Dimethyl sulfide (DMS) and dimethyl sulfoxide (DMSO) have important microbial-driven roles in global nutrient cycling, chemotaxis and/or climate regulation. Microbial DMSO and DMS assimilation were thought to require their enzymatic reduction to methanethiol. However, reactive oxygen species were recently shown to mediate methane production from DMS and DMSO. Here, we show that this oxidative mechanism can sustain microbial growth without the need for enzymes to directly reduce DMS or oxidize DMSO. Both, light and heat were effective geochemical drivers of this mechanism that yielded methanesulfonic acid and sulfite, and which mimicked the stepwise oxidation of DMSO by monooxygenases that only enzymatically enhance this oxidation reaction. Furthermore, we demonstrated intracellular DMSO degradation, in which sulfur and the simultaneously released carbon were both utilized by microbes. This study emphasizes that metabolic pathways are not necessarily enzyme-driven, with putatively ancient, non-enzymatic reaction networks taking place at a transition between geochemistry and biochemistry.

Extreme anoxic environments are hotspots of sulfur cycling and harbor numerous novel uncharacterized microbial lineages. Although the phylum Joyebacterota was recently proposed, its internal phylogenetic architecture and evolutionary adaptations remain poorly understood. Here, we significantly expand the genomic diversity and metabolic framework of this phylum by integrating recovered metagenome-assembled genomes, and propose a novel genus, Cavimicrobium. Phylogenomic analysis placed Cavimicrobium as a distinct clade and further divided into four species-level subgroups associated with diverse anoxic sources, including sediments from the Salton Sea, the Eastern Gotland Basin, and the anoxic waters of the Sansha Yongle Blue Hole (SYBH). Unlike previous broad surveys, our study revealed that this lineage evolved from a facultatively anaerobic ancestor and underwent adaptive gene gain and loss through phylogenetic reconstruction. Genomic evidence suggested that this lineage harbored a previously overlooked anaerobic sulfite reduction (asrABC) pathway that likely mediating thiosulfate uptake and conversion to sulfite and sulfide. Notably, Cavimicrobium was particularly abundant in the anoxic waters of SYBH, comprising up to one-third of the bacterial community in particle-associated fraction below 100 m, where it is likely a major contributor to sulfide accumulation. Analysis of MAGs and global amplicon datasets revealed that Cavimicrobium is widespread across anoxic environments, comprising up to 0.32% of the bacterial community in 354 200 publicly available 16S rRNA gene amplicon samples. Together, these findings reveal a new lineage dominant in certain anoxic environments where they are likely important mediators of sulfur cycling, and broaden our understanding of biogeochemical potential of Joyebacterota.

Dimethylsulfoniopropionate (DMSP) is a globally significant marine organosulfur compound with diverse ecological roles, including environmental stress protection, chemotaxis, and nutrient cycling. Its microbial catabolism is crucial for the marine sulfur cycle, generating dimethyl sulfide (DMS), a volatile gas that influences global sulfur fluxes, cloud formation, and climate regulation. Despite its importance, the metabolic regulatory mechanisms governing bacterial DMSP cleavage and DMS production remain unclear. Here, using the model DMSP-catabolizing bacterium Halomonas sp. D47, a complex regulatory mechanism involving two transcriptional regulators, AcuR and AcuZ, was elucidated through integrated genetic and biochemical analyses, in which they coordinate the orderly progression of DMSP catabolism. These regulators sense external signals from DMSP and its metabolites, fine-tuning gene expression to balance metabolism and detoxification, thereby maintaining cellular integrity. Bioinformatics analyses suggest that this regulatory scheme is conserved among certain efficient DMSP-metabolizing bacteria. Our findings provide key insights into the regulation of DMSP catabolism and highlight a potentially bacterial strategy for balancing metabolic demands with cellular homeostasis.

Hadal subseafloor sediments host abundant and active microbial biosphere with considerable heterotrophic activity. However, carbon and nutrient cycling processes and mechanisms driven by hadal subsurface microorganisms remain poorly understood. Using culture-dependent and culture-independent methods, we characterized the diversity, metabolism, and vertical dynamics of hydrocarbon-degrading (HYD) bacteria in a subsurface sediment core (MT20-750, ~750 cm below seafloor [cmbsf]) collected from the Challenger Deep (10,816 m below sea level) in the Mariana Trench. The sediment core contained high concentrations of mid- and long-chain n-alkanes (310-8,724 ng/g), although no <C18 n-alkanes at detectable levels were present, in contrast to proximal hadal seawater samples where these compounds were highly abundant. Metagenomic analysis identified diverse genes for aerobic and anaerobic degradation of n-alkanes and aromatic compounds, distributed across a wide range of taxa, dominated by Chloroflexota, Planctomycetes, Proteobacteria, and Actinobacteria, alongside six novel HYD phyla. Metabolic reconstruction of 120 HYD metagenome-assembled genomes (MAGs) suggests distinct hydrocarbon degradation preferences and metabolic strategies among different bacterial groups. Additionally, hadal bacterial isolates from Proteobacteria, Actinobacteria, and Firmicutes were able to degrade n-alkanes (C18-36), with Dietzia maris HXX048 removing ~50% of n-eicosane within 45 days under 5°C and 50 MPa. Predicted substrate binding of C10 and C20 with AhyA and heterologous expression of almA in Chloroflexota genomes supported their degradative capacity under anaerobic and aerobic conditions. The detection of putative hydrocarbon synthesis genes, specifically oleBC and oleC, suggests that hadal heterotrophic microorganisms may synthesize hydrocarbons. These findings provide evidence for microbial hydrocarbon production and thereby support a previously unrecognized sedimentary hydrocarbon cycle.IMPORTANCEOur findings suggest that hydrocarbon degradation may play an important role in organic matter decomposition and carbon cycling in the hadal subseafloor. This degradation capacity is likely distributed through diverse metabolic pathways across a wide range of phylogenetic taxa. The detection of genes likely encoding enzymes involved in aerobic and anaerobic hydrocarbon degradation, as well as the identification of novel hydrocarbon-degrading (HYD) phyla, highlights the complexity and significance of microbial processes in hadal subsurface sediment. The widespread distribution of hydrocarbon degradation capacity in different hadal sediments suggests hydrocarbons as a potential carbon source sustaining microbial life in this extreme environment. Moreover, the presence of genes associated with hydrocarbon synthesis suggests that hadal sediment microbes possess the genetic potential for both degrading and producing hydrocarbons, pointing to a dynamic and multifaceted hydrocarbon cycle within hadal subsurface sediment.

Dimethylsulfoniopropionate (DMSP) catabolism by marine Roseobacters is important for global biogeochemical cycling and the climate. Many Roseobacters contain competing DMSP demethylation and cleavage pathways, but only cleavage produces the climate-cooling gas dimethylsulfide. Here, we identify the "switch" regulator in Roseobacters, DmdR, which transcriptionally represses demethylation (dmdA, encoding DMSP demethylase), cleavage (acuI, encoding acryloyl-CoA reductase) and oxidative stress protection (dmdEF, dinB) genes under low intracellular DMSP levels. Increased DMSP levels lead to DMSP cleavage and accumulation of cytotoxic cleavage product acryloyl-CoA. Acryloyl-CoA binding to DmdR derepresses dmdA-acuI transcription to stimulate acryloyl-CoA catabolism and DMSP demethylation. Upregulation of the newly identified peroxidase DmdF, and possibly also of DmdE and DinB, counteracts oxidative stress associated with DMSP demethylation. Thus, DmdR, along with DmdR-independent regulators of DMSP cleavage, likely maintains cellular DMSP levels to allow its antistress functions, but accelerates demethylation and catabolism of toxic intermediates at higher DMSP levels. Of note, DmdR appears to control acryloyl-CoA catabolism/detoxification even in abundant marine bacteria lacking dmdA, suggesting additional mechanisms. DmdR and DmdEF are widespread in Earth's oceans and important for biogeochemical cycling and climate-active gas production.

Abstract The allododecaploid cordgrass Spartina anglica thrives in saltmarshes, where it grows vigorously despite facing extreme environmental stresses. The species was formed through a genome duplication of an infertile hybrid in ∼1870, and is today listed amongst 100 of the World’s Worst Invasive Alien Species. Here, we use long-read sequencing to provide a genomic sequence of S. anglica and undertake a detailed transcriptomic analysis of different tissues. We demonstrate that S. anglica has undergone at least two whole-genome duplication events and exhibits segmental allopolyploidy. We also show that S. anglica has evolved novel mechanisms to tolerate abiotic stress, including expansion and neofunctionalization of genes involved in sucrose synthesis, detoxification of reactive oxygen species and heavy metals, and calcium signalling associated with salt, ionic, and nutrient stress. Furthermore, we demonstrate that S. anglica produces a diverse array of osmolytes, including dimethylsulfoniopropionate (DMSP), and reveal that a retrotransposon with a unique 55 bp insertion causes high-level expression of the DMSP-amine oxidase (DOX) gene and contributes to the exceptionally high levels of DMSP production. Taken together, our results highlight the specialised genomic, transcriptomic, and biochemical adaptations that S. anglica has evolved to tolerate severe abiotic stresses in saltmarshes.

Root-associated microbiota play a critical role in plant tolerance to salt stress. However, the conservation of beneficial interactions across diverse crops and soils and the underlying mechanisms remain unclear. Here, we show that pseudomonads were consistently enriched in salt-stressed plant roots across multiple soil types and most crop species. Comparative genomics revealed that these pseudomonads harbored unique genomic signatures associated with high salinity tolerance, such as Na + transporters. Pseudomonad isolates from salt-stressed plants robustly colonized soybean roots and significantly improved salt tolerance under both greenhouse and field conditions. Pseudomonads-dependent plant salt stress tolerance was mediated through plant lignin biosynthesis stimulation rather than the canonical mechanism of Na + homeostasis. Overexpression of the key plant lignin biosynthesis genes, including GmCAD , GmCOMT , and Gm4CL , significantly enhanced soybean growth under salt stress. Furthermore, mutant plants deficient in lignin biosynthesis no longer showed pseudomonads-induced salt tolerance. Collectively, our findings reveal a previously unrecognized microbial-mediated pathway that enhances plant resilience to salt stress.

Ubiquitous marine microalgae and bacteria produce the abundant organosulfur compound dimethylsulfoniopropionate (DMSP) and/or catabolize it to climate-active gases, such as dimethylsulfide (DMS), with major consequences for global biogeochemistry and climate. However, their relative and dynamic roles in DMSP synthesis and catabolism remain poorly resolved, particularly during natural bloom events. Here, we combined metagenomics and metatranscriptomics, with measurements of intracellular/particulate DMSP (DMSPp), DMS concentrations, and DMSPp production rates, as well as microscopy and flow cytometry, to predict the key microbes and enzymes driving DMSP/DMS dynamics during a spring-summer bloom in the Western English Channel. Microalgae and bacteria expressing the DMSP synthesis genes DSYB/DSYE and dsyB were likely major and significant DMSP producers, respectively, except during the largest observed DMSP spike. This spike coincided with elevated Synechococcus and autotrophic flagellate biomass but minimal DMSP synthesis gene expression. Axenic Synechococcus strains contained no detectable DMSP, implying that flagellates with novel DMSP synthesis genes were likely responsible. Microbial DMSP import potential far exceeded catabolism, suggesting strong selection for DMSP uptake. Bacteria were the major predicted DMSP degraders, with DMSP demethylation potential dwarfing cleavage. However, the highest DMS concentrations were linked to Haptophyta expressing the DMSP lyase gene Alma, implying the significance of algal DMSP cleavage. Methanethiol-dependent DMS production was also likely important, with bacterial mddH transcripts coinciding with another major DMS spike. Overall, these results imply dynamic and contrasting roles of microalgae and bacteria, and their pathways, in coastal DMSP/DMS and sulfur cycling.

Dimethylsulfoniopropionate (DMSP) is a highly abundant marine organosulfur compound, with important roles in stress protection and climate-cooling gases production. Polar regions, particularly seawater and sea ice interfaces, are critical yet understudied DMSP cycling hotspots. Here, we reveal up to 38-fold higher DMSP concentrations in Southern Ocean sea ice versus seawaters, identifying sea ice as a concentrated reservoir of DMSP with implications for microbial stress tolerance and sulfur recycling. Eukaryotic algae harboring DSYB and DSYE genes were predicted to dominate DMSP production, but diverse and previously unidentified bacterial producers were also detected. This elevated abundance of algal biosynthetic genes likely underpins the higher DMSP concentrations in sea ice. Notably, DMSP catabolism, particularly the dmdA demethylase and dddD and dddK lyase genes, were more abundant than biosynthesis genes. Taken together, these findings reveal the widespread metabolism for DMSP cycling and underscore a dynamic reservoir and transformation hub influencing polar climate-cooling sulfur fluxes.

Carbon fixation in marine ecosystems is a vital process that contributes to climate regulation, with ocean sediments playing a critical role in carbon sequestration. This process is driven by chemolithoautotrophy in marine sediments, fueled by reduced compounds, such as those containing nitrogen and sulfur. However, the vertical distribution of microbial autotrophs and their energy coupling systems remain poorly understood in many sediments. In this study, we investigated a 750 cm sediment core from the Challenger Deep, the deepest point on Earth, which harbors abundant and diverse microbes under extreme conditions. To explore the autotrophic characteristics across redox conditions in this core, we characterized the microbial community, metagenome, and metagenome-assembled genomes (MAGs), and their potential for carbon fixation processes and associated energy metabolism. The Wood-Ljungdahl (WL) pathway, primarily driven by Planctomycetota and Aerophobota, and the reverse oxidative TCA (roTCA) cycle, primarily driven by Bacteroidota and Gemmatimonadota, were the dominant predicted carbon fixation pathways, with hydrogen as the primary energy source, coupled to nitrogen and sulfur metabolism. Notably, the 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle, mediated by Nitrososphaeria, showed the highest abundance in the oxidized environment (15–27 cm below the seafloor), where ammonia oxidation likely served as the primary energy source. Gammaproteobacteria were predicted to utilise sulfur oxidation, whereas Alphaproteobacteria and Chloroflexota used hydrogen to drive the Calvin-Benson-Bassham (CBB), reductive glycine pathway (rGly) in Alphaproteobacteria and the dicarboxylate/4-hydroxybutyrate cycle (DC/4HB) in Chloroflexota, respectively. The abundance of carbon fixation, and nitrogen, sulfur and hydrogen cycling functional genes were significantly correlated with environmental factors (NH4+ and SiO32−) based on Pearson’s correlation analysis. This study reveals the vertical distribution of microbial carbon fixation potential and diversity in sediments driven by redox conditions, highlights the crucial role of hydrogen as an energy source, and provides new insights for optimizing global deep-sea carbon cycle models. Collectively, these findings extend the redox tower theory by revealing a hadal-sediment specific distribution of autotrophic genes, characterized by persistent enrichment of energetically efficient pathways and dominant hydrogen-based energy coupling across deep sediment layers.

Dimethylsulfoniopropionate (DMSP) is a ubiquitous marine organosulfur compound central to microbial stress responses, chemotaxis, and nutrient cycling. Its catabolism produces dimethylsulfide (DMS), a climate-active gas, and plays a key role in the global sulfur cycle. However, the molecular basis of DMSP import, underpinning its microbial metabolism, remains poorly understood. Here, we identify and characterize the BCCT-family transporter DddT from Psychrobacter sp. D2, a marine gamma-proteobacterium that utilizes DMSP as a carbon source. DddT is essential for DMSP uptake and functions as a Na+-coupled symporter driven by the transmembrane sodium gradient. Using cryo-electron microscopy, we determined DddT structures in multiple conformational states, revealing its Na+-dependent transport mechanism involving two sodium ions, one coordinated by a previously uncharacterized binding site. Sequence analysis shows that DddT-like proteins with conserved sodium-binding features are widespread in marine bacteria, suggesting this Na+-coupled transport mechanism represents a broadly conserved feature of the BCCT family. Our findings provide mechanistic insights into sodium-driven substrate uptake and marine sulfur cycling.

Understanding past Earth system processes is an essential component of placing current climate changes in context and testing climate model output. In this context, reconstructing patterns in marine or terrestrial temperatures is as important as understanding the mode of the hydrological cycle. However, there is only limited research on past hydrological systems, as the interplay between evapotranspiration, precipitation and runoff makes comprehensive reconstructions challenging. To overcome this issue, the spatiotemporal distribution of precipitation and riverine runoff can be estimated by reconstructing the dynamics of enhanced fresh water input into marginal sea.Here, we focus on the hydrological conditions of shallow marine areas around the southern paleo-North Sea during the Eocene, including the Paris, Hampshire and Belgium Basins. We utilised fossil bivalve shells (Venericor planicosta and Crassatella ponderosa) as archives as they can be used to reconstruct both long-term climate changes due to their widespread abundance and temporal continuity in the geological record as well as short-term variability via the time-distinct (sub-seasonal) layering of their shells. We reconstruct fresh water flux to these basins at different spatiotemporal resolutions, ranging from regional differences across millions of years to (sub-)seasonally resolved local variations. Depending on the targeted spatiotemporal resolution, different proxy systems were used. For the reconstruction of large scale changes in the input of terrigenous material by riverine runoff, Ba/Ca and 87Sr/86Sr are employed. In addition, δ18O and Δ47+Δ48 measurementswere conductedto detect sub-annual changes in the isotopic composition of the sea water by isotopically lighter fresh-water influx.Result exhibit regionally specific Ba/Ca and 87Sr/86Sr values for each of the examined basins, generally reflecting the hinterland geology. However, these values show time dependent variations throughout the Eocene, suggesting variable degrees of terrigenous input by varying riverine runoff. The detected changes in riverine runoff are generally congruent to the depositional evolution of the basins, as derived from the sedimentary record, revealing less terrigenous input signal with increasing open marine conditions and vice versa. A specimen of V. planicosta from the Paris Basin, showing a distinct riverine signal in Ba/Ca and 87Sr/86Sr, was used for combined δ18O and Δ47+Δ48 measurements to identify seasonal variations in the oxygen isotopic composition of the sea water (δ18OSW). The resulting δ18OSW values show a minimum seasonal variability of 0.9‰ and an enhanced fresh water input during the summer.These results shed new light on the hydrological conditions in Western Europe during the Eocene and show how different proxy systems can be interlinked to reconstruct basin hydrology on different spatiotemporal scales.

Hydrogen sulfide (H2S), methanethiol (MeSH), and dimethylsulfide (DMS) are abundant sulfur gases with crucial roles in global sulfur cycling, chemotaxis, and climate regulation. Microorganisms can S-methylate H2S and MeSH, which can be cytotoxic, to yield non-toxic DMS via MddA or MddH enzymes in largely terrestrial or marine environments, respectively. However, the potential of many important and abundant bacteria like Actinomycetota is underestimated due to unknown Mdd enzymes. Here, two novel S-adenosine-methionine-dependent H2S and MeSH S-methyltransferases, MddM1 and MddM2 are identified, in the DMS-producing actinomycete Mycolicibacterium poriferae (M. poriferae) ZYF656, isolated from the Mariana Trench. M. poriferae ZYF656 MddM1 and MddM2 likely detoxify H2S and MeSH and alleviate oxidative stress, since mddM1 and mddM2 transcription is induced by H2S, MeSH, and oxidative stress, and their expression in E. coli enhances H2S, MeSH, and oxidative stress tolerance. MddM1 and/or MddM2 are in >50% of actinomycetota, including the model Streptomyces species, S. venezuelae, but are also seen in some Chloroflexota, Acidobacteriota, and Proteobacteria. mddM1 is always more abundant than mddM2 in diverse environments and is prevalent in soils and marsh sediments. This study highlights the significance of H2S- and MeSH-dependent DMS production and, principally, of Actinomycetota in global DMS production and sulfur cycling.

Organosulfur compounds play an important role in chemotaxis, stress protection, and nutrition in many marine symbioses. Lucinidae, an ancient and species-rich family of marine bivalves, host chemosynthetic sulphur-oxidising bacteria within gill epithelial cells, and is well-known for its contribution to inorganic sulphur cycling in marine sediments worldwide. Little is known about organosulfur transformations by lucinid-associated microbiota or the host's potential contribution. Here, we integrated field measurements, genomics, transcriptomics, and experimental assays to investigate organosulfur cycling in three lucinid species from temperate and tropical environments. Concentrations of the osmolyte dimethylsulphoniopropionate (DMSP) in lucinids were typically much higher than in their surrounding environment, and varied with host species and season, but not with symbiont abundance. Indeed, candidate DMSP synthesis DSYB genes were expressed by the animal hosts implying that the host may be the source of DMSP. Furthermore, a newly identified and isolated Candidatus Endozoicomonas endolucinida symbiont was capable of DMSP catabolism to dimethylsulphide (DMS), which could be further syntrophically oxidised by the sulphur-oxidising symbionts that encode methanethiol oxidase genes in their genomes. Finally, incubation experiments supported a combined role of the host and its associated microbiome in organosulfur cycling during stress, with the highest DMSP concentrations measured when holobionts were incubated with antibiotics under anoxic conditions. This study identified a previously unrecognised microbial partner in lucinid symbioses and revealed its potential organosulphur-based metabolic interactions with both the host and the sulphur-oxidising symbionts, highlighting the capacity of these widespread associations to influence global organosulfur cycling.

Dimethylsulfoniopropionate (DMSP) is a globally abundant organosulfur compound produced by marine organisms, where it plays key physiological roles in stress protection and serves as a major source of carbon, sulfur, and energy for microbial communities. Importantly, DMSP degradation contributes to the formation of the climate-active gas dimethyl sulfide (DMS), which can drive the production of potent greenhouse gases, methane and carbon dioxide, in anoxic environments. While aerobic DMSP degradation is well studied, its fate under anoxic conditions remains poorly understood, and the microbial populations and metabolic pathways underlying these biotransformations are virtually unknown. Here, we present the first detailed investigation of microbial DMSP cycling in anoxic saltmarsh sediments. Our sediment samples had high in situ DMSP concentrations (up to 7.7 μmol/g) and the conversion efficiencies of DMSP to DMS under anoxic conditions (~68%) were comparable to those in oxic environments. Furthermore, using 13C-labelled DMSP in stable isotope probing (SIP) experiments, combined with 16S rRNA gene sequencing and metagenomics, we identified Amphritea (Oceanospirillales) as a key active DMSP degrader, likely operating via the dddD-encoded lysis pathway. Additional taxa, including Geopsychrobacter, were implicated as potential secondary consumers, while Arcobacteraceae may contribute to sulfur cycling rather than direct DMSP catabolism. This study uncovers a previously overlooked route for DMSP transformation via anaerobic metabolism, expands the known metabolic roles of saltmarsh microorganisms and highlights the potential for DMSP to drive climate-active gas production in anoxic coastal ecosystems.

Sulfur isotope fractionation during microbial sulfate reduction is often preserved in the mineral pyrite (FeS2), which has been used to reconstruct the biogeochemical sulfur cycle and redox geochemistry of the oceans over the Earth history. Understanding what controls the preserved sulfur isotopic composition of pyrite is therefore of paramount importance, but it has been difficult to deconvolve the influence of environmental changes from changes in sedimentation rate. We present a 16-month record of pore fluid geochemical profiles with in situ sampling apparatus installed in coastal sediments, one of which is dominated by microbial sulfate reduction and the other dominated by bacterial iron reduction. Our data include monthly sulfate (SO42-) and chloride concentrations (Cl-), dissolved iron concentrations (Fe2+), and the sulfur isotopic composition of dissolved sulfate (delta 34SSO4) up to 36 cm below the sediment-water interface. We use a reactive transport model to determine the expressed sulfur isotopic fractionation factor for each month and a Monte Carlo simulation to calculate net sulfate flux into the sediment based on pore fluid profiles from the sulfidic sediment. Net rates of sulfate reduction in the sulfidic sediment vary by three orders of magnitude over the seasonal cycle and are positively correlated with air temperature. The expressed sulfur isotope fractionation factor varies between 20 and 70 parts per thousand and reaches the thermodynamic limit in the colder months. Our data suggest that the correlation between temperature and the subsurface microbial sulfur biogeochemical cycle should be considered when interpreting sulfur isotope ratios in pyrite over Earth history.

The organosulfur cycle involves active microbial transformations of dimethylsulfoniopropionate (DMSP) to yield the climate active gas dimethyl sulfide (DMS) and other compounds. The lack of rapid and accurate methods to quantify the DMSP metabolic potential hinders a deeper understanding of this cycling. We developed a high-throughput qPCR (HT-qPCR) chip, DSMG-chip, to quantify the absolute abundance of DMSP and related organic sulfur metabolic genes. DSMG-chip contains 42 degenerate primer sets targeting 27 organosulfur metabolic genes, with the 16S rRNA gene as a reference, allowing for the detection of 41 environmental samples simultaneously. In silico analysis indicated that the DSMG-chip possesses broad taxonomic coverage (1.4-91.3%, spanning 12 phyla and 275 genera) and high specificity (44.4-100%, mean: 85.34%). Validation experiments using conventional PCR, qPCR, and HT-qPCR confirmed the primers' strict specificity, robust amplification efficiency (0.677 to 0.997, mean: 0.771), and excellent accuracy, correlating well with conventional qPCR (Pearson's r = 0.914). Finally, application of the DSMG-chip accurately reflected variations in DMSP metabolism across diverse seawater and sediment samples, highlighting the active microbial DMSP cycling in Pacific Ocean (section P) seawater and the contribution of the methanethiol (MeSH) methylation pathway (via mddA) in sediments. Our findings provide a powerful, novel tool for studying the organosulfur cycle.

Deep-sea sediments contain a large number of Thaumarchaeota that are phylogenetically distinct from their pelagic counterparts. However, their ecology and evolutionary adaptations are not well understood. Metagenomic analyses were conducted on samples from various depths of a 750-cm sediment core collected from the Mariana Trench Challenger Deep. The abundance of Thaumarchaeota and archaeal amoA generally decreased with depth, except for an unexpected peak midway through the core. The thaumarchaeotal metagenome-assembled genomes were classified into diverse phylogenetic clusters associated with amoA-NP-γ, amoA-NP-θ, and amoA-NP-δ of ammonia-oxidising Thaumarchaeota and non-ammonia-oxidising lineages. The most abundant group was within amoA-NP-γ, which is usually found in coastal and shallow habitats, indicating potential niche expansion from marine shallow to hadal environments. This benthic group showed within-species genomic variations compared to the previously identified Hadal water group, suggesting microdiversification of hadal Thaumarchaeota along with niche separation between benthic and pelagic environments. Evolutionary adaptations associated with the benthic-to-pelagic transition included reduced genome size, loss of motility/cell adhesion, altered energy metabolism, and different mechanisms for substrate acquisition and regulation (e.g., ammonium). These findings offer new insights into the evolution of hadal Thaumarchaeota and demonstrate, for the first time, intraspecies-level genomic variation in Thaumarchaeota related to the benthic-versus-pelagic niche partitioning in the deep ocean.

Ocean circulations and water mass exchange can exert significant influences on seawater biogeochemistry, microbial communities, and carbon cycling in marine systems. However, the detailed mechanisms of the impacts of physical processes in the open ocean on the cycle of greenhouse gases, particularly methane, remain poorly understood. In this study, we integrated high-resolution underway observations, experimental incubations, radioisotope labelling, and molecular analysis to constrain the controls of methanogenic pathways, methanotrophic activity, and emission fluxes in the highly hydrodynamic Kuroshio and Oyashio Extension (KOE) region of the Northwest Pacific. The mixing of high-temperature, nutrient-rich Kuroshio waters with methane-rich Oyashio currents significantly affected not only methane abundance, but also methane production pathways and oxidation rates. Water mass mixing caused changes in the dominance of phytoplankton communities to Bacillariophyta, with less production of the methane precursor dimethylsulphoniopropionate, thus reducing dimethylsulphoniopropionate-dependent methanogenesis. The alteration of nutrient levels due to mixing of Kuroshio and Oyashio at KOE is also likely to affect microbial utilization of dissolved organic phosphorus, thus influencing methane production from the C-P cleavage of methylphosphonate. Furthermore, the abundances of methanotrophs, such as Methylocystis and Methylosinus, were much higher at the KOE sites than those observed at the Oyashio Extension, which contributed to elevated methane oxidation rates in the mixing region. Microbial oxidation as a biological sink of methane accounted for ~43.7% ± 28.8% of the total methane loss, which reduced methane emissions to the atmosphere. These data highlight the physical controls on biogeochemical methane cycling, indicating that intensive mixing of water masses may regulate methane emissions from the open oceans.

Billions of tons of dimethylsulfoniopropionate (DMSP) are produced every year in marine and coastal ecosystems such as saltmarshes and estuaries. DMSP has far-reaching roles in global carbon and sulfur cycling, also as an osmotolerant and signalling molecule. Furthermore, the microbial degradation of DMSP contributes significantly to the formation of dimethylsulfide (DMS) and methanethiol (MT), other abundant organosulfur compounds with ecological significance. Particularly, in anaerobic sediments, microbial DMS and MT degradation leads to the formation of methane, a powerful greenhouse gas. However, research to date has predominantly focused on aerobic settings, revealing diverse groups of microbes and enzymes mediating DMSP degradation. DMSP concentrations in anaerobic ecosystems and microbial populations underlying DMSP breakdown have never been studied, prohibiting improvements in our understanding of global carbon and sulfur cycles. To address this key knowledge gap, we applied stable-isotope probing combined with 16S rRNA sequencing to identify the active DMSP-degraders in anaerobic saltmarsh sediments.We collected sediments from a 5-10 cm depth of Medway Saltmarshes (UK) using 3.5cm Perspex corers. We transferred the samples to the laboratory and measured in situ DMSP concentrations of 7.7 (±0.5) μmol g−1 wet sediment. In line with the in situ concentrations, we set up replicated incubations anaerobically with 8 μmol g−113C- and 12C-labelled DMSP, and applied stable-isotope probing combined with 16S rRNA sequencing.We observed immediate degradation of DMSP in the sediment incubations and DMS production, suggesting the existence of a resident microbial community actively carrying out this process. A total of 48 μmol/g 13C- or 12C-DMSP was amended and a total of 34 (±3.2) μmol/g DMS was produced in the incubations over 12 days. DNA was extracted and ultracentrifugation was applied to separate heavy and light DNA fractions for downstream analysis. 16S rRNA sequencing of the fractions from 13C and 12C-labelled DNA demonstrated significant enrichment of the family Nitrincolaceae within the order Oceanospirillales in 13C-heavy fractions compared to 13C- light and 12C-heavy fractions (P