (TW), and enclosed rivers (ER). Metagenomic high-throughput sequencing and the Diting pipeline were utilized to investigate the microbial mechanisms involved in sediment C/N/S geochemical cycling during low-water-level regulation. The results reveal that the degree of pollution in LW sediment is lower compared to TW and ER sediment. LW sediment exhibits a higher capacity for pollutant degradation and elimination of black, odorous substances due to its stronger microbial methane oxidation, nitrification, denitrification, anammox, and oxidation of sulfide, sulfite, and thiosulfate. Conversely, TW and ER sediment showcase greater microbial methanogenesis, anaerobic fermentation, and sulfide generation abilities, leading to the persistence of black, odorous substances. Factors such as grit and silt content, nitrate, and ammonia concentrations impacted microbial metabolic pathways. Low-water-level regulation improved the micro-environment for functional microbes, facilitating pollutant removal and preventing black odorous substance accumulation. These findings provide insights into the microbial mechanisms underlying low-water-level regulation technology for sediment restoration in urban rivers.

Controlling organic carbon increase in oxygenated marine sediment by using decarburization slag

The chemical oxygen demand (COD) in the Seto Inland Sea, Japan has increased in the recent decades due to the increase of bottom dissolved oxygen (DO) concentration which stimulated several autotrophic microorganisms, specially sulfur oxidizing bacteria (SOB). This increased SOB activity due to the oxygenation of the bottom sediment synthesized new organic matter (OM) which contributed dissolved organic carbon to the overlying seawater. This phenomenon further led to hypoxia in some subareas in the Seto Inland Sea. Higher pH or alkaline environment has been found to be an unfavorable condition for SOB. In this research, we used decarburization slag to elevate the pH of sediment to control the SOB activity and consequently reduce OM production in the sediment. Ignition loss of the surface sediment increased from 5.14% 6.38% after 21 days of incubation with aeration; whereas the sediment showed the less ignition loss of 5.71% after 21 days when the slag was incubated in the same experimental setup. Microbial community analysis showed less SOB activity in the slag added aerated sediment which accounts for the controlled increase of OM in the sediment. An additional experiment was conducted with magnesium oxide to confirm whether elevated pH can control the OM increase in sediment due to rising DO. All these results showed that decarburization slag can elevate the pH of the sediment to a certain level which can control the SOB activity followed by controlled increase of OM in the sediment. The findings may be beneficial to control accumulation of sedimentary OM which can act as a source of organic carbon in the overlying seawater.

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.

Sulfur oxidation and reduction are coupled to nitrogen fixation in the roots of the salt marsh foundation plant Spartina alterniflora

Heterotrophic activity, primarily driven by sulfate-reducing prokaryotes, has traditionally been linked to nitrogen fixation in the root zone of coastal marine plants, leaving the role of chemolithoautotrophy in this process unexplored. Here, we show that sulfur oxidation coupled to nitrogen fixation is a previously overlooked process providing nitrogen to coastal marine macrophytes. In this study, we recovered 239 metagenome-assembled genomes from a salt marsh dominated by the foundation plant Spartina alterniflora, including diazotrophic sulfate-reducing and sulfur-oxidizing bacteria. Abundant sulfur-oxidizing bacteria encode and highly express genes for carbon fixation (RuBisCO), nitrogen fixation (nifHDK) and sulfur oxidation (oxidative-dsrAB), especially in roots stressed by sulfidic and reduced sediment conditions. Stressed roots exhibited the highest rates of nitrogen fixation and expression level of sulfur oxidation and sulfate reduction genes. Close relatives of marine symbionts from the Candidatus Thiodiazotropha genus contributed ~30% and ~20% of all sulfur-oxidizing dsrA and nitrogen-fixing nifK transcripts in stressed roots, respectively. Based on these findings, we propose that the symbiosis between S. alterniflora and sulfur-oxidizing bacteria is key to ecosystem functioning of coastal salt marshes.

Microorganisms uptake zero-valent sulfur via membrane lipid dissolution of octasulfur and intracellular solubilization as persulfide

Zero-valent sulfur, commonly utilized as a fertilizer or fungicide, is prevalent in various environmental contexts. Its most stable and predominant form, octasulfur (S8), plays a crucial role in microbial sulfur metabolism, either through oxidation or reduction. However, the mechanism underlying its cellular uptake remains elusive. We presented evidence that zero-valent sulfur was adsorbed to the cell surface and then dissolved into the membrane lipid layer as lipid-soluble S8 molecules, which reacted with cellular low-molecular thiols to form persulfide, e.g., glutathione persulfide (GSSH), in the cytoplasm. The process brought extracellular zero-valent sulfur into the cells. When persulfide dioxygenase is present in the cells, GSSH will be oxidized. Otherwise, GSSH will react with another glutathione (GSH) to produce glutathione disulfide (GSSG) and hydrogen sulfide (H2S). The mechanism is different from simple diffusion, as insoluble S8 becomes soluble GSSH after crossing the cytoplasmic membrane. The uptake process is limited by physical contact of insoluble zero-valent sulfur with microbial cells and the regeneration of cellular thiols. Our findings elucidate the cellular uptake mechanism of zero-valent sulfur, which provides critical information for its application in agricultural practices and the bioremediation of sulfur contaminants and heavy metals.

Impact of microplastics on microbial-mediated soil sulfur transformations in flooded conditions

As emerging environmental pollutants, microplastics have become a crucial focus in environmental science research. Despite this, the impact of microplastics on soil in flooding conditions remains largely unexplored. Addressing this gap, our study examined the influence of polystyrene (PS) and polyphenylene sulfide (PPS) on the microbial populations in black soil, meadow soil, and paddy soil under flooded conditions. Given the significant regulatory influence exerted by microorganisms on sulfur transformations, our study was primarily focused on evaluating the microbial contributions to alterations in soil sulfur species. Our findings revealed several notable trends: In black soil, both PS and PPS led to a marked increase in the abundance of γ-proteobacteria and Subgroup_6, while reducing Clostridia. Ignavibacteria were found to be lower under PPS compared to PS. In meadow soil, the introduction of PPS resulted in increased levels of KD4-96 and γ-proteobacteria, while α-proteobacteria decreased. Chloroflexia under PPS was observed to be lower than under PS conditions. In paddy soil, our study identified a significant rise in Bacteroidia and Ignavibacteria, accompanied by a decrease in α-proteobacteria and γ-proteobacteria. γ-proteobacteria levels under PPS were notably higher than those under PS conditions. These shifts in microbial communities induced by both PS and PPS had a direct impact on adenosine 5'-phosphosulfate reductase, sulfite reductase, and polysulfide dioxygenase. Consequently, these changes led to soil organic sulfur decrease and sulfide increase. This study not only offers a theoretical framework but also provides empirical evidence for understanding the effects of microplastics on soil microorganisms and their role in regulating nutrient cycling, particularly in flood-prone conditions. Furthermore, this study underscores the importance of ensuring an adequate supply of sulfur in agricultural practices, such as rice and lotus root cultivation, to support optimal crop growth in the presence of microplastic pollution.

Activity-Based Fluorescent Probes for Hydrogen Sulfide and Related Reactive Sulfur Species

Hydrogen sulfide (H2S) is not only a well-established toxic gas but also an important small molecule bioregulator in all kingdoms of life. In contemporary biology, H2S is often classified as a "gasotransmitter," meaning that it is an endogenously produced membrane permeable gas that carries out essential cellular processes. Fluorescent probes for H2S and related reactive sulfur species (RSS) detection provide an important cornerstone for investigating the multifaceted roles of these important small molecules in complex biological systems. A now common approach to develop such tools is to develop "activity-based probes" that couple a specific H2S-mediated chemical reaction to a fluorescent output. This Review covers the different types of such probes and also highlights the chemical mechanisms by which each probe type is activated by specific RSS. Common examples include reduction of oxidized nitrogen motifs, disulfide exchange, electrophilic reactions, metal precipitation, and metal coordination. In addition, we also outline complementary activity-based probes for imaging reductant-labile and sulfane sulfur species, including persulfides and polysulfides. For probes highlighted in this Review, we focus on small molecule systems with demonstrated compatibility in cellular systems or related applications. Building from breadth of reported activity-based strategies and application, we also highlight key unmet challenges and future opportunities for advancing activity-based probes for H2S and related RSS.

Species-resolved, single-cell respiration rates reveal dominance of sulfate reduction in a deep continental subsurface ecosystem

Rates of microbial processes are fundamental to understanding the significance of microbial impacts on environmental chemical cycling. However, it is often difficult to quantify rates or to link processes to specific taxa or individual cells, especially in environments where there are few cultured representatives with known physiology. Here, we describe the use of the redox-enzyme-sensitive molecular probe RedoxSensor™ Green to measure rates of anaerobic electron transfer physiology (i.e., sulfate reduction and methanogenesis) in individual cells and link those measurements to genomic sequencing of the same single cells. We used this method to investigate microbial activity in hot, anoxic, low-biomass (~103 cells mL-1) groundwater of the Death Valley Regional Flow System, California. Combining this method with electron donor amendment experiments and metatranscriptomics confirmed that the abundant spore formers including Candidatus Desulforudis audaxviator were actively reducing sulfate in this environment, most likely with acetate and hydrogen as electron donors. Using this approach, we measured environmental sulfate reduction rates at 0.14 to 26.9 fmol cell-1 h-1. Scaled to volume, this equates to a bulk environmental rate of ~103 pmol sulfate L-1 d-1, similar to potential rates determined with radiotracer methods. Despite methane in the system, there was no evidence for active microbial methanogenesis at the time of sampling. Overall, this method is a powerful tool for estimating species-resolved, single-cell rates of anaerobic metabolism in low-biomass environments while simultaneously linking genomes to phenomes at the single-cell level. We reveal active elemental cycling conducted by several species, with a large portion attributable to Ca. Desulforudis audaxviator.

A preliminary study on benthic nutrient exchange across sediment-water interfaces in a shallow marine protected area of the Northwestern Arabian Gulf

Sedimentary processes are expected to play a crucial role in macronutrient cycling of the shallow Arabian Gulf. To investigate this aspect, sediment cores were collected from the shallow intertidal and subtidal expanses of the first Marine Protected Area (MPA) of Kuwait in the Northwestern Arabian Gulf (NAG). Porewater nutrient profiling and whole core incubation experiments were conducted to measure the nutrient fluxes, both with and without the addition of the nitrification inhibitor allylthiourea (ATU). The porewater data confirmed the potential of sediments to host multiple aerobic and anaerobic pathways of nutrient regeneration. The average (±SD) of net nutrient fluxes from several incubation experiments indicated that ammonium (NH4+) predominantly fluxed out of the sediment (3.81 ± 2.53 mmol m-2 d-1), followed by SiO44- (3.07 ± 1.21 mmol m-2 d-1). In contrast, the average PO43- flux was minimal, at only 0.06 ± 0.05 mmol m-2 d-1. Fluxes of NO3- (ranged from 0.07 ± 0.005 to 1.16 ± 0.35 mmol m-2 d-1) and NO2- (0.03 ± 0.003 to 0.71 ± 0.21 mmol m-2 d-1) were moderate, which either reduced or reversed in the presence of ATU (-0.001 ± 0.0001 to 0.01 ± 0.0001 mmol m-2 d-1 and -0.001 ± 0.0003 to 0.006 ± 0.001 mmol m-2 d-1 for NO3- and NO2- respectively). Thus, this study provides preliminary experimental evidence that nitrification can act as a source of NO3- and NO2- as well as contribute towards the relatively high concentrations of NO2- (>1 in the gulf waters.

The impact of microplastics on sulfur REDOX processes in different soil types: A mechanism study

Microplastics can potentially affect the physical and chemical properties of soil, as well as soil microbial communities. This could, in turn, influence soil sulfur REDOX processes and the ability of soil to supply sulfur effectively. However, the specific mechanisms driving these effects remain unclear. To explore this, soil microcosm experiments were conducted to assess the impacts of polystyrene (PS) and polyphenylene sulfide (PPS) microplastics on sulfur reduction-oxidation (REDOX) processes in black, meadow, and paddy soils. The findings revealed that PS and PPS most significantly decreased SO42- in black soil by 9.4%, elevated SO42- in meadow soil by 20.8%, and increased S2- in paddy soil by 20.5%. PS and PPS microplastics impacted the oxidation process of sulfur in soil by influencing the activity of sulfur dioxygenase, which was mediated by α-proteobacteria and γ-proteobacteria, and the oxidation process was negatively influenced by soil organic matter. PS and PPS microplastics impacted the reduction process of sulfur in soil by influencing the activity of adenosine-5'-phosphosulfate reductase, sulfite reductase, which was mediated by Desulfuromonadales and Desulfarculales, and the reduction process was positively influenced by soil organic matter. In addition to their impacts on microorganisms, it was found that PP and PPS microplastics directly influenced the structure of soil enzymes, leading to alterations in soil enzyme activity. This study sheds light on the mechanisms by which microplastics impact soil sulfur REDOX processes, providing valuable insights into how microplastics influence soil health and functioning, which is essential for optimizing crop growth and maximizing yield in future agricultural practices.

Polyethylene microplastic-induced microbial shifts affected greenhouse gas emissions during litter decomposition in coastal wetland sediments

Microplastic contamination has become increasingly aggravated in coastal environments, further affecting biogeochemical processes involved with microbial community shifts. As a key biogeochemical process mainly driven by microbiota in coastal wetland sediments, litter decomposition contributes greatly to the global greenhouse gas (GHG) budget. However, under microplastic pollution, the relationship between microbial alterations and GHG emissions during litter decomposition in coastal wetlands remains largely unknown. Here, we explored the microbial mechanism by which polyethylene microplastic (PE-MP) influenced greenhouse gas (i.e., CH4, CO2 and N2O) emissions during litter decomposition in coastal sediments through a 75-day microcosm experiment. During litter decomposition, PE-MP exposure significantly decreased cumulative CH4 and CO2 emissions by 41.07% and 25.79%, respectively. However, there was no significant change in cumulative N2O emissions under PE-MP exposure. The bacterial, archaeal, and fungal communities in sediments exhibited varied responses to PE-MP exposure over time, as reflected by the altered structure and changed functional groups of the microbiota. The altered microbial functional groups ascribed to PE-MP exposure and sediment property changes might contribute to suppressing CH4 and CO2 emissions during litter decomposition. This study yielded valuable information regarding the effects of PE-MP on GHG emissions during litter decomposition in coastal wetland sediments.

In-situ measurement of dissolved sulfide in surface sediment porewater using diffusive gradients in thin films (DGT) coupled with digital imaging

Dissolved sulfide in sediment porewater significantly influences aquatic ecosystems. Conventionally, sulfide determination in sediment porewater relies on ex-situ analytical methods, susceptible to measurement errors due to sulfide oxidation and volatilization during sample analysis. In this study, we introduced an innovative in-situ method for assessing dissolved sulfide in surface sediment porewater, leveraging the integration of diffusive gradients in thin films (DGT) with digital imaging. The DGT device effectively concentrates sulfide in sediment porewater, inducing observable color changes in the binding gel. Recordings of these changes, captured by imaging equipment, facilitated the establishment of calibration curves correlating grayscale value alterations in the binding gel to sulfide concentrations. Under optimal conditions, the developed method demonstrated a linear detection range of 3.0-200 μmol L-1 at 20 °C, particularly when the exposure time exceeded 180 min. The developed method is insensitive to salinity and suitable for measuring sulfide concentrations in various natural water environments. Compared to traditional ex-situ methods, our approach circumvents challenges linked to intricate pre-treatment, prolonged analysis duration, and significant systemic errors. This proposed method presents a real-time solution for sulfide concentration assessment in surface sediment porewater, empowering researchers with an efficient means to monitor and study dynamic sulfide levels.

Groundwater microbial communities reflect geothermal activity on volcanic island

Studies of the effects of volcanic activity on the Hawaiian Islands are extremely relevant due to the past and current co-eruptions at both Mauna Loa and Kīlauea. The Big Island of Hawai'i is one of the most seismically monitored volcanic systems in the world, and recent investigations of the Big Island suggest a widespread subsurface connectivity between volcanoes. Volcanic activity has the potential to add mineral contaminants into groundwater ecosystems, thus affecting water quality, and making inhabitants of volcanic islands particularly vulnerable due to dependence on groundwater aquifers. As part of an interdisciplinary study on groundwater aquifers in Kona, Hawai'i, over 40 groundwater wells were sampled quarterly from August 2017 through March 2019, before and after the destructive eruption of the Kīlauea East Rift Zone in May 2018. Sample sites occurred at great distance (~80 km) from Kīlauea, allowing us to pose questions of how volcanic groundwater aquifers might be influenced by volcanic subsurface activity. Approximately 400 water samples were analyzed and temporally split by pre-eruption and post-eruption for biogeochemical analysis. While most geochemical constituents did not differ across quarterly sampling, microbial communities varied temporally (pre- and post-eruption). When a salinity threshold amongst samples was set, the greatest microbial community differences were observed in the freshest groundwater samples. Differential analysis indicated bacterial families with sulfur (S) metabolisms (sulfate reducers, sulfide oxidation, and disproportionation of S-intermediates) were enriched post-eruption. The diversity in S-cyclers without a corresponding change in sulfate geochemistry suggests cryptic cycling may occur in groundwater aquifers as a result of distant volcanic subsurface activity. Microbial communities, including taxa that cycle S, may be superior tracers to changes in groundwater quality, especially from direct inputs of subsurface volcanic activity.

Passive sampling of herbicides above sediments at sites with losses of submerged macrophytes in a mesotrophic lake

Declines of submerged macrophytes (SUM) were monitored in littoral zones of the deep, mesotrophic lake Suhrer See (Northern Germany) since 2017. Drastic losses coincided with intense agriculture in sandy sub-catchments and precipitation. All lines of evidence pointed to a causal connection with subsurface discharge indicating that herbicide application might have caused the effects. Passive sampling was applied in 2022 to elucidate, whether herbicides were really present at sites of losses and if so, in ecotoxicological relevant concentrations. Samplers were exposed on top of lake sediments in 2 m depth and under worst case conditions, i.e., at sites, known for losses of the whole functional group of SUM and at the beginning of the vegetation period. At this time, SUM diaspores were most vulnerable to repression of development and the subsurface discharge was high in the same instance. The potential ecotoxicological relevance of detected herbicide concentrations was assessed with a toxic units (TU) approach, with reference to acute effect concentrations (EC50 of green algae, 72 h, growth). The TU ranged from 0.001 to 0.03. Most concentrations exceeded the threshold of relevance set by an assessment factor of 1000, i.e., TU > 0.001. Locally applied herbicides acted by suppressing developmental stages, and the sum of TU exceeded 0.02 at all sites, mainly due to diflufenican. Not applied locally, terbuthylazine and its relevant metabolites, including terbutryn, acted by inhibiting photosynthesis, and the sum of TU reached 0.005. On this base, diflufenican was assessed to be likely a main stressor, all other detected herbicides to be potentially relevant. Uncertainties and knowledge gaps were specified. The result of the chemical risk assessment was counterchecked for consistence with biological monitoring data within a whole lake perspective. Concepts of empirical and advanced causal attribution methodology were applied to get a grip to the ecological causal field and to protection.

DsrMKJOP is the terminal reductase complex in anaerobic sulfate respiration

Microbial dissimilatory sulfate reduction (DSR) is a key process in the Earth biogeochemical sulfur cycle. In spite of its importance to the sulfur and carbon cycles, industrial processes, and human health, it is still not clear how reduction of sulfate to sulfide is coupled to energy conservation. A central step in the pathway is the reduction of sulfite by the DsrAB dissimilatory sulfite reductase, which leads to the production of a DsrC-trisulfide. A membrane-bound complex, DsrMKJOP, is present in most organisms that have DsrAB and DsrC, and its involvement in energy conservation has been inferred from sequence analysis, but its precise function was so far not determined. Here, we present studies revealing that the DsrMKJOP complex of the sulfate reducer Archaeoglobus fulgidus works as a menadiol:DsrC-trisulfide oxidoreductase. Our results reveal a close interaction between the DsrC-trisulfide and the DsrMKJOP complex and show that electrons from the quinone pool reduce consecutively the DsrM hemes b, the DsrK noncubane [4Fe-4S]3+/2+ catalytic center, and finally the DsrC-trisulfide with concomitant release of sulfide. These results clarify the role of this widespread respiratory membrane complex and support the suggestion that DsrMKJOP contributes to energy conservation upon reduction of the DsrC-trisulfide in the last step of DSR.

Adaptability of sulfur-disproportionating bacteria for mine water remediation under the pressures of heavy metal ions and high sulfate content

Biological sulfide production processes mediated by sulfate/sulfur reduction have gained attention for metal removal from industrial wastewater (e.g., mine water (MW) and metallurgical wastewater) via forming insoluble metal sulfides. However, these processes often necessitate the addition of external organic compounds as electron donors, which poses a constraint on the broad application of this technology. A recent proof of concept study reported that microbial sulfur disproportionation (SD) produced sulfide with no demand for organics, which could achieve more cost-benefit MW treatment against the above-mentioned processes. However, the resistance of SD bioprocess to different metals and high sulfate content in MW remains mysterious, which may substantially affect the practical applicability of such process. In this study, the sulfur-disproportionating bacteria (SDB)-dominated consortium was enriched from a previously established SD-driven bioreactor, in which Dissulfurimicrobium sp. with a relative abundance of 39.9 % was the predominated SDB. When exposed to the real pretreated acidic MW after the pretreatment process of pH amelioration, the sulfur-disproportionating activity remained active, and metals were effectively removed from the MW. Metal tolerance assays further demonstrated that the consortium had a good tolerance to different metal ions (i.e., Pb2+, Cu2+, Ni2+, Mn2+, Zn2+), especially for Mn2+ with a concentration of approximately 20 mg/L. It suggested the robustness of Dissulfurimicrobium sp. likely due to the presence of genes encoding for the enzymes associated with metal(loid) resistance/uptake. Additionally, although high sulfate content resulted in a slight inhibition on the sulfur-disproportionating activity, the consortium still achieved sulfide production rates of 27.3 mg S/g VSS-d on average under an environmentally relevant sulfate level (i.e., 1100 mg S/L), which is comparable to those reported in sulfate reduction. Taken together, these findings imply that SDB could ensure sustainable MW treatment in a more cost-effective and organic-free way.

Available sulfur and phosphorus transformation mechanism and functional microorganisms during sheep manure composting on Qinghai-Tibet Plateau under two moisture contents

Understanding the mechanisms of sulfur and phosphorus transformation during composting is important for improving compost fertility. This study aims to investigate the microbial mechanism of available sulfur and phosphorus transformation during sheep manure composting under different moisture contents (45%: M45 and 60%: M60) on the Qinghai-Tibet Plateau using metagenomics technology. The results showed that the final available sulfur and phosphorus contents of M45 were 11% and 13% higher than those of M60, respectively. M45 enhanced sulfur oxidation, sulfate reduction, and thiosulfate disproportionation. These steps were significantly positively correlated with available sulfur, and Pseudomonas, Thermobifida, Luteimonas, Brevibacterium, Planifilum, and Xinfangfangia were the main participants. Available phosphorus was significantly positively correlated with polyphosphate degradation and inorganic P solubilization, and the main participants in these steps were Luteimonas, Brachybacterium, Corynebacterium, Jeotgalicoccus, Microbacterium, Streptomyces, and Pseudoxanthomonas. These findings reveal the microbial mechanisms of available and phosphorus transformation during composting at two moisture contents.

Unexpected carbon utilization activity of sulfate-reducing microorganisms in temperate and permanently cold marine sediments

Significant amounts of organic carbon in marine sediments are degraded, coupled with sulfate reduction. However, the actual carbon and energy sources used in situ have not been assigned to each group of diverse sulfate-reducing microorganisms (SRM) owing to the microbial and environmental complexity in sediments. Here, we probed microbial activity in temperate and permanently cold marine sediments by using potential SRM substrates, organic fermentation products at very low concentrations (15-30 μM), with RNA-based stable isotope probing. Unexpectedly, SRM were involved only to a minor degree in organic fermentation product mineralization, whereas metal-reducing microbes were dominant. Contrastingly, distinct SRM strongly assimilated 13C-DIC (dissolved inorganic carbon) with H2 as the electron donor. Our study suggests that canonical SRM prefer autotrophic lifestyle, with hydrogen as the electron donor, while metal-reducing microorganisms are involved in heterotrophic organic matter turnover, and thus regulate carbon fluxes in an unexpected way in marine sediments.

Metabolic and phylogenetic diversity in the phylum Nitrospinota revealed by comparative genome analyses

The most abundant known nitrite-oxidizing bacteria in the marine water column belong to the phylum Nitrospinota. Despite their importance in marine nitrogen cycling and primary production, there are only few cultured representatives that all belong to the class Nitrospinia. Moreover, although Nitrospinota were traditionally thought to be restricted to marine environments, metagenome-assembled genomes have also been recovered from groundwater. Over the recent years, metagenomic sequencing has led to the discovery of several novel classes of Nitrospinota (UBA9942, UBA7883, 2-12-FULL-45-22, JACRGO01, JADGAW01), which remain uncultivated and have not been analyzed in detail. Here, we analyzed a nonredundant set of 98 Nitrospinota genomes with focus on these understudied Nitrospinota classes and compared their metabolic profiles to get insights into their potential role in biogeochemical element cycling. Based on phylogenomic analysis and average amino acid identities, the highly diverse phylum Nitrospinota could be divided into at least 33 different genera, partly with quite distinct metabolic capacities. Our analysis shows that not all Nitrospinota are nitrite oxidizers and that members of this phylum have the genomic potential to use sulfide and hydrogen for energy conservation. This study expands our knowledge of the phylogeny and potential ecophysiology of the phylum Nitrospinota and offers new avenues for the isolation and cultivation of these elusive bacteria.

Effect of alkaline leaching of phosphogypsum on sulfate reduction activity and bacterial community composition using different sources of anaerobic microbial inoculum

Phosphogypsum (PG), a by-product of the phosphate industry, is high in sulfate, (SO42-), which makes it an excellent substrate for sulfate-reducing bacteria (SRB) to produce hydrogen sulfide. This work aimed to optimize SO42- leaching from PG to achieve a high biological reduction of SO42- and generate high sulfide concentrations for subsequent use in the biological recovery of elemental sulfur. Five SRB consortia were isolated and enriched from: IS (Industrial sludges), MS (Marine sediments), WC (Winogradsky column), SNV (petroleum industry sediments) and PG (stored Phosphogypsum). The five consortia showed reduction activity when using PG leachate (with water) as source of SO42- and lactate, acetate, or glucose as the electron donor. The highest reduction rate (81.5 %) was registered using lactate and the IS consortium (81.5 %) followed by MS (79 %) and PG (71 %). To enhance the concentration of leached SO42- from PG for future utilization with the isolated consortia, PG was treated with NaOH solutions (2 % and 5 %). SO42- release of 97 % was achieved with a 5 % concentration and the resulting leachate was further diluted to target a SO42- concentration of 12.4 g·L-1 for utilization with the isolated consortia. Compared to water leachate, a significantly higher reduction rate was registered (2 g·L-1 of SO42) using the IS consortium, demonstrating limited inhibition effect of sulfide- concentration on SRB functionalities. Moreover, metagenomic analysis of the consortia revealed that using PG as a source of SO42- increased the abundance of Deltaproteobacteria, including known SRB like Desulfovibrio, Desulfomicrobium, and Desulfosporosinus, as well as novel SRB genera (Cupidesulfovibrio, Desulfocurvus, Desulfococcus) that showed, for the first time, significant potential as novel sulfate-reducers using PG as a SO42- source.

Co-occurrence of toxic metals, bacterial communities and metal resistance genes in coastal sediments from Bohai bay

Sediment heavy metal contamination poses substantial risks to microbial community composition and functional gene distribution. Bohai Bay (BHB), the second-largest bay in the Bohai Sea, is subject to severe anthropogenic pollution. However, to date, there have been no studies conducted to evaluate the distribution of metal resistance genes (MRGs) and bacterial communities in the coastal sediments of BHB. In this study, we employed high-throughput sequencing based on 16S rRNA genes and real-time quantitative PCR (qPCR) to provide a comprehensive view of toxic metals, MRGs, and bacterial communities in BHB's coastal sediment samples across two seasons. We detected high levels of Cd in the summer samples and As in the autumn samples. The metal content in most autumn samples and all summer samples, based on ecological indices, indicated low ecological risk. Proteobacteria dominated all samples, followed by Desulfobacterota, Bacteroidota and Campilobacterota. Bacterial community variability was higher between autumn sampling sites but more stable in summer. We detected 9 MRG subtypes in all samples, with abundances ranging from 4.58 × 10-1 to 2.25 copies/16S rRNA copies. arsB exhibited the highest relative abundance, followed by acr3, czcA and arrA. The efflux mechanism is a common mechanism for sediment resistance to metal stress in Bohai Bay. Procrustes analysis indicated that bacterial community composition may be a determinant of MRGs composition in BHB sediments. Network analysis suggested that eight classes could be potential hosts for six MRGs. However, this type of correlation requires further validation. To summarize, our study offers preliminary insights into bacterial community and MRG distribution patterns in heavy metal-exposed sediments, laying the groundwork for understanding microbial community adaptations in multi-metal polluted environments and supporting ecological restoration efforts.

Practical Guide to Measuring Wetland Carbon Pools and Fluxes

Wetlands cover a small portion of the world, but have disproportionate influence on global carbon (C) sequestration, carbon dioxide and methane emissions, and aquatic C fluxes. However, the underlying biogeochemical processes that affect wetland C pools and fluxes are complex and dynamic, making measurements of wetland C challenging. Over decades of research, many observational, experimental, and analytical approaches have been developed to understand and quantify pools and fluxes of wetland C. Sampling approaches range in their representation of wetland C from short to long timeframes and local to landscape spatial scales. This review summarizes common and cutting-edge methodological approaches for quantifying wetland C pools and fluxes. We first define each of the major C pools and fluxes and provide rationale for their importance to wetland C dynamics. For each approach, we clarify what component of wetland C is measured and its spatial and temporal representativeness and constraints. We describe practical considerations for each approach, such as where and when an approach is typically used, who can conduct the measurements (expertise, training requirements), and how approaches are conducted, including considerations on equipment complexity and costs. Finally, we review key covariates and ancillary measurements that enhance the interpretation of findings and facilitate model development. The protocols that we describe to measure soil, water, vegetation, and gases are also relevant for related disciplines such as ecology. Improved quality and consistency of data collection and reporting across studies will help reduce global uncertainties and develop management strategies to use wetlands as nature-based climate solutions.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13157-023-01722-2.

Sedimentary parameters control the sulfur isotope composition of marine pyrite

Reconstructions of coupled carbon, oxygen, and sulfur cycles rely heavily on sedimentary pyrite sulfur isotope compositions (δ34Spyr). With a model of sediment diagenesis, paired with global datasets of sedimentary parameters, we show that the wide range of δ34Spyr (~100 per mil) in modern marine sediments arises from geographic patterns in the relative rates of diffusion, burial, and microbial reduction of sulfate. By contrast, the microbial sulfur isotope fractionation remains large and relatively uniform. Over Earth history, the effect of increasing seawater sulfate and oxygen concentrations on sulfate and sulfide transport and reaction may explain the corresponding increase observed in the δ34S offset between sulfate and pyrite. More subtle variations may be related to changes in depositional environments associated with sea level fluctuations and supercontinent cycles.

Advances and Opportunities in H2S Measurement in Chemical Biology

Hydrogen sulfide (H2S) is an important biological mediator across all kingdoms of life and plays intertwined roles in various disciplines, ranging from geochemical cycles to industrial processes. A common need across these broad disciplines is the ability to detect and measure H2S in complex sample environments. This Perspective focuses on key advances and opportunities for H2S detection and quantification that are relevant to chemical biology. Specifically, we focus on methods for H2S detection and quantification most commonly used in biological samples, including activity-based H2S probes, the methylene blue assay, the monobromobimane assay, and H2S-sensitive electrode measurements. Our goal is to help simplify what at first may seem to be an overwhelming array of detection and measurement choices, to articulate the strengths and limitations of individual techniques, and to highlight key unmet needs and opportunities in the field.

Integration of molecular and computational approaches paints a holistic portrait of obscure metabolisms

Microorganisms are essential drivers of earth's geochemical cycles. However, the significance of elemental redox cycling mediated by microorganisms is often underestimated beyond the most well-studied nutrient cycles. Phosphite, (per)chlorate, and iodate are each considered esoteric substrates metabolized by microorganisms. However, recent investigations have indicated that these metabolisms are widespread and ubiquitous, affirming a need to continue studying the underlying microbiology to understand their biogeochemical effects and their interface with each other and our biosphere. This review focuses on combining canonical techniques of culturing microorganisms with modern omic approaches to further our understanding of obscure metabolic pathways and elucidate their importance in global biogeochemical cycles. Using these approaches, marker genes of interest have already been identified for phosphite, (per)chlorate, and iodate using traditional microbial physiology and genetics. Subsequently, their presence was queried to reveal the distribution of metabolic pathways in the environment using publicly available databases. In conjunction with each other, computational and experimental techniques provide a more comprehensive understanding of the location of these microorganisms, their underlying biochemistry and genetics, and how they tie into our planet's geochemical cycles.

Impact of redox fluctuations on microbe-mediated elemental sulfur disproportionation and coupled redox cycling of iron

Elemental sulfur (S0) plays a vital role in the coupled cycling of sulfur and iron, which in turn affects the transformation of carbon and various pollutants. These processes have been well characterized under static anoxic or oxic conditions, however, how the natural redox fluctuations affect the bio-mediated sulfur cycling and coupled iron cycling remain enigmatic. The present work examined S0 disproportionation as driven by natural microbial communities under fluctuating redox conditions and the contribution of S0 disproportionation to ferrihydrite transformation. Samples were incubated at either neutral or alkaline pH values, applying sequential anaerobic, aerobic and anaerobic conditions over 60 days. Under anaerobic conditions, S0 was found to undergo disproportionation to sulfate and sulfide, which subsequently reduced ferrihydrite at both pH 7.4 and 9.5. Ferrihydrite promoted S0 disproportionation by scavenging biogenic sulfide and maintaining a suitable degree of sulfate formation. After an oxic period, during the subsequent anoxic incubation, bioreduction of sulfate occurred and the biogenic sulfide reduced iron (hydr)oxides at a rate approximately 25 % lower than that observed during the former anoxic period. A 16S rDNA-based microbial community analysis revealed changes in the microbial community in response to the redox fluctuations, implying an intimate association with the coupled cycling of sulfur and iron. Microscopic and spectroscopic analyses confirmed the S0-mediated transformation of ferrihydrite to crystalline iron (hydr)oxide minerals such as lepidocrocite and magnetite and the formation of iron sulfides precipitated under fluctuating redox conditions. Finally, a reaction mechanism based on mass balance was proposed, demonstrating that bio-mediated sulfur transformation maintained a sustainable redox reaction with iron (hydr)oxides under fluctuating anaerobic-aerobic-anaerobic conditions tested in this study. Altogether, the finding of our study is critical for obtaining a more complete understanding of the dynamics of iron redox reactions and pollutant transformation in sulfur-rich aquatic environments.

Anaerobic biodegradation of phenanthrene and pyrene by sulfate-reducing cultures enriched from contaminated freshwater lake sediments

Our current understanding of the susceptibility of hazardous polycyclic aromatic hydrocarbons (PAHs) to anaerobic microbial degradation is very limited. In the present study, we obtained phenanthrene- and pyrene-degrading strictly anaerobic sulfate-reducing enrichments using contaminated freshwater lake sediments as the source material. The highly enriched phenanthrene-degrading culture, MMKS23, was dominated (98%) by a sulfate-reducing bacterium belonging to the genus Desulfovibrio. While Desulfovibrio sp. was also predominant (79%) in the pyrene-degrading enrichment culture, MMKS44, an anoxygenic purple non-sulfur bacterium, Rhodopseudomonas sp., constituted a significant fraction (18%) of the total microbial community. Phenanthrene or pyrene biodegradation by the enrichment cultures was coupled with sulfate reduction, as evident from near stoichiometric consumption of sulfate and accumulation of sulfide. Also, there was almost complete inhibition of substrate degradation in the presence of an inhibitor of sulfate reduction, i.e., 20 mM MoO42-, in the culture medium. After 180 days of incubation, about 79.40 μM phenanthrene was degraded in the MMKS23 culture, resulting in the consumption of 806.80 μM sulfate and accumulation of 625.80 μM sulfide. Anaerobic pyrene biodegradation by the MMKS44 culture was relatively slow. About 22.30 μM of the substrate was degraded after 180 days resulting in the depletion of 239 μM sulfate and accumulation of 196.90 μM sulfide. Biodegradation of phenanthrene by the enrichment yielded a metabolite, phenanthrene-2-carboxylic acid, suggesting that carboxylation could be a widespread initial step of phenanthrene activation under sulfate-reducing conditions. Overall, this novel study demonstrates the ability of sulfate-reducing bacteria (SRB), dwelling in contaminated freshwater sediments to anaerobically biodegrade three-ringed phenanthrene and highly recalcitrant four-ringed pyrene. Our findings suggest that SRB could play a crucial role in the natural attenuation of PAHs in anoxic freshwater sediments.

New Mechanism via Dichlorocarbene Intermediate for Activated Carbon-Mediated Reductive Dechlorination of Carbon Tetrachloride by Sulfide in Aqueous Solutions

Although activated carbon (AC) is widely used as an adsorbent and barrier for contaminated sediment remediation, little attention has been paid to its mediation effects on reductive dechlorination of chlorinated solvents by commonly presenting sulfide. Here, we reported that highly porous, graphitized AC (250 mg L-1) suspended in deoxygenated aqueous solutions could increase the pseudo-first-order rate constant of sulfide-induced dechlorination of carbon tetrachloride (CCl4) by more than 1 order of magnitude. Carbon disulfide (CS2) was the only main product, with no production of chloroform or dichloromethane. The minimum promotion of CCl4 reduction observed with electro-conductive but nonporous graphite and a microporous but electro-insulative resin (XAD-4) indicates that graphitic carbons and micropores both play key roles in AC-mediated dechlorination of CCl4 by sulfide. The detection of dichlorocarbene (:CCl2) by free radical trapping experiments combined with the high suitability of the Langmuir-Hinshelwood model led us to propose a new mediation mechanism: CCl4 molecules adsorbed within the deep regions of AC micropores formed by graphitic carbons accept two electrons transferred from sulfide to form :CCl2, which is impeded from hydrolysis and hydrogenolysis by the hydrophobic micropore and further reacts with sulfide to generate CS2. Consistently, the production of :CCl2 was very low when AC was replaced with graphite or XAD-4. The proposed mechanism was further validated by the enhanced mediation effects of another two carbonaceous materials (template-synthesized mesoporous carbon and covalent triazine-based framework) that are electro-conductive and have well-developed micropore structures. These findings highlight the importance of pore properties of carbonaceous materials as mediators or catalysts for reductive dechlorination reactions and shed light on the development of coupled adsorption-reaction systems for remediation.

Non-conservative mixing behaviors of mercury in subterranean estuary: Coupling effect of hydrological and biogeochemical processes and implications for rapidly changing world

Coastal ecosystem is an important zone of mercury (Hg) storage and hotspot of neurotoxic methylmercury (MMHg) production and bioaccumulation. The releases of Hg from coastal aquifer or subterranean estuary (STE) via submarine groundwater discharge (SGD) to coastal waters provide an important source of Hg from land to seas. However, the transport and biogeochemical transformation of Hg in STEs are less quantified. In this study, we documented total Hg (THg) and MMHg dynamics in two distinct STEs (a sandflat at an open coast versus a mudflat at a bay) during two different seasons (December versus August) in the temperate coast of northern China, and further applied the salinity-based conservative mixing model (CMM) to quantify the coupling effect of hydrological and biogeochemical processes on STE Hg cycle. Our field data presented large variations of THg and MMHg concentrations and%MMHg/THg of groundwater and sediment in both STEs over time and space. The CMM results clearly displayed substantial divergences of dissolved THg and MMHg from salinity in groundwater between sites and seasons, and the concentration and percent deviations in the Hg-rich mudflat were significantly higher than those in the Hg-poor sandflat. Our findings indicate the non-conservative mixing behaviors of Hg along the groundwater flow paths of both STEs, and the Hg-rich intertidal zone could be hotspot for the production and source of dissolved THg and MMHg to coastal waters via SGD. Our results provide field evidence to highlight that the hydrological shifts and biogeochemical processes collectively drive complex transport and biogeochemical transformation of Hg in STEs. The non-conservative mixing behaviors of Hg in STEs also highlight that, for more accurately calculating SGD-derived Hg fluxes to coastal seas, we need to carefully select the groundwater zonation of STE to better represent the output endmember. Our findings also address that human activities and climate change will profoundly alter the Hg biogeochemical cycle and toxicology in global coastal aquifers.

Global diversity and inferred ecophysiology of microorganisms with the potential for dissimilatory sulfate/sulfite reduction

Sulfate/sulfite-reducing microorganisms (SRM) are ubiquitous in nature, driving the global sulfur cycle. A hallmark of SRM is the dissimilatory sulfite reductase encoded by the genes dsrAB. Based on analysis of 950 mainly metagenome-derived dsrAB-carrying genomes, we redefine the global diversity of microorganisms with the potential for dissimilatory sulfate/sulfite reduction and uncover genetic repertoires that challenge earlier generalizations regarding their mode of energy metabolism. We show: (i) 19 out of 23 bacterial and 2 out of 4 archaeal phyla harbor uncharacterized SRM, (ii) four phyla including the Desulfobacterota harbor microorganisms with the genetic potential to switch between sulfate/sulfite reduction and sulfur oxidation, and (iii) the combination as well as presence/absence of different dsrAB-types, dsrL-types and dsrD provides guidance on the inferred direction of dissimilatory sulfur metabolism. We further provide an updated dsrAB database including > 60% taxonomically resolved, uncultured family-level lineages and recommendations on existing dsrAB-targeted primers for environmental surveys. Our work summarizes insights into the inferred ecophysiology of newly discovered SRM, puts SRM diversity into context of the major recent changes in bacterial and archaeal taxonomy, and provides an up-to-date framework to study SRM in a global context.

Analogous assembly mechanisms and functional guilds govern prokaryotic communities in mangrove ecosystems of China and South America

As an important coastal "blue carbon sink," mangrove ecosystems contain microbial communities with an as-yet-unknown high species diversity. Exploring the assemblage and structure of sediment microbial communities therein can aid in a better understanding of their ecosystem functioning, such as carbon sequestration and other biogeochemical cycles in mangrove wetlands. However, compared to other biomes, the study of mangrove sediment microbiomes is limited, especially in diverse mangrove ecosystems at a large spatial scale, which may harbor microbial communities with distinct compositions and functioning. Here, we analyzed 380 sediment samples from 13 and 8 representative mangrove ecosystems, respectively, in China and South America and compared their microbial features. Although the microbial community compositions exhibited strong distinctions, the community assemblage in the two locations followed analogous patterns: the assemblages of the entire community, abundant taxa, rare taxa, and generalists were predominantly driven by stochastic processes with significant distance-decay patterns, while the assembly of specialists was more likely related to the behaviors of other organisms in or surrounding the mangrove ecosystems. In addition, co-occurrence and topological network analysis of mangrove sediment microbiomes underlined the dominance of sulfate-reducing prokaryotes in both the regions. Moreover, we found that more than 70% of the keystone and hub taxa were sulfate-reducing prokaryotes, implying their important roles in maintaining the linkage and stability of the mangrove sediment microbial communities. This study fills a gap in the large-scale analysis of microbiome features covering distantly located and diverse mangrove ecosystems. Here, we propose a suggestion to the Mangrove Microbiome Initiative that 16S rRNA sequencing protocols should be standardized with a unified primer to facilitate the global-scale analysis of mangrove microbiomes and further comparisons with the reference data sets from other biomes.IMPORTANCEMangrove wetlands are important ecosystems possessing valuable ecological functions for carbon storage, species diversity maintenance, and coastline stabilization. These functions are greatly driven or supported by microorganisms that make essential contributions to biogeochemical cycles in mangrove ecosystems. The mechanisms governing the microbial community assembly, structure, and functions are vital to microbial ecology but remain unclear. Moreover, studying these mechanisms of mangrove microbiomes at a large spatial scale can provide a more comprehensive insight into their universal features and can help untangle microbial interaction patterns and microbiome functions. In this study, we compared the mangrove microbiomes in a large spatial range and found that the assembly patterns and key functional guilds of the Chinese and South American mangrove microbiomes were analogous. The entire communities exhibited significant distance-decay patterns and were strongly governed by stochastic processes, while the assemblage of specialists may be merely associated with the behaviors of the organisms in mangrove ecosystems. Furthermore, our results highlight the dominance of sulfate-reducing prokaryotes in mangrove microbiomes and their key roles in maintaining the stability of community structure and functions.

Major contribution of sulfide-derived sulfur to the benthic food web in a large freshwater lake

In freshwater systems, contributions of chemosynthetic products by sulfur-oxidizing bacteria in sediments as nutritional resources in benthic food webs remain unclear, even though chemosynthetic products might be an important nutritional resource for benthic food webs in deep-sea hydrothermal vents and shallow marine systems. To study geochemical aspects of this trophic pathway, we sampled sediment cores and benthic animals at two sites (90 and 50 m water depths) in the largest freshwater (mesotrophic) lake in Japan: Lake Biwa. Stable carbon, nitrogen, and sulfur isotopes of the sediments and animals were measured to elucidate the sulfur nutritional resources for the benthic food web precisely by calculating the contributions of the incorporation of sulfide-derived sulfur to the biomass and of the biogeochemical sulfur cycle supporting the sulfur nutritional resource. The recovered sediment cores showed increases in 34 S-depleted sulfide at 5 cm sediment depth and showed low sulfide concentration with high δ34 S in deeper layers, suggesting an association of microbial activities with sulfate reduction and sulfide oxidation in the sediments. The sulfur-oxidizing bacteria may contribute to benthic animal biomass. Calculations based on the biomass, sulfur content, and contribution to sulfide-derived sulfur of each animal comprising the benthic food web revealed that 58%-67% of the total biomass sulfur in the benthic food web of Lake Biwa is occupied by sulfide-derived sulfur. Such a large contribution implies that the chemosynthetic products of sulfur-oxidizing bacteria are important nutritional resources supporting benthic food webs in the lake ecosystems, at least in terms of sulfur. The results present a new trophic pathway for sulfur that has been overlooked in lake ecosystems with low-sulfate concentrations.

Development of microbial enrichments for simultaneous removal of sulfur and nitrogenous metabolites in saline water aquaculture

AIM

The aim of the study was to develop microbial enrichments from the nitrifying microbial consortia and the environment for simultaneous removal of ammonia, nitrate, and sulfide in aquaculture systems at varied salinities.

METHODS AND RESULTS

Sulfur and nitrogen metabolites are the major factors affecting the farmed aquatic animal species and deteriorate the receiving environments causing ecological damage. The present study reports the development of microbial enrichments from the nitrifying microbial consortia and the environment. The enrichments used thiosulfate or thiocyanate as an energy source and simultaneously removed sulfur, ammonia, and nitrite in spiked medium (125 mg/l ammonia; 145 mg/l nitrite). Further, the microbes in the enrichments could grow up to 30 g/l salinity. Metagenomic studies revealed limited microbial diversity suggesting the enrichment of highly specialized taxa, and co-occurrence network analysis showed the formation of three micro-niches with multiple interactions at different taxonomic levels.

CONCLUSIONS

The ability of the enrichments to grow in both organic and inorganic medium and simultaneous removal of sulfide, ammonia, and nitrite under varied salinities suggests their potential application in sulfur, nitrogen, and organic matter-rich aquaculture pond environments and other industrial effluents.

Remediation of marine dead zones by enhancing microbial sulfide oxidation using electrodes

Marine dead zones caused by hypoxia have expanded over the last decades and pose a serious threat to coastal marine life. We tested sediment microbial fuel cells (SMFCs) for their potential to reduce the release of sulfide from sediments, in order to potentially protect the marine environment from the formation of such dead zones. Steel electrodes as well as charcoal-amended electrodes and corresponding non-connected controls of a size of together 24 m2 were installed in a marine harbour, and the effects on water quality were monitored for several months. Both pure steel electrodes and charcoal-amended electrodes were able to reduce sulfide concentrations in bottom water (92 % to 98 % reduction, in comparison to disconnected control steel electrodes). Also phosphate concentrations and ammonium were drastically reduced. SMFCs might be used to eliminate hypoxia at sites with high organic matter deposition and should be further investigated for this purpose.

Distinct microbial structure and metabolic potential shaped by significant environmental gradient impacted by ferrous slag weathering

Alkaline ferrous slags pose global environmental issues and long-term risks to ambient environments. To explore the under-investigated microbial structure and biogeochemistry in such unique ecosystems, combined geochemical, microbial, ecological and metagenomic analyses were performed in the areas adjacent to a ferrous slag disposal plant in Sichuan, China. Different levels of exposure to ultrabasic slag leachate had resulted in a significant geochemical gradient of pH (8.0-12.4), electric potential (-126.9 to 437.9 mV), total organic carbon (TOC, 1.5-17.3 mg/L), and total nitrogen (TN, 0.17-1.01 mg/L). Distinct microbial communities were observed depending on their exposure to the strongly alkaline leachate. High pH and Ca2+ concentrations were associated with low microbial diversity and enrichment of bacterial classes Gamma-proteobacteria and Deinococci in the microbial communities exposed to the leachate. Combined metagenomic analyses of 4 leachate-unimpacted and 2-impacted microbial communities led to the assembly of one Serpentinomonas pangenome and 81 phylogenetically diversified metagenome assembled genomes (MAGs). The prevailing taxa in the leachate-impacted habitats (e.g., Serpentinomonas and Meiothermus spp.) were phylogenetically related to those in active serpentinizing ecosystems, suggesting the analogous processes between the man-made and natural systems. More importantly, they accounted for significant abundance of most functional genes associated with environmental adaptation and major element cycling. Their metabolic potential (e.g., cation/H+ antiporters, carbon fixation on lithospheric carbon source, and respiration coupling sulfur oxidization and oxygen or nitrate reduction) may support these taxa to survive and prosper in these unique geochemical niches. This study provides fundamental understandings of the adaptive strategies of microorganisms in response to the strong environmental perturbation by alkali tailings. It also contributes to a better comprehension of how to remediate environments affected by alkaline industrial material.

The evolution and spread of sulfur cycling enzymes reflect the redox state of the early Earth

The biogeochemical sulfur cycle plays a central role in fueling microbial metabolisms, regulating the Earth's redox state, and affecting climate. However, geochemical reconstructions of the ancient sulfur cycle are confounded by ambiguous isotopic signals. We use phylogenetic reconciliation to ascertain the timing of ancient sulfur cycling gene events across the tree of life. Our results suggest that metabolisms using sulfide oxidation emerged in the Archean, but those involving thiosulfate emerged only after the Great Oxidation Event. Our data reveal that observed geochemical signatures resulted not from the expansion of a single type of organism but were instead associated with genomic innovation across the biosphere. Moreover, our results provide the first indication of organic sulfur cycling from the Mid-Proterozoic onwards, with implications for climate regulation and atmospheric biosignatures. Overall, our results provide insights into how the biological sulfur cycle evolved in tandem with the redox state of the early Earth.

Liquid scintillation counting at the limit of detection in biogeosciences

Liquid scintillation is widely used to quantify the activity of radioisotopes. We present an overview of the technique and its application to biogeosciences, particularly for turnover rate measurements. Microbial communities and their metabolism are notoriously difficult to analyze in low energy environments as biomass is exceedingly sparse and turnover rates low. Highly sensitive methods, such as liquid scintillation counting, are required to investigate low metabolic rates and conclusively differentiate them from the background noise of the respective analyzer. We conducted a series of experiments to explore the effects of luminescence, measurement time and temperature on scintillation measurements. Luminescence, the spontaneous emission of photons, disproportionally affects samples within the first few hours after sample preparation and can be minimized by following simple guidelines. Short measurement times will negatively affect liquid scintillation analysis or if background noise makes up a significant proportion of the detected events. Measurement temperature affected liquid scintillation analysis only when the temperature during the measurement reached approximately 30°C or higher, i.e. the liquid scintillation analyzer was placed in an environment without temperature control, but not in cases where chemicals were stored at elevated temperatures prior to measurement. Basic understanding on the functionality of a liquid scintillation analyzer and simple precautions prior to the measurement can significantly lower the minimum detection limit and therefore allow for determination of low turnover rates previously lost in the background noise.

Bacterial enzymatic degradation of recalcitrant organic pollutants: catabolic pathways and genetic regulations

Contamination of soil and natural water bodies driven by increased organic pollutants remains a universal concern. Naturally, organic pollutants contain carcinogenic and toxic properties threatening all known life forms. The conventional physical and chemical methods employed to remove these organic pollutants ironically produce toxic and non-ecofriendly end-products. Whereas microbial-based degradation of organic pollutants provides an edge, they are usually cost-effective and take an eco-friendly approach towards remediation. Bacterial species, including Pseudomonas, Comamonas, Burkholderia, and Xanthomonas, have the unique genetic makeup to metabolically degrade toxic pollutants, conferring their survival in toxic environments. Several catabolic genes, such as alkB, xylE, catA, and nahAc, that encode enzymes and allow bacteria to degrade organic pollutants have been identified, characterized, and even engineered for better efficacy. Aerobic and anaerobic processes are followed by bacteria to metabolize aliphatic saturated and unsaturated hydrocarbons such as alkanes, cycloalkanes, aldehydes, and ethers. Bacteria use a variety of degrading pathways, including catechol, protocatechuate, gentisate, benzoate, and biphenyl, to remove aromatic organic contaminants such as polychlorinated biphenyls, polycyclic aromatic hydrocarbons, and pesticides from the environment. A better understanding of the principle, mechanisms, and genetics would be beneficial for improving the metabolic efficacy of bacteria to such ends. With a focus on comprehending the mechanisms involved in various catabolic pathways and the genetics of the biotransformation of these xenobiotic compounds, the present review offers insight into the various sources and types of known organic pollutants and their toxic effects on health and the environment.

A New Approach for Investigating Iron Mineral Transformations in Soils and Sediments Using 57Fe-Labeled Minerals and 57Fe Mössbauer Spectroscopy

Iron minerals in soils and sediments play important roles in many biogeochemical processes and therefore influence the cycling of major and trace elements and the fate of pollutants in the environment. However, the kinetics and pathways of Fe mineral recrystallization and transformation processes under environmentally relevant conditions are still elusive. Here, we present a novel approach enabling us to follow the transformations of Fe minerals added to soils or sediments in close spatial association with complex solid matrices including other minerals, organic matter, and microorganisms. Minerals enriched with the stable isotope ⁵⁷Fe are mixed with soil or sediment, and changes in Fe speciation are subsequently studied by ⁵⁷Fe Mössbauer spectroscopy, which exclusively detects ⁵⁷Fe. In this study, ⁵⁷Fe-labeled ferrihydrite was synthesized, mixed with four soils differing in chemical and physical properties, and incubated for 12+ weeks under anoxic conditions. Our results reveal that the formation of crystalline Fe(III)(oxyhydr)oxides such as lepidocrocite and goethite was strongly suppressed, and instead formation of a green rust-like phase was observed in all soils. These results contrast those from Fe(II)-catalyzed ferrihydrite transformation experiments, where formation of lepidocrocite, goethite, and/or magnetite often occurs. The presented approach allows control over the composition and crystallinity of the initial Fe mineral, and it can be easily adapted to other experimental setups or Fe minerals. It thus offers great potential for future investigations of Fe mineral transformations in situ under environmentally relevant conditions, in both the laboratory and the field.