Phylogenetic and environmental diversity of DsrAB-type dissimilatory (bi)sulfite reductases

Key role of macrophyte-dominated habitats over cyanobacteria-dominated habitats in stability of microbial sulfur cycling in freshwater lakes

Despite extensive studies on sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB) in marine and deep stratified ecosystems, their spatiotemporal dynamics and ecological roles in shallow freshwater lakes remain poorly understood, especially with habitat shifts driven by eutrophication and climate change. Here, we monitored seasonal changes in sediment and porewater chemical parameters, and applied high-throughput sequencing and co-occurrence network analysis to compare SRB and SOB communities in surface sediments from cyanobacteria-dominated (ZSB) and macrophyte-dominated (XKB) habitats of Lake Taihu across four seasons. In ZSB, seasonal variations in acid volatile sulfide (AVS), dissolved sulfide (∑H2S), and Fe(II) were the primary drivers of sulfur bacterial communities. In contrast, SRB in XKB were mainly influenced by total nitrogen (TN) and total phosphorus (TP), while SOB were regulated by spatial heterogeneity, with AVS as the key driver. Spore-forming SRB such as Desulfotomaculum were distinctly enriched in ZSB, indicating an adaptive strategy to environmental fluctuations. Notably, Cupriavidus, a genus rarely linked to sulfur oxidation, was the dominant SOB genus in both habitats. Co-occurrence network analysis showed that dominant genera in ZSB acted as network hubs, indicating greater vulnerability to environmental changes in cyanobacteria-dominated habitats. Conversely, XKB displayed evenly distributed interaction networks without dominant network hubs, enhancing resilience to environmental fluctuations. These findings provide new insight into how macrophyte-dominated habitats enhance the resilience of shallow freshwater lakes to algal bloom expansion via stabilized sulfur cycling. Hydrological and hydrodynamic factors should be considered in future to better elucidate sulfur cycling in freshwater lakes.

Metagenomic insights into taxonomic and functional patterns in shallow coastal and deep subseafloor sediments in the Western Pacific

Marine sediments are vast, underexplored habitats and represent one of the largest carbon deposits on our planet. Microbial communities drive nutrient cycling in these sediments, but the full extent of their taxonomic and metabolic diversity remains to be explored. Here, we analysed shallow coastal and deep subseafloor sediment cores from 0.01 to nearly 600 metres below the seafloor, in the Western Pacific Region. Applying metagenomics, we identified several taxonomic clusters across all samples, which mainly aligned with depth and sediment type. Inferring functional patterns provided insights into possible ecological roles of the main microbial taxa. These included Chloroflexota, the most abundant phylum across all samples, whereby the classes Dehalococcoida and Anaerolineae dominated deep-subsurface and most shallow coastal sediments, respectively. Thermoproteota and Asgardarchaeota were the most abundant phyla among Archaea, contributing to high relative abundances of Archaea reaching over 50% in some samples. We recovered high-quality metagenome-assembled genomes for all main prokaryotic lineages and proposed names for three phyla, i.e. Tangaroaeota phyl. nov. (former RBG-13-66-14), Ryujiniota phyl. nov. (former UBA6262) and Spongiamicota phyl. nov. (former UBA8248). Metabolic capabilities across all samples ranged from aerobic respiration and photosynthesis in the shallowest sediment layers to heterotrophic carbon utilization, sulphate reduction and methanogenesis in deeper anoxic sediments. We also identified taxa with the potential to be involved in nitrogen and sulphur cycling and heterotrophic carbon utilization. In summary, this study contributes to our understanding of the taxonomic and functional diversity in benthic prokaryotic communities across marine sediments in the Western Pacific Region.

Large Filamentous Bacteria Isolated From Sulphidic Sediments Reveal Novel Species and Distinct Energy and Defence Mechanisms for Survival

Various morphotypes of large filamentous bacteria were isolated through micromanipulation from sulphidic sediment mats in the Bay of Concepción, central Chile. This study employed DNA amplification, whole-genome sequencing and bioinformatics analyses to unveil the taxonomic and genomic features of previously unidentified bacteria. The results revealed several novel genera, families and species, including three specimens belonging to Beggiatoales (Beggiatoaceae family), five to Desulfobacterales (Desulfobacteraceae family), two to the Chloroflexi phylum and one to the phylum Firmicutes. Metabolically, Beggiatoaceae bacteria exhibit a flexible and versatile genomic repertoire, enabling them to adapt to variable conditions at the sediment-water interface. All the bacteria demonstrated a mixotrophic mode, gaining energy from both inorganic and organic carbon sources. Except for the Firmicutes bacterium, all others displayed the ability to grow chemolithoautotrophically using H2 and CO2. Remarkably, the reverse tricarboxylic acid (rTCA) and Calvin-Benson-Bassham (CBB) pathways coexisted in one Beggiatoaceae bacterium. Additionally, various defence systems, such as CRISPR-Cas, along with evidence of viral interactions, have been identified. These defence mechanisms suggest that large filamentous bacteria inhabiting sulphidic sediments frequently encounter bacteriophages. Thus, robust defence mechanisms coupled with multicellularity may determine the survival or death of these large bacteria.

Role of Methanosarcina in mercuric mercury transportation and methylation in sulfate-driven anaerobic oxidation of methane with municipal wastewater sludge

Sulfate-driven anaerobic oxidation of methane (AOM) and anaerobic digestion (AD) with municipal wastewater sludge containing heavy metals may provide favorable conditions for the biogeochemical transformation of mercury (Hg) by methanogens and methanotrophs. However, it remains largely unclear what Hg-methylators functioned and what role Methanosarcina played in these processes. Here, we performed sulfate-driven AOM following AD with Hg-containing wastewater sludge and investigated the role of microbes, especially Methanosarcina, in the biogeochemical transformation of Hg based on 16S rRNA amplicon and metatranscriptomic sequencing. Results showed that methylmercury (MeHg) concentrations and MeHg/total Hg ratios increased significantly, implying mercuric Hg [Hg(II)] methylation predominated MeHg demethylation. Desulfovibrio, Desulfobulbus and Methanosarcina dominated and thus likely played important roles in Hg(II) methylation, while Methanosarcina dominated and functioned in methane metabolism. In the presence of sulfate, differentially-expressed genes (DEGs) related to Hg transporting ATPase increased significantly, indicating Methanosarcina absorbed a large amount of Hg(II) and likely further methylated it to MeHg. No Hg response DEGs were found in the absence of sulfate, further confirming sulfate played an essential role in Hg cycle. Overall, these results suggest that controlling sulfate levels and Methanosarcina abundances in municipal wastewater could potentially mitigate MeHg risks to humans.

Diversity and ecology of microbial sulfur metabolism

Sulfur plays a pivotal role in interactions within the atmosphere, lithosphere, pedosphere, hydrosphere and biosphere, and the functioning of living organisms. In the Earth's crust, mantle, and atmosphere, sulfur undergoes geochemical transformations due to natural and anthropogenic factors. In the biosphere, sulfur participates in the formation of amino acids, proteins, coenzymes and vitamins. Microorganisms in the biosphere are crucial for cycling sulfur compounds through oxidation, reduction and disproportionation reactions, facilitating their bioassimilation and energy generation. Microbial sulfur metabolism is abundant in both aerobic and anaerobic environments and is interconnected with biogeochemical cycles of important elements such as carbon, nitrogen and iron. Through metabolism, competition or cooperation, microorganisms metabolizing sulfur can drive the consumption of organic carbon, loss of fixed nitrogen and production of climate-active gases. Given the increasing significance of sulfur metabolism in environmental alteration and the intricate involvement of microorganisms in sulfur dynamics, a timely re-evaluation of the sulfur cycle is imperative. This Review explores our understanding of microbial sulfur metabolism, primarily focusing on the transformations of inorganic sulfur. We comprehensively overview the sulfur cycle in the face of rapidly changing ecosystems on Earth, highlighting the importance of microbially-mediated sulfur transformation reactions across different environments, ecosystems and microbiomes.

Biodesulfurization of high-sulfur oil from the Karazhanbas field of Kazakhstan with deep eutectic solvents

The Karazhanbas oil field in the Mangystau region of Kazakhstan contains high-sulfur oil (1.6-2.2 %). It is known that sulfur negatively affects the operational properties of petroleum products, causes the corrosion of pipelines, and adversely affects the environment and the human body. Therefore, the development of biodesulfurization technology, taking into account local features, is relevant for this field. The purpose of the study is to develop biodesulfurization of high-sulfur oil from the Karazhanbas field in Kazakhstan using deep eutectic solvents. Research objectives: isolation of sulfate-oxidizing and sulfate-reducing bacteria from the studied oils; identification of isolated bacteria; study of the effect of heavy metal Cr(VI) and sulfur on microbial activity; testing of native strains for the potential for desulfurization of crude oil. The research methodology was based on the application of the Koch methods to determine the total number of microorganisms; light microscopy - for the study of microbiological preparations; genetic identification of bacteria based on the analysis of the nucleotide sequence of a fragment of the 16S rRNA gene; synthesis of deep eutectic solvents; testing of isolated bacteria - for sensitivity to Cr (VI), for the ability of microorganisms to use hydrocarbons of high-sulfur oil, for activity in sulfur-containing crude oil, for determination of the mass fraction of sulfur. From 12 aerobic bacterial cultures isolated from oil samples, 9 strains with active and moderate growth in a medium with high-sulfur oil were selected during testing, followed by two strains (Bacillus paramycoides SFN-1, Bacillus cereus SFN-2), which were the most resistant to Cr (VI) and two strains (Bacillus cereus SFN2, Bacillus thuringiensis SFN3), which have shown sulfur-oxidizing abilities. The native bacterial strains selected during the study showed high disulfurization activity without the addition of deep eutectic solvents (hereinafter referred to as DES) (Bacillus thuringiensis SFN3), with the addition of DES-1 (Bacillus cereus SFN2) and with the addition of DES-2 (Bacillus thuringiensis SFN3). As a result of a comparative analysis of microbial desulfurization processes, it was found that the highest biodesulfurization rate at the end of the experiment was recorded in cultures of Pseudomonas aeruginosa B-5807 (96.3 %), Bacillus thuringiensis SFN-3 (96.1 %), and Rhodococcus erythropolis AC 1039 (96 %).

Multidisciplinary methodologies used in the study of cable bacteria

Cable bacteria are a unique type of filamentous microorganism that can grow up to centimetres long and are capable of long-distance electron transport over their entire lengths. Due to their unique metabolism and conductive capacities, the study of cable bacteria has required technical innovations, both in adapting existing techniques and developing entirely new ones. This review discusses the existing methods used to study eight distinct aspects of cable bacteria research, including the challenges of culturing them in laboratory conditions, performing physical and biochemical extractions, and analysing the conductive mechanism. As cable bacteria research requires an interdisciplinary approach, methods from a range of fields are discussed, such as biogeochemistry, genomics, materials science, and electrochemistry. A critical analysis of the current state of each approach is presented, highlighting the advantages and drawbacks of both commonly used and emerging methods.

Characterization of DsrD and its interaction with the DsrAB dissimilatory sulfite reductase

Microbial dissimilatory sulfate reduction is a key process in the global sulfur and carbon cycles in anoxic ecosystems. In this anaerobic respiration, sulfate is phosphorylated and reduced to sulfite, which is further reduced to a DsrC-trisulfide by the dissimilatory sulfite reductase DsrAB. DsrD is a small protein that acts as an allosteric activator of DsrAB, increasing the efficiency of sulfite reduction. Here, we report a detailed study of DsrD and its interaction with DsrAB. Sequence similarity analyses show that there are three groups of DsrD in organisms with a reductive-type DsrAB. The protein regions involved in the DsrD-DsrAB interaction and activity-promoting effect were investigated through in vitro and in silico studies, including mutations of conserved DsrD residues. The results reveal that the conserved β-loop of DsrD is involved in the interaction, contributing to a better understanding of its mechanism of action.

Phylogeny and evolution of dissimilatory sulfite reduction in prokaryotes

Sulfate is the second most common nonmetallic ion in modern oceans, as its concentration dramatically increased alongside tectonic activity and atmospheric oxidation in the Proterozoic. Microbial sulfate/sulfite metabolism, involving organic carbon or hydrogen oxidation, is linked to sulfur and carbon biogeochemical cycles. However, the coevolution of microbial sulfate/sulfite metabolism and Earth's history remains unclear. Here, we conducted a comprehensive phylogenetic analysis to explore the evolutionary history of the dissimilatory sulfite reduction (Dsr) pathway. The phylogenies of the Dsr-related genes presented similar branching patterns but also some incongruencies, indicating the complex origin and evolution of Dsr. Among these genes, dsrAB is the hallmark of sulfur-metabolizing prokaryotes. Our detailed analyses suggested that the evolution of dsrAB was shaped by vertical inheritance and multiple horizontal gene transfer events and that selection pressure varied across distinct lineages. Dated phylogenetic trees indicated that key evolutionary events of dissimilatory sulfur-metabolizing prokaryotes were related to the Great Oxygenation Event (2.4-2.0 Ga) and several geological events in the "Boring Billion" (1.8-0.8 Ga), including the fragmentation of the Columbia supercontinent (approximately 1.6 Ga), the rapid increase in marine sulfate (1.3-1.2 Ga), and the Neoproterozoic glaciation event (approximately 1.0 Ga). We also proposed that the voluminous iron formations (approximately 1.88 Ga) might have induced the metabolic innovation of iron reduction. In summary, our study provides new insights into Dsr evolution and a systematic view of the coevolution of dissimilatory sulfur-metabolizing prokaryotes and the Earth's environment.

Effective cadmium immobilization in paddy soil by the interaction of sulfate reducing bacteria and manganese fertilizer

Manganese fertilizer (MnSO4) was widely applied to control the Cadmium (Cd) uptake by rice, but the overall process of microbial activities controlling Cd mobilization in paddy soil is poorly understood. This study investigated the stimulation effect of sulfate reducing bacteria (SRB) on Cd bioavailability with the input of different doses MnSO4 (0.5, 1.0, 2.0 g/kg) under the anaerobic paddy soil. The results show that the input of MnSO4 generated soil H+ release. However, the stimulation of SRB remarkedly increased soil pH and reduced the redox potential (Eh) by inhibiting the exchange of Mn2+ and H+, resulting in the available Cd decreased and the amorphous Fe/Mn Oxide-Cd increased significantly. In the co-existed SRB and 1.0 g/kg MnSO4, the available Cd decreased remarkedly by 40.18%, which was transformed to reducible Cd. Meanwhile, the addition of MnSO4 and SRB enhanced the abundance of Cd immobilization related bacteria, including Desulfobacterota, Chloroflexi, Bacteroidota, and Myxococcota. KEGG results showed that MnSO4 and SRB treatment enhanced the ability of microbial sulfur and secondary metabolites. Furthermore, the sulfate reduction related genes (i.e. aprA, sat) obviously enriched in soils. Structural equation modeling showed that Mn, Fe, DOC, Eh, and pH are the key factors affecting available Cd. These findings add to the current knowledge of how MnSO4 and microorganisms affect the mobilization and availability of Cd under paddy soil media, providing new ideas and a theoretical basis for reducing the environmental risk of Cd.

On the diversity, phylogeny and biogeography of cable bacteria

Cable bacteria have acquired a unique metabolism, which induces long-distance electron transport along their centimeter-long multicellular filaments. At present, cable bacteria are thought to form a monophyletic clade with two described genera. However, their diversity has not been systematically investigated. To investigate the phylogenetic relationships within the cable bacteria clade, 16S rRNA gene sequences were compiled from literature and public databases (SILVA 138 SSU and NCBI GenBank). These were complemented with novel sequences obtained from natural sediment enrichments across a wide range of salinities (2-34). To enable taxonomic resolution at the species level, we designed a procedure to attain full-length 16S rRNA gene sequences from individual cable bacterium filaments using an optimized nested PCR protocol and Sanger sequencing. The final database contained 1,876 long 16S rRNA gene sequences (≥800 bp) originating from 92 aquatic locations, ranging from polar to tropical regions and from intertidal to deep sea sediments. The resulting phylogenetic tree reveals 90 potential species-level clades (based on a delineation value of 98.7% 16S rRNA gene sequence identity) that reside within six genus-level clusters. Hence, the diversity of cable bacteria appears to be substantially larger than the two genera and 13 species that have been officially named up to now. Particularly brackish environments with strong salinity fluctuations, as well as sediments with low free sulfide concentrations and deep sea sediments harbor a large pool of novel and undescribed cable bacteria taxa.

Artificial subsurface lithoautotrophic microbial ecosystems and gas storage in deep subsurface

Over the next few years, it is planned to convert all or part of the underground gas storage (UGS) facilities used for natural gas (salt caverns, depleted hydrocarbon reservoirs, and deep aquifers) into underground dihydrogen (H2) storage reservoirs. These deep environments host microbial communities, some of which are hydrogenotrophic (sulfate reducers, acetogens, and methanogens). The current state of microbiological knowledge is thus presented for the three types of UGS facilities. In the mid-1990s, the concept of anaerobic subsurface lithoautotrophic microbial ecosystems, or SLiMEs, emerged. It is expected that the large-scale injection of H2 into subsurface environments will generate new microbial ecosystems called artificial SLiMEs, which could persist over time. These artificial SLiMEs could lead to H2 loss, an intense methanogenic activity, a degradation of gas quality and a risk to installations through sulfide production. However, recent studies on salt caverns and deep aquifers suggest that hydrogenotrophic microbial activity also leads to alkalinization (up to pH 10), which can constrain hydrogenotrophy. Therefore, studying and understanding these artificial SLiMEs is both a necessity for the development of the H2 industry and presents an opportunity for ecologists to monitor the evolution of deep environments in real time.

Mechanism of Intracellular Elemental Sulfur Oxidation in Beggiatoa leptomitoformis, Where Persulfide Dioxygenase Plays a Key Role

Representatives of the colorless sulfur bacteria of the genus Beggiatoa use reduced sulfur compounds in the processes of lithotrophic growth, which is accompanied by the storage of intracellular sulfur. However, it is still unknown how the transformation of intracellular sulfur occurs in Beggiatoa representatives. Annotation of the genome of Beggiatoa leptomitoformis D-402 did not identify any genes for the oxidation or reduction of elemental sulfur. By searching BLASTP, two putative persulfide dioxygenase (PDO) homologs were found in the genome of B. leptomitoformis. In some heterotrophic prokaryotes, PDO is involved in the oxidation of sulfane sulfur. According to HPLC-MS/MS, the revealed protein was reliably detected in a culture sample grown only in the presence of endogenous sulfur and CO2. The recombinant protein from B. leptomitoformis was active in the presence of glutathione persulfide. The crystal structure of recombinant PDO exhibited consistency with known structures of type I PDO. Thus, it was shown that B. leptomitoformis uses PDO to oxidize endogenous sulfur. Additionally, on the basis of HPLC-MS/MS, RT-qPCR, and the study of PDO reaction products, we predicted the interrelation of PDO and Sox-system function in the oxidation of endogenous sulfur in B. leptomitoformis and the connection of this process with energy metabolism.

Microbial acidification by N, S, Fe and Mn oxidation as a key mechanism for deterioration of subsea tunnel sprayed concrete

The deterioration of fibre-reinforced sprayed concrete was studied in the Oslofjord subsea tunnel (Norway). At sites with intrusion of saline groundwater resulting in biofilm growth, the concrete exhibited significant concrete deterioration and steel fibre corrosion. Using amplicon sequencing and shotgun metagenomics, the microbial taxa and surveyed potential microbial mechanisms of concrete degradation at two sites over five years were identified. The concrete beneath the biofilm was investigated with polarised light microscopy, scanning electron microscopy and X-ray diffraction. The oxic environment in the tunnel favoured aerobic oxidation processes in nitrogen, sulfur and metal biogeochemical cycling as evidenced by large abundances of metagenome-assembled genomes (MAGs) with potential for oxidation of nitrogen, sulfur, manganese and iron, observed mild acidification of the concrete, and the presence of manganese- and iron oxides. These results suggest that autotrophic microbial populations involved in the cycling of several elements contributed to the corrosion of steel fibres and acidification causing concrete deterioration.

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.

Electromicrobiological concentration cells are an overlooked potential energy conservation mechanism for subsurface microorganisms

Thermodynamics has predicted many different kinds of microbial metabolism by determining which pairs of electron acceptors and donors will react to produce an exergonic reaction (a negative net change in Gibbs free energy). In energy-limited environments, such as the deep subsurface, such an approach can reveal the potential for unexpected or counter-intuitive energy sources for microbial metabolism. Up until recently, these thermodynamic calculations have been carried out with the assumption that chemical species appearing on the reactant and product side of a reaction formula have a constant concentration, and thus do not count towards net concentration changes and the overall direction of the reaction. This assumption is reasonable considering microorganisms are too small (~1 μm) for any significant differences in concentration to overcome diffusion. However, recent discoveries have demonstrated that the reductive and oxidative halves of reactions can be separated by much larger distances, from millimetres to centimetres via conductive filamentous bacteria, mineral conductivity, and biofilm conductivity. This means that the concentrations of reactants and products can indeed be different, and that concentration differences can contribute to the net negative change in Gibbs free energy. It even means that the same redox reaction, simultaneously running in forward and reverse, can drive energy conservation, in an ElectroMicrobiological Concentration Cell (EMCC). This paper presents a model to investigate this phenomenon and predict under which circumstances such concentration-driven metabolism might take place. The specific cases of oxygen concentration cells, sulfide concentration cells, and hydrogen concentration cells are examined in more detail.

Microbial metabolic potential of hydrothermal vent chimneys along the submarine ring of fire

Hydrothermal vents host a diverse community of microorganisms that utilize chemical gradients from the venting fluid for their metabolisms. The venting fluid can solidify to form chimney structures that these microbes adhere to and colonize. These chimney structures are found throughout many different locations in the world's oceans. In this study, comparative metagenomic analyses of microbial communities on five chimney structures from around the Pacific Ocean were elucidated focusing on the core taxa and genes that are characteristic of each of these hydrothermal vent chimneys. The differences among the taxa and genes found at each chimney due to parameters such as physical characteristics, chemistry, and activity of the vents were highlighted. DNA from the chimneys was sequenced, assembled into contigs, and annotated for gene function. Genes used for carbon, oxygen, sulfur, nitrogen, iron, and arsenic metabolisms were found at varying abundances at each of the chimneys, largely from either Gammaproteobacteria or Campylobacteria. Many taxa shared an overlap of these functional metabolic genes, indicating that functional redundancy is critical for life at these hydrothermal vents. A high relative abundance of oxygen metabolism genes coupled with a low abundance of carbon fixation genes could be used as a unique identifier for inactive chimneys. Genes used for DNA repair, chemotaxis, and transposases were found at high abundances at each of these hydrothermal chimneys allowing for enhanced adaptations to the ever-changing chemical and physical conditions encountered.

Deciphering microbial communities involved in marine steel corrosion using high-throughput amplicon sequencing

To characterize the source and effects of bacterial communities on corrosion of intertidal structures, three different UK coastal sites were sampled for corrosion materials, sediment and seawater. Chemical analyses indicate the activity of sulfate-reducing microbes (SRBs) at 2 sites (Shoreham and Newhaven), but not at the third (Southend-on-Sea). Microbial communities in the deep sediment and corrosion samples are similar. The phylum Proteobacteria is dominant (40.4% of the total ASV), followed by Campilobacterota (11.3%), Desulfobacterota and Firmicutes (4%-5%). At lower taxonomic levels, corrosion causing bacteria, such as Shewanella sp. (6%), Colwellia sp. (7%) and Mariprofundus sp. (1%), are present. At Southend-on-sea, the relative abundance of Campilobacterota is higher compared to the other two sites. The mechanism of action of microorganisms at Shoreham and Newhaven involves biogenic sulfuric acid corrosion of iron by the combined action of SRBs and sulfur-oxidizing microbes. However, at Southend-on-sea, sulfur compounds are not implicated in corrosion, but SRBs and other electroactive microbes may play a role in which cathodic reactions (electrical MIC) and microbial enzymes (chemical MIC) are involved. To contribute to diagnosis of accelerated intertidal corrosion types, we developed a rapid identification method for SRBs using quantitative polymerase chain reaction high-resolution melt curve analysis of the dsrB gene.

The highly differentiated gut of Pachnoda marginata hosts sequential microbiomes: microbial ecology and potential applications

Insect gut microbiomes play a crucial role in the insect development and are shaped, among other factors, by the specialized insect diet habits as well as the morphological structure of the gut. Rose chafers (Pachnoda spp.; Coleoptera: Scarabaeidae) have a highly differentiated gut characterized by a pronounced hindgut dilation which resembles a miniaturized rumen. Specifically, the species Pachnoda marginata has not been previously studied in detail in terms of microbial ecology. Here, we show a fine scale study of the highly compartmentalized gut of P. marginata by using amplicon and metagenomic sequencing to shed light on the bacterial, archaeal and fungal communities thriving in each section of the gut. We found a microbial gradient along the gut from aerobic (foregut) to strictly anaerobic communities (hindgut). In addition, we have characterized interesting biological activities and metabolic pathways of gut microbial communities related to cellulose degradation, methane production and sulfate reduction. Taken together, our results reveal the highly diverse microbial community and the potential of P. marginata gut as a source of industrially relevant microbial diversity.

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

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

Metagenomes from microbial populations beneath a chromium waste tip give insight into the mechanism of Cr (VI) reduction

Dumped Chromium Ore Processing Residue (COPR) at legacy sites poses a threat to health through leaching of toxic Cr(VI) into groundwater. Previous work implicates microbial activity in reducing Cr(VI) to less mobile and toxic Cr(III), but the mechanism has not been explored. To address this question a combined metagenomic and geochemical study was undertaken. Soil samples from below the COPR waste were used to establish anaerobic microcosms which were challenged with Cr(VI), with or without acetate as an electron donor, and incubated for 70 days. Cr was rapidly reduced in both systems, which also reduced nitrate, nitrite then sulfate, but this sequence was accelerated in the acetate amended microcosms. 16S rRNA gene sequencing revealed that the original soil sample was diverse but both microcosm systems became less diverse by the end of the experiment. A high proportion of 16S rRNA gene reads and metagenome-assembled genomes (MAGs) with high completeness could not be taxonomically classified, highlighting the distinctiveness of these alkaline Cr impacted systems. Examination of the coding capacity revealed widespread capability for metal tolerance and Fe uptake and storage, and both populations possessed metabolic capability to degrade a wide range of organic molecules. The relative abundance of genes for fatty acid degradation was 4× higher in the unamended compared to the acetate amended system, whereas the capacity for dissimilatory sulfate metabolism was 3× higher in the acetate amended system. We demonstrate that naturally occurring in situ bacterial populations have the metabolic capability to couple acetate oxidation to sequential reduction of electron acceptors which can reduce Cr(VI) to less mobile and toxic Cr(III), and that microbially produced sulfide may be important in reductive precipitation of chromate. This capability could be harnessed to create a Cr(VI) trap-zone beneath COPR tips without the need to disturb the waste.

Assessment of the in situ biomethanation potential of a deep aquifer used for natural gas storage

The dihydrogen (H2) sector is undergoing development and will require massive storage solutions. To minimize costs, the conversion of underground geological storage sites, such as deep aquifers, used for natural gas storage into future underground hydrogen storage sites is the favored scenario. However, these sites contain microorganisms capable of consuming H2, mainly sulfate reducers and methanogens. Methanogenesis is, therefore expected but its intensity must be evaluated. Here, in a deep aquifer used for underground geological storage, 17 sites were sampled, with low sulfate concentrations ranging from 21.9 to 197.8 µM and a slow renewal of formation water. H2-selected communities mainly were composed of the families Methanobacteriaceae and Methanothermobacteriaceae and the genera Desulfovibrio, Thermodesulfovibrio, and Desulforamulus. Experiments were done under different conditions, and sulfate reduction, as well as methanogenesis, were demonstrated in the presence of a H2 or H2/CO2 (80/20) gas phase, with or without calcite/site rock. These metabolisms led to an increase in pH up to 10.2 under certain conditions (without CO2). The results suggest competition for CO2 between lithoautotrophs and carbonate mineral precipitation, which could limit microbial H2 consumption.

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.

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.

A mixed blessing of influent leachate microbes in downstream biotreatment systems of a full-scale landfill leachate treatment plant

In landfill leachate treatment plants (LLTPs), the microbiome plays a pivotal role in the decomposition of organic compounds, reduction in nutrient levels, and elimination of toxins. However, the effects of microbes in landfill leachate influents on downstream treatment systems remain poorly understood. To address this knowledge gap, we collected 23 metagenomic and 12 metatranscriptomic samples from landfill leachate and activated sludge from various treatment units in a full-scale LLTP. We successfully recovered 1,152 non-redundant metagenome-assembled genomes (MAGs), encompassing a wide taxonomic range, including 48 phyla, 95 classes, 166 orders, 247 families, 238 genera, and 1,152 species. More diverse microbes were observed in the influent leachate than in the downstream biotreatment systems, among which, an unprecedented ∼30 % of microbes with transcriptional expression migrated from the influent to the biological treatment units. Network analysis revealed that 399 shared MAGs across the four units exhibited high node centrality and degree, thus supporting enhanced interactions and increased stability of microbial communities. Functional reconstruction and genome characterization of MAGs indicated that these shared MAGs possessed greater capabilities for carbon, nitrogen, sulfur, and arsenic metabolism compared to non-shared MAGs. We further identified a novel species of Zixibacteria in the leachate influent with discrete lineages from those in other environments that accounted for up to 17 % of the abundance of the shared microbial community and exhibited notable metabolic versatility. Meanwhile, we presented groundbreaking evidence of the involvement of Zixibacteria-encoded genes in the production of harmful gas emissions, such as N2O and H2S, at the transcriptional level, thus suggesting that influent microbes may pose safety risks to downstream treatment systems. In summary, this study revealed the complex impact of the influent microbiome on LLTP and emphasizes the need to consider these microbial characteristics when designing treatment technologies and strategies for landfill leachate management.

Effect of target gene sequence evenness and dominance on real-time PCR quantification of artificial sulfate-reducing microbial communities

Quantitative real-time PCR of phylogenetic and functional marker genes is among the most commonly used techniques to quantify the abundance of microbial taxa in environmental samples. However, in most environmental applications, the approach is a rough assessment of population abundance rather than an exact absolute quantification method because of PCR-based estimation biases caused by multiple factors. Previous studies on these technical issues have focused on primer or template sequence features or PCR reaction conditions. However, how target gene sequence characteristics (e.g., evenness and dominance) in environmental samples affect qPCR quantifications has not been well studied. Here, we compared three primer sets targeting the beta subunit of the dissimilatory sulfite reductase (dsrB) to investigate qPCR quantification performance under different target gene sequence evenness and dominance conditions using artificial gBlock template mixtures designed accordingly. Our results suggested that the qPCR quantification performance of all tested primer sets was determined by the comprehensive effect of the target gene sequence evenness and dominance in environmental samples. Generally, highly degenerate primer sets have equivalent or better qPCR quantification results than a more target-specific primer set. Low template concentration in this study (~105 copies/L) will exaggerate the qPCR quantification results difference among tested primer sets. Improvements to the accuracy and reproducibility of qPCR assays for gene copy number quantification in environmental microbiology and microbial ecology studies should be based on prior knowledge of target gene sequence information acquired by metagenomic analysis or other approaches, careful selection of primer sets, and proper reaction conditions optimization.

Evolutionary history and origins of Dsr-mediated sulfur oxidation

Microorganisms play vital roles in sulfur cycling through the oxidation of elemental sulfur and reduction of sulfite. These metabolisms are catalyzed by dissimilatory sulfite reductases (Dsr) functioning in either the reductive or reverse, oxidative direction. Dsr-mediated sulfite reduction is an ancient metabolism proposed to have fueled energy metabolism in some of Earth's earliest microorganisms, whereas sulfur oxidation is believed to have evolved later in association with the widespread availability of oxygen on Earth. Organisms are generally believed to carry out either the reductive or oxidative pathway, yet organisms from diverse phyla have been discovered with gene combinations that implicate them in both pathways. A comprehensive investigation into the metabolisms of these phyla regarding Dsr is currently lacking. Here, we selected one of these phyla, the metabolically versatile candidate phylum SAR324, to study the ecology and evolution of Dsr-mediated metabolism. We confirmed that diverse SAR324 encode genes associated with reductive Dsr, oxidative Dsr, or both. Comparative analyses with other Dsr-encoding bacterial and archaeal phyla revealed that organisms encoding both reductive and oxidative Dsr proteins are constrained to a few phyla. Further, DsrAB sequences from genomes belonging to these phyla are phylogenetically positioned at the interface between well-defined oxidative and reductive bacterial clades. The phylogenetic context and dsr gene content in these organisms points to an evolutionary transition event that ultimately gave way to oxidative Dsr-mediated metabolism. Together, this research suggests that SAR324 and other phyla with mixed dsr gene content are associated with the evolution and origins of Dsr-mediated sulfur oxidation.

Effects of operating conditions on the in situ control of sulfur-containing odors by using a novel alternative landfill cover and its transformation mechanism

Sulfur-containing gases are main sources of landfill odors, which has become a big issue for pollution to environment and human health. Biocover is promising for treating landfill odors, with advantages of durability and environmental friendliness. In this study, charcoal sludge compost was utilized as the main effective component of a novel alternative landfill cover and the in situ control of sulfur-containing odors from municipal solid waste landfilling process was simulated under nine different operating conditions. Results showed that five sulfur-containing odors (hydrogen sulfide, H2S; methyl mercaptan, CH3SH; dimethyl sulfide, CH3SCH3; ethylmercaptan, CH3CH2SH; carbon disulfide, CS2) were monitored and removed by the biocover, with the highest removal efficiencies of 77.18% for H2S, 87.36% for CH3SH, and 92.19% for CH3SCH3 in reactor 8#, and 95.94% for CH3CH2SH and 94.44% for CS2 in reactor 3#. The orthogonal experiment showed that the factors influencing the removal efficiencies of sulfur-containing odors were ranked from high to low as follows: temperature > weight ratio > humidity content. The combination of parameters of 20% weight ratio, 25°C temperature, and 30% water content was more recommended based on the consideration of the removal efficiencies and economic benefits. The mechanisms of sulfur conversion inside biocover were analyzed. Most organic sulfur was firstly degraded to reduced sulfides or element sulfur, and then oxidized to sulfate which could be stable in the layer as the final state. In this process, sulfur-oxidizing bacteria play a great role, and the distribution of them in reactor 1#, 5#, and 8# was specifically monitored. Bradyrhizobiaceae and Rhodospirillaceae were the dominant species which can utilize sulfide as substance to produce sulfate and element sulfur, respectively. Based on the results of OUTs, the biodiversity of these sulfur-oxidizing bacteria, these microorganisms, was demonstrated to be affected by the different parameters. These results indicate that the novel alternative landfill cover modified with bamboo charcoal compost is effective in removing sulfur odors from landfills. Meanwhile, the findings have direct implications for addressing landfill odor problems through parameter adjustment.

Assessing the effect of sulfate on the anaerobic oxidation of methane coupled with Cr(VI) bioreduction by sludge characteristic and metagenomics analysis

Methane-driven hexavalent chromium (Cr(VI)) reduction in a microbial fuel cell (MFC) has attracted much attention. However, whether the presence of sulfate (SO42-) affects the reduction of Cr(VI) is still lacking in systematic studies. This study involved constructing a MFC-granular sludge (MFC-GS) coupling system with dissolved methane (CH4) was used as the electron donor to investigate the effect of SO42- on Cr(VI) bioreduction, sludge characteristic, and functional metabolic mechanisms. When the SO42- concentration was 10 mg/L, the average removal rate of Cr(VI) in the anaerobic stage decreased to the lowest value (22.25 ± 2.06%). Adding 10 mg/L SO42- obviously inhibited the electrochemical performance of the system. Increasing SO42- concentration weakened the fluorescence peaks of tryptophan and aromatic proteins in the extracellular polymeric substance of sludge. Under the influence of SO42-, Methanothrix_soehngenii decreased from 14.44% to 5.89%. The relative abundance of methane metabolic was down-regulated from 1.47% to 0.98%, while the sulfur metabolic was up-regulated from 0.09% to 0.21% when SO42- was added. These findings provided some reference for the treatment of wastewater containing Cr(VI) and SO42- complex pollutants in the MFC-GS coupling system.

Gallionellaceae pangenomic analysis reveals insight into phylogeny, metabolic flexibility, and iron oxidation mechanisms

IMPORTANCE

Neutrophilic iron-oxidizing bacteria (FeOB) produce copious iron (oxyhydr)oxides that can profoundly influence biogeochemical cycles, notably the fate of carbon and many metals. To fully understand environmental microbial iron oxidation, we need a thorough accounting of iron oxidation mechanisms. In this study, we show the Gallionellaceae FeOB genomes encode both characterized iron oxidases as well as uncharacterized multiheme cytochromes (MHCs). MHCs are predicted to transfer electrons from extracellular substrates and likely confer metabolic capabilities that help Gallionellaceae occupy a range of different iron- and mineral-rich niches. Gallionellaceae appear to specialize in iron oxidation, so it would be advantageous for them to have multiple mechanisms to oxidize various forms of iron, given the many iron minerals on Earth, as well as the physiological and kinetic challenges faced by FeOB. The multiple iron/mineral oxidation mechanisms may help drive the widespread ecological success of Gallionellaceae.

Phylogenetic diversity of functional genes in deep-sea cold seeps: a novel perspective on metagenomics

BACKGROUND

Leakages of cold, methane-rich fluids from subsurface reservoirs to the sea floor are termed cold seeps. Recent exploration of the deep sea has shed new light on the microbial communities in cold seeps. However, conventional metagenomic methods largely rely on reference databases and neglect the phylogeny of functional genes.

RESULTS

In this study, we developed the REMIRGE program to retrieve the full-length functional genes from shotgun metagenomic reads and fully explored the phylogenetic diversity in cold seep sediments. The abundance and diversity of functional genes involved in the methane, sulfur, and nitrogen cycles differed in the non-seep site and five cold seep sites. In one Haima cold seep site, the divergence of functional groups was observed at the centimeter scale of sediment depths, with the surface layer potentially acting as a reservoir of microbial species and functions. Additionally, positive correlations were found between specific gene sequence clusters of relevant genes, indicating coupling occurred within specific functional groups.

CONCLUSION

REMIRGE revealed divergent phylogenetic diversity of functional groups and functional pathway preferences in a deep-sea cold seep at finer scales, which could not be detected by conventional methods. Our work highlights that phylogenetic information is conducive to more comprehensive functional profiles, and REMIRGE has the potential to uncover more new insights from shotgun metagenomic data. Video Abstract.

A quantitative sequencing method using synthetic internal standards including functional and phylogenetic marker genes

The method of spiking synthetic internal standard genes (ISGs) to samples for amplicon sequencing, generating sequences and converting absolute gene numbers from read counts has been used only for phylogenetic markers and has not been applied to functional markers. In this study, we developed ISGs, including gene sequences of the 16S rRNA, pmoA, encoding a subunit of particulate methane monooxygenase and amoA, encoding a subunit of ammonia monooxygenase. We added ISGs to the samples, amplified the target genes and performed amplicon sequencing. For the mock community, the copy numbers converted from read counts using ISGs were equivalent to those obtained by the quantitative real-time polymerase chain reaction (4.0 × 104 versus 4.1 × 104 and 3.0 × 103 versus 4.0 × 103 copies μL-DNA-1 for 16S rRNA and pmoA genes, respectively), but we also identified underestimation, possibly due to primer coverage (7.8 × 102 versus 3.7 × 103  μL-DNA-1 for amoA gene). We then applied this method to environmental samples and analysed phylogeny, functional diversity and absolute quantities. One Methylocystis population was most abundant in the sludge samples [16S rRNA gene (3.8 × 109 copies g-1 ) and the pmoA gene (2.3 × 109 copies g-1 )] and were potentially interrelated. This study demonstrates that ISG spiking is useful for evaluating sequencing data processing and quantifying functional markers.

Biogeochemical characterization of four depleted gas reservoirs for conversion into underground hydrogen storage

Depleted gas reservoirs are a valuable option for underground hydrogen storage (UHS). However, different classes of microorganisms, which are capable of using free H2 as a reducing agent for their metabolism, inhabit deep underground formations and can potentially affect the storage. This study integrates metagenomics based on Illumina-NGS sequencing of bacterial and archaeal 16S rRNA and dsrB and mcrA functional genes to unveil the composition and the variability of indigenous microbial populations of four Italian depleted reservoirs. The obtained mcrA sequences allow us to implement the existing taxonomic database for mcrA gene sequences with newly classified sequences obtained from the Italian gas reservoirs. Moreover, the KEGG and COG predictive functional annotation was used to highlight the metabolic pathways potentially associated with hydrogenotrophic metabolisms. The analyses revealed the specificity of each reservoir microbial community, and taxonomic and functional data highlighted the presence of an enriched number of taxa, whose activity depends on both reservoir hydrochemical composition and nutrient availability, of potential relevance in the context of UHS. This study is the very first to address the profiling of the microbial population and allowed us to perform a preliminary assessment of UHS feasibility in Italy.

Shifts in the coral microbiome in response to in situ experimental deoxygenation

IMPORTANCE

Marine hypoxia is a threat for corals but has remained understudied in tropical regions where coral reefs are abundant. Though microbial symbioses can alleviate the effects of ecological stress, we do not yet understand the taxonomic or functional response of the coral microbiome to hypoxia. In this study, we experimentally lowered oxygen levels around Siderastrea siderea and Agaricia lamarcki colonies in situ to observe changes in the coral microbiome in response to deoxygenation. Our results show that hypoxia triggers a stochastic change of the microbiome overall, with some bacterial families changing deterministically after just 48 hours of exposure. These families represent an increase in anaerobic and opportunistic taxa in the microbiomes of both coral species. Thus, marine deoxygenation destabilizes the coral microbiome and increases bacterial opportunism. This work provides novel and fundamental knowledge of the microbial response in coral during hypoxia and may provide insight into holobiont function during stress.

Diversity at single nucleotide to pangenome scales among sulfur cycling bacteria in salt marshes

IMPORTANCE

Salt marshes are known for their significant carbon storage capacity, and sulfur cycling is closely linked with the ecosystem-scale carbon cycling in these ecosystems. Sulfate reducers are key for the decomposition of organic matter, and sulfur oxidizers remove toxic sulfide, supporting the productivity of marsh plants. To date, the complexity of coastal environments, heterogeneity of the rhizosphere, high microbial diversity, and uncultured majority hindered our understanding of the genomic diversity of sulfur-cycling microbes in salt marshes. Here, we use comparative genomics to overcome these challenges and provide an in-depth characterization of sulfur-cycling microbial diversity in salt marshes. We characterize communities across distinct sites and plant species and uncover extensive genomic diversity at the taxon level and specific genomic features present in MAGs affiliated with uncultivated sulfur-cycling lineages. Our work provides insights into the partnerships in salt marshes and a roadmap for multiscale analyses of diversity in complex biological systems.

In situ enrichment of sulphate-reducing microbial communities with different carbon sources stimulating the acid mine drainage sediments

The applications of sulphate-reducing microorganisms (SRMs) in acid mine drainage (AMD) treatment systems have received extensive attention due to their ability to reduce sulphate and stabilize metal(loid)s. Despite great phylogenetic diversity of SRMs, only a few have been used in AMD treatment bioreactors. In situ enrichment could be an efficient approach to select new effective SRMs for AMD treatment. Here, we performed in situ enrichment of SRMs in highly stratified AMD sediment cores using different kinds of carbon source mixture. The dsrAB (dissimilatory sulfite reductase) genes affiliated with nine phyla (two archaeal and seven bacterial phyla) and 26 genera were enriched. Remarkably, those genes affiliated with Aciduliprofundum and Vulcanisaeta were enriched in situ in AMD-related environments for the first time, and their relative abundances were negatively correlated with pH. Furthermore, 107 dsrAB-containing metagenome-assembled genomes (MAGs) were recovered from metagenomic datasets, with 14 phyla (two archaeal and 12 bacterial phyla) and 15 genera. The relative abundances of MAGs were positively correlated with total carbon and sulphate contents. Our findings expanded the diversity of SRMs that can be enriched in AMD sediment, and revealed the physiochemical properties that might affect the growth of SRMs, which provided guidance for AMD treatment bioreators.

Unraveling prokaryotic diversity distribution and functional pattern on nitrogen and methane cycling in the subtropical Western North Pacific Ocean

Prokaryotes play an important role in marine nitrogen and methane cycles. However, their community changes and metabolic modifications to the concurrent impact of ocean warming (OW), acidification (OA), deoxygenation (OD), and anthropogenic‑nitrogen-deposition (AND) from the surface to the deep ocean remains unknown. We examined here the amplicon sequencing approach across the surface (0-200 m; SL), intermediate (200-1000 m; IL), and deep layers (1000-2200 m; DL), and characterized the simultaneous impacts of OW, OA, OD, and AND on the Western North Pacific Ocean prokaryotic changes and their functional pattern in nitrogen and methane cycles. Results showed that SL possesses higher ammonium oxidation community/metabolic composition assumably the reason for excess nitrogen input from AND and modification of their kinetic properties to OW adaptation. Expanding OD at IL showed hypoxic conditions in the oxygen minimum layer, inducing higher microbial respiration that elevates the dimerization of nitrification genes for higher nitrous oxide production. The aerobic methane-oxidation composition was dominant in SL presumably the reason for adjustment in prokaryotic optimal temperature to OW, while anaerobic oxidation composition was dominant at IL due to the evolutionary changes coupling with higher nitrification. Our findings refocus on climate-change impacts on the open ocean ecosystem from the surface to the deep-environment integrating climate-drivers as key factors for higher nitrous-oxide and methane emissions.

Biogeochemical transformation of mercury driven by microbes involved in anaerobic digestion of municipal wastewater

Anaerobic digestion (AD) with municipal wastewater contained heavy metal mercury (Hg) highly affects the utilization of activated sludge, and poses severe threat to the health of human beings. However, the biogeochemical transformation of Hg during AD remains unclear. Here, we investigated the biogeochemical transformation and environmental characteristics of Hg and the variations of dominant microbes during AD. The results showed that Hg(II) methylation is dominant in the early stage of AD, while methylmercury (MeHg) demethylation dominates in the later stage. Dissolved total Hg (DTHg) in the effluent sludge decreased with time, while THg levels enhanced to varying degrees at the final stage. Sulfate significant inhibits MeHg formation, reduces bioavailability of Hg(II) by microbes and thus inhibits Hg(II) methylation. Microbial community analysis reveals that strains in Methanosarcina and Aminobacterium from the class of Methanomicrobia, rather than Deltaproteobacteria, may be directly related to Hg(II) methylation and MeHg demethylation. Overall, this research provide insights into the biogeochemical transformation of Hg in the anaerobic digestion of municipal wastewater treatment. This work is beneficial for scientific treatment of municipal wastewater and effluent sludge, thus reducing the risk of MeHg to human beings.

Stepwise pathway for early evolutionary assembly of dissimilatory sulfite and sulfate reduction

Microbial dissimilatory sulfur metabolism utilizing dissimilatory sulfite reductases (Dsr) influenced the biochemical sulfur cycle during Earth's history and the Dsr pathway is thought to be an ancient metabolic process. Here we performed comparative genomics, phylogenetic, and synteny analyses of several Dsr proteins involved in or associated with the Dsr pathway across over 195,000 prokaryotic metagenomes. The results point to an archaeal origin of the minimal DsrABCMK(N) protein set, having as primordial function sulfite reduction. The acquisition of additional Dsr proteins (DsrJOPT) increased the Dsr pathway complexity. Archaeoglobus would originally possess the archaeal-type Dsr pathway and the archaeal DsrAB proteins were replaced with the bacterial reductive-type version, possibly at the same time as the acquisition of the QmoABC and DsrD proteins. Further inventions of two Qmo complex types, which are more spread than previously thought, allowed microorganisms to use sulfate as electron acceptor. The ability to use the Dsr pathway for sulfur oxidation evolved at least twice, with Chlorobi and Proteobacteria being extant descendants of these two independent adaptations.

Ecophysiology and interactions of a taurine-respiring bacterium in the mouse gut

Taurine-respiring gut bacteria produce H2S with ambivalent impact on host health. We report the isolation and ecophysiological characterization of a taurine-respiring mouse gut bacterium. Taurinivorans muris strain LT0009 represents a new widespread species that differs from the human gut sulfidogen Bilophila wadsworthia in its sulfur metabolism pathways and host distribution. T. muris specializes in taurine respiration in vivo, seemingly unaffected by mouse diet and genotype, but is dependent on other bacteria for release of taurine from bile acids. Colonization of T. muris in gnotobiotic mice increased deconjugation of taurine-conjugated bile acids and transcriptional activity of a sulfur metabolism gene-encoding prophage in other commensals, and slightly decreased the abundance of Salmonella enterica, which showed reduced expression of galactonate catabolism genes. Re-analysis of metagenome data from a previous study further suggested that T. muris can contribute to protection against pathogens by the commensal mouse gut microbiota. Together, we show the realized physiological niche of a key murine gut sulfidogen and its interactions with selected gut microbiota members.

The low-temperature germinating spores of the thermophilic Desulfofundulus contribute to an extremely high sulfate reduction in burning coal seams

Burning coal seams, characterized by massive carbon monoxide (CO) emissions, the presence of secondary sulfates, and high temperatures, represent suitable environments for thermophilic sulfate reduction. The diversity and activity of dissimilatory sulfate reducers in these environments remain unexplored. In this study, using metagenomic approaches, in situ activity measurements with a radioactive tracer, and cultivation we have shown that members of the genus Desulfofundulus are responsible for the extremely high sulfate reduction rate (SRR) in burning lignite seams in the Altai Mountains. The maximum SRR reached 564 ± 21.9 nmol S cm-3 day-1 at 60°C and was of the same order of magnitude for both thermophilic (60°C) and mesophilic (23°C) incubations. The 16S rRNA profiles and the search for dsr gene sequences in the metagenome revealed members of the genus Desulfofundulus as the main sulfate reducers. The thermophilic Desulfofundulus sp. strain Al36 isolated in pure culture, did not grow at temperatures below 50°C, but produced spores that germinated into metabolically active cells at 20 and 15°C. Vegetative cells germinating from spores produced up to 0.738 ± 0.026 mM H2S at 20°C and up to 0.629 ± 0.007 mM H2S at 15°C when CO was used as the sole electron donor. The Al36 strain maintains significant production of H2S from sulfate over a wide temperature range from 15°C to 65°C, which is important in variable temperature biotopes such as lignite burning seams. Burning coal seams producing CO are ubiquitous throughout the world, and biogenic H2S may represent an overlooked significant flux to the atmosphere. The thermophilic spore outgrowth and their metabolic activity at temperatures below the growth minimum may be important for other spore-forming bacteria of environmental, industrial and clinical importance.

Sulfur-cycling chemolithoautotrophic microbial community dominates a cold, anoxic, hypersaline Arctic spring

BACKGROUND

Gypsum Hill Spring, located in Nunavut in the Canadian High Arctic, is a rare example of a cold saline spring arising through thick permafrost. It perennially discharges cold (~ 7 °C), hypersaline (7-8% salinity), anoxic (~ 0.04 ppm O2), and highly reducing (~ - 430 mV) brines rich in sulfate (2.2 g.L-1) and sulfide (9.5 ppm), making Gypsum Hill an analog to putative sulfate-rich briny habitats on extraterrestrial bodies such as Mars.

RESULTS

Genome-resolved metagenomics and metatranscriptomics were utilized to describe an active microbial community containing novel metagenome-assembled genomes and dominated by sulfur-cycling Desulfobacterota and Gammaproteobacteria. Sulfate reduction was dominated by hydrogen-oxidizing chemolithoautotrophic Desulfovibrionaceae sp. and was identified in phyla not typically associated with sulfate reduction in novel lineages of Spirochaetota and Bacteroidota. Highly abundant and active sulfur-reducing Desulfuromusa sp. highly transcribed non-coding RNAs associated with transcriptional regulation, showing potential evidence of putative metabolic flexibility in response to substrate availability. Despite low oxygen availability, sulfide oxidation was primarily attributed to aerobic chemolithoautotrophic Halothiobacillaceae. Low abundance and transcription of photoautotrophs indicated sulfur-based chemolithoautotrophy drives primary productivity even during periods of constant illumination.

CONCLUSIONS

We identified a rare surficial chemolithoautotrophic, sulfur-cycling microbial community active in a unique anoxic, cold, hypersaline Arctic spring. We detected Mars-relevant metabolisms including hydrogenotrophic sulfate reduction, sulfur reduction, and sulfide oxidation, which indicate the potential for microbial life in analogous S-rich brines on past and present Mars. Video Abstract.

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.

Microbial functionalities and immobilization of environmental lead: Biogeochemical and molecular mechanisms and implications for bioremediation

The increasing environmental and human health concerns about lead in the environment have stimulated scientists to search for microbial processes as innovative bioremediation strategies for a suite of different contaminated media. In this paper, we provide a compressive synthesis of existing research on microbial mediated biogeochemical processes that transform lead into recalcitrant precipitates of phosphate, sulfide, and carbonate, in a genetic, metabolic, and systematics context as they relate to application in both laboratory and field immobilization of environmental lead. Specifically, we focus on microbial functionalities of phosphate solubilization, sulfate reduction, and carbonate synthesis related to their respective mechanisms that immobilize lead through biomineralization and biosorption. The contributions of specific microbes, both single isolates or consortia, to actual or potential applications in environmental remediation are discussed. While many of the approaches are successful under carefully controlled laboratory conditions, field application requires optimization for a host of variables, including microbial competitiveness, soil physical and chemical parameters, metal concentrations, and co-contaminants. This review challenges the reader to consider bioremediation approaches that maximize microbial competitiveness, metabolism, and the associated molecular mechanisms for future engineering applications. Ultimately, we outline important research directions to bridge future scientific research activities with practical applications for bioremediation of lead and other toxic metals in environmental systems.

Decadal evolution of an acidic pit lake: Insights into the biogeochemical impacts of microbial community succession

Acidic pit lakes represent hydrological features resulting from the accumulation of acid mine drainage in mining operations. Long-term monitoring is essential for these extreme and contaminated environments, yet tracking investigations integrating microbial geochemical dynamics in acidic pit lakes have been lacking thus far. This study integrated historical data with field sampling to track decadal biogeochemical changes in an acidic pit lake. With limited artificial disturbance, significant and sustained biogeochemical changes were observed over the past decade. Surface water pH slowly increased from 2.8 to a maximum of 3.6, with a corresponding increase in bottom water pH to around 3.9, despite the accumulation of externally imported sulfate and metals. Elevated nutrient levels stimulated the macroscopic growth of Chlorophyta, resulting in a shift from reddish-brown to green water with floating algal bodies. Furthermore, microalgae-fixed organic carbon promoted the transition from the initial chemolithotrophy-based population dominated by Acidiphilium and Ferrovum to a heterotrophic community. The increase in heterotrophic iron- and sulfate-reducers may cause an elevation in ferrous levels and a decline in copper concentrations. However, most metals were not removed from the water column, potentially due to insufficient biosulfidogenesis or sulfide reoxidation. These findings offer novel insights into microbial succession in extreme ecosystem evolution and contribute to the management and remediation of acidic pit lakes.

Microbial communities related to the sulfur cycle in the Sansha Yongle Blue Hole

The Sansha Yongle Blue Hole (SYBH), the deepest blue hole in the world, is an excellent habitat for revealing biogeochemical cycles in the anaerobic environment. However, how sulfur cycling is mediated by microorganisms in the SYBH hasn't been fully understood. In this study, the water layers of the SYBH were divided into oxic zone, hypoxic zone, anoxic zone I and II, and microbial-mediated sulfur cycling in the SYBH was comprehensively interpreted. The 16S rRNA genes/transcripts analyses showed that the microbial community structures associated with the sulfur cycling in each zone had distinctive features. Sulfur-oxidizing bacteria were mostly constituted by Gammaproteobacteria, Alphaproteobacteria, Campylobacterota, and Chlorobia above the anoxic zone I and sulfate-reducing bacteria were dominated by Desulfobacterota in anoxic zones. Metagenomic analyses showed that the sulfide-oxidation-related gene sqr and genes encoding the Sox system were mainly distributed in the anoxic zone I, while genes related to dissimilatory sulfate reduction and sulfur intermediate metabolite reduction were mainly distributed in the anoxic zone II, indicating different sulfur metabolic processes between these two zones. Moreover, sulfur-metabolism-related genes were identified in 81 metagenome-assembled genomes (MAGs), indicating a high diversity of microbial communities involved in sulfur cycling. Among them, three MAGs from the candidate phyla JdFR-76 and AABM5-125-24 with genes related to dissimilatory sulfate reduction exhibited distinctive metabolic features. Our results showed unique and novel microbial populations in the SYBH sulfur cycle correlated to the sharp redox gradients, revealing complex biogeochemical processes in this extreme environment. IMPORTANCE Oxygen-deficient regions in the global ocean are expanding rapidly and affect the growth, reproduction and ecological processes of marine organisms. The anaerobic water body of about 150 m in the Sansha Yongle Blue Hole (SYBH) provided a suitable environment to study the specific microbial metabolism in anaerobic seawater. Here, we found that the vertical distributions of the total and active communities of sulfur-oxidizing bacteria (SOB) and sulfate-reducing bacteria (SRB) were different in each water layer of the SYBH according to the dissolved oxygen content. Genes related to sulfur metabolism also showed distinct stratification characteristics. Furthermore, we have obtained diverse metagenome-assembled genomes, some of which exhibit special sulfur metabolic characteristics, especially candidate phyla JdFR-76 and AABM5-125-24 were identified as potential novel SRB. The results of this study will promote further understanding of the sulfur cycle in extreme environments, as well as the environmental adaptability of microorganisms in blue holes.

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.

Decreasing lactate input for cost-effective sulfidogenic metal removal in sulfate-rich effluents: Mechanistic insights from (bio)chemical kinetics to microbiome response

High material cost is the biggest barrier for the industrial use of low-molecular-weight organics (i.e. lactate) as external carbon and electron source for sulfidogenic metal removal in sulfate-rich effluents. This study aims to provide mechanistic evidence from kinetics to microbiome analysis by batch modeling to support the possibility of decreasing the lactate input to achieve cost-effective application. The results showed that gradient COD/SO42- ratios at a low level had promising treatment performance, reaching neutralized pH with nearly total elimination of COD (91%-99%), SO42- (85%-99%), metals (80%-99%) including Cu, Zn, and Mn. First-order kinetics exhibited the best fit (R2 = 0.81-0.98) to (bio)chemical reactions, and the simulation results revealed that higher COD/SO42- accelerated the reaction rate of SO42- and COD but not suitable to that of metals. On the other hand, we found that the decreasing COD/SO42- ratio increased average path distance but decreased clustering coefficient and heterogeneity in microbial interaction network. Genetic prediction found that the sulfate-reduction-related functions were significantly correlated with the reaction kinetics changed with COD/SO42- ratios. Our study, combining reaction kinetics with microbiome analysis, demonstrates that the use of lactate as a carbon source under low COD/SO42- ratios entails significant efficiency of metal removal in sulfate-rich effluent using SRB-based technology. However, further studies should be carried out, including parameter-driven optimization and life cycle assessments are necessary, for its practical application.

Insight into the metabolic potential and ecological function of a novel Magnetotactic Nitrospirota in coral reef habitat

Magnetotactic bacteria (MTB) within the Nitrospirota phylum play important roles in biogeochemical cycles due to their outstanding ability to biomineralize large amounts of magnetite magnetosomes and intracellular sulfur globules. For several decades, Nitrospirota MTB were believed to only live in freshwater or low-salinity environments. While this group have recently been found in marine sediments, their physiological features and ecological roles have remained unclear. In this study, we combine electron microscopy with genomics to characterize a novel population of Nitrospirota MTB in a coral reef area of the South China Sea. Both phylogenetic and genomic analyses revealed it as representative of a novel genus, named as Candidatus Magnetocorallium paracelense XS-1. The cells of XS-1 are small and vibrioid-shaped, and have bundled chains of bullet-shaped magnetite magnetosomes, sulfur globules, and cytoplasmic vacuole-like structures. Genomic analysis revealed that XS-1 has the potential to respire sulfate and nitrate, and utilize the Wood-Ljungdahl pathway for carbon fixation. XS-1 has versatile metabolic traits that make it different from freshwater Nitrospirota MTB, including Pta-ackA pathway, anaerobic sulfite reduction, and thiosulfate disproportionation. XS-1 also encodes both the cbb₃-type and the aa₃-type cytochrome c oxidases, which may function as respiratory energy-transducing enzymes under high oxygen conditions and anaerobic or microaerophilic conditions, respectively. XS-1 has multiple copies of circadian related genes in response to variability in coral reef habitat. Our results implied that XS-1 has a remarkable plasticity to adapt the environment and can play a beneficial role in coral reef ecosystems.

Hallmarks of the relationship between host and Trypanosoma cruzi sulfated glycoconjugates along the course of Chagas disease

American Trypanosomiasis or Chagas disease (ChD), a major problem that is still endemic in large areas of Latin America, is caused by Trypanosoma cruzi. This agent holds a major antigen, cruzipain (Cz). Its C-terminal domain (C-T) is retained in the glycoprotein mature form and bears several post-translational modifications. Glycoproteins containing sulfated N-linked oligosaccharides have been mostly implicated in numerous specific procedures of molecular recognition. The presence of sulfated oligosaccharides was demonstrated in Cz, also in a minor abundant antigen with serine-carboxypeptidase (SCP) activity, as well as in parasite sulfatides. Sulfate-bearing glycoproteins in Trypanosomatids are targets of specific immune responses. T. cruzi chronically infected subjects mount specific humoral immune responses to sulfated Cz. Unexpectedly, in the absence of infection, mice immunized with C-T, but not with sulfate-depleted C-T, showed ultrastructural heart anomalous pathological effects. Moreover, the synthetic anionic sugar conjugate GlcNAc₆SO₃-BSA showed to mimic the N-glycan-linked sulfated epitope (sulfotope) humoral responses that natural Cz elicits. Furthermore, it has been reported that sulfotopes participate via the binding of sialic acid Ig-like-specific lectins (Siglecs) to sulfosialylated glycoproteins in the immunomodulation by host-parasite interaction as well as in the parasite infection process. Strikingly, recent evidence involved Cz-sulfotope-specific antibodies in the immunopathogenesis and infection processes during the experimental ChD. Remarkably, sera from chronically T. cruzi-infected individuals with mild disease displayed higher levels of IgG₂ antibodies specific for sulfated glycoproteins and sulfatides than those with more severe forms of the disease, evidencing that T. cruzi sulfotopes are antigenic independently of the sulfated glycoconjugate type. Ongoing assays indicate that antibodies specific for sulfotopes might be considered biomarkers of human cardiac ChD progression, playing a role as predictors of stability from the early mild stages of chronic ChD.