Climate-active Gas Dimethylsulfide Research Articles

An S-methyltransferase that produces the climate-active gas dimethylsulfide is widespread across diverse marine bacteria.

Hydrogen sulfide (H2S), methanethiol (MeSH) and dimethylsulfide (DMS) are abundant sulfur gases with roles in biogeochemical cycling, chemotaxis and/or climate regulation. Catabolism of the marine osmolyte dimethylsulfoniopropionate (DMSP) is a major source of DMS and MeSH, but both also result from S-methylation of H2S via MddA, an H2S and MeSH S-methyltransferase whose gene is abundant in soil but scarce in marine environments. Here we identify the S-adenosine methionine (SAM)-dependent MeSH and H2S S-methyltransferase 'MddH', which is widespread in diverse marine bacteria and some freshwater and soil bacteria. mddH is predicted in up to ~5% and ~15% of seawater and coastal sediment bacteria, respectively, which is considerably higher than mddA. Furthermore, marine mddH transcript levels are similar to those for the most abundant DMSP lyase gene dddP. This study implies that the importance of H2S and MeSH S-methylation pathways in marine environments is significantly underestimated.

Gephyrocapsa huxleyi (Emiliania huxleyi) as a model system for coccolithophore biology.

Coccolithophores are the most abundant calcifying organisms in modern oceans and are important primary producers in many marine ecosystems. Their ability to generate a cellular covering of calcium carbonate plates (coccoliths) plays a major role in marine biogeochemistry and the global carbon cycle. Coccolithophores also play an important role in sulfur cycling through the production of the climate-active gas dimethyl sulfide. The primary model organism for coccolithophore research is Emiliania huxleyi, now named Gephyrocapsa huxleyi. G. huxleyi has a cosmopolitan distribution, occupying coastal and oceanic environments across the globe, and is the most abundant coccolithophore in modern oceans. Research in G. huxleyi has identified many aspects of coccolithophore biology, from cell biology to ecological interactions. In this perspective, we summarize the key advances made using G. huxleyi and examine the emerging tools for research in this model organism. We discuss the key steps that need to be taken by the research community to advance G. huxleyi as a model organism and the suitability of other species as models for specific aspects of coccolithophore biology.

Climate Change Impacts on the Marine Cycling of Biogenic Sulfur: A Review.

A key component of the marine sulfur cycle is the climate-active gas dimethylsulfide (DMS), which is synthesized by a range of organisms from phytoplankton to corals, and accounts for up to 80% of global biogenic sulfur emissions. The DMS cycle starts with the intracellular synthesis of the non-gaseous precursor dimethylsulfoniopropionate (DMSP), which is released to the water column by various food web processes such as zooplankton grazing. This dissolved DMSP pool is rapidly turned over by microbially mediated conversion using two known pathways: demethylation (releasing methanethiol) and cleavage (producing DMS). Some of the formed DMS is ventilated to the atmosphere, where it undergoes rapid oxidation and contributes to the formation of sulfate aerosols, with the potential to affect cloud microphysics, and thus the regional climate. The marine phase cycling of DMS is complex, however, as heterotrophs also contribute to the consumption of the newly formed dissolved DMS. Interestingly, due to microbial consumption and other water column sinks such as photolysis, the amount of DMS that enters the atmosphere is currently thought to be a relatively minor fraction of the total amount cycled through the marine food web—less than 10%. These microbial processes are mediated by water column temperature, but the response of marine microbial assemblages to ocean warming is poorly characterized, although bacterial degradation appears to increase with an increase in temperature. This review will focus on the potential impact of climate change on the key microbially mediated processes in the marine cycling of DMS. It is likely that the impact will vary across different biogeographical regions from polar to tropical. For example, in the rapidly warming polar oceans, microbial communities associated with the DMS cycle will likely change dramatically during the 21st century with the decline in sea ice. At lower latitudes, where corals form an important source of DMS (P), shifts in the microbiome composition have been observed during thermal stress with the potential to alter the DMS cycle.

Oceanospirillales containing the DMSP lyase DddD are key utilisers of carbon from DMSP in coastal seawater

BackgroundUbiquitous and diverse marine microorganisms utilise the abundant organosulfur molecule dimethylsulfoniopropionate (DMSP), the main precursor of the climate-active gas dimethylsulfide (DMS), as a source of carbon, sulfur and/or signalling molecules. However, it is currently difficult to discern which microbes actively catabolise DMSP in the environment, why they do so and the pathways used.ResultsHere, a novel DNA-stable isotope probing (SIP) approach, where only the propionate and not the DMS moiety of DMSP was 13C-labelled, was strategically applied to identify key microorganisms actively using DMSP and also likely DMS as a carbon source, and their catabolic enzymes, in North Sea water. Metagenomic analysis of natural seawater suggested that Rhodobacterales (Roseobacter group) and SAR11 bacteria were the major microorganisms degrading DMSP via demethylation and, to a lesser extent, DddP-driven DMSP lysis pathways. However, neither Rhodobacterales and SAR11 bacteria nor their DMSP catabolic genes were prominently labelled in DNA-SIP experiments, suggesting they use DMSP as a sulfur source and/or in signalling pathways, and not primarily for carbon requirements. Instead, DNA-SIP identified gammaproteobacterial Oceanospirillales, e.g. Amphritea, and their DMSP lyase DddD as the dominant microorganisms/enzymes using DMSP as a carbon source. Supporting this, most gammaproteobacterial (with DddD) but few alphaproteobacterial seawater isolates grew on DMSP as sole carbon source and produced DMS. Furthermore, our DNA-SIP strategy also identified Methylophaga and other Piscirickettsiaceae as key bacteria likely using the DMS, generated from DMSP lysis, as a carbon source.ConclusionsThis is the first study to use DNA-SIP with 13C-labelled DMSP and, in a novel way, it identifies the dominant microbes utilising DMSP and DMS as carbon sources. It highlights that whilst metagenomic analyses of marine environments can predict microorganisms/genes that degrade DMSP and DMS based on their abundance, it cannot disentangle those using these important organosulfur compounds for their carbon requirements. Note, the most abundant DMSP degraders, e.g. Rhodobacterales with DmdA, are not always the key microorganisms using DMSP for carbon and releasing DMS, which in this coastal system were Oceanospirillales containing DddD.98tW24pEex88JAHxuSH5r1Video abstract.

Patterns and drivers of dimethylsulfide concentration in the northeast subarctic Pacific across multiple spatial and temporal scales

Abstract. The northeast subarctic Pacific (NESAP) is a globally important source of the climate-active gas dimethylsulfide (DMS), yet the processes driving DMS variability across this region are poorly understood. Here we examine the spatial distribution of DMS at various spatial scales in contrasting oceanographic regimes of the NESAP. We present new high-spatial-resolution measurements of DMS across hydrographic frontal zones along the British Columbia continental shelf, together with key environmental variables and biological rate measurements. We combine these new data with existing observations to produce a revised summertime DMS climatology for the NESAP, yielding a broader context for our sub-mesoscale process studies. Our results demonstrate sharp DMS concentration gradients across hydrographic frontal zones and suggest the presence of two distinct DMS cycling regimes in the NESAP, corresponding to microphytoplankton-dominated waters along the continental shelf and nanoplankton-dominated waters in the cross-shelf transitional zone. DMS concentrations across the continental shelf transition (range < 1–10 nM, mean 3.9 nM) exhibited positive correlations to salinity (r=0.80), sea surface height anomaly (SSHA; r=0.51), and the relative abundance of prymnesiophyte and dinoflagellates (r=0.89). In contrast, DMS concentrations in nearshore coastal transects (range < 1–24 nM, mean 6.1 nM) showed a negative correlation with salinity (r=-0.69; r=-0.78) and SSHA (r=-0.81; r=-0.75) and a positive correlation to relative diatom abundance (r=0.88; r=0.86). These results highlight the importance of bloom-driven DMS production in continental shelf waters of this region and the role of prymnesiophytes and dinoflagellates in DMS cycling further offshore. In all areas, the rate of DMS consumption appeared to be an important control on observed concentration gradients, with higher DMS consumption rate constants associated with lower DMS concentrations. We compiled a data set of all available summertime DMS observations for the NESAP (including previously unpublished results) to examine the performance of several existing algorithms for predicting regional DMS concentrations. None of these existing algorithms was able to accurately reproduce observed DMS distributions across the NESAP, although performance was improved by the use of regionally tuned coefficients. Based on our compiled observations, we derived an average summertime distribution map for DMS concentrations and sea–air fluxes across the NESAP, estimating a mean regional flux of 0.30 Tg of DMS-derived sulfur to the atmosphere during the summer season.

Structure-Function Analysis Indicates that an Active-Site Water Molecule Participates in Dimethylsulfoniopropionate Cleavage by DddK.

The osmolyte dimethylsulfoniopropionate (DMSP) is produced in petagram quantities in marine environments and has important roles in global sulfur and carbon cycling. Many marine microorganisms catabolize DMSP via DMSP lyases, generating the climate-active gas dimethyl sulfide (DMS). DMS oxidation products participate in forming cloud condensation nuclei and, thus, may influence weather and climate. SAR11 bacteria are the most abundant marine heterotrophic bacteria; many of them contain the DMSP lyase DddK, and their dddK transcripts are relatively abundant in seawater. In a recently described catalytic mechanism for DddK, Tyr64 is predicted to act as the catalytic base initiating the β-elimination reaction of DMSP. Tyr64 was proposed to be deprotonated by coordination to the metal cofactor or its neighboring His96. To further probe this mechanism, we purified and characterized the DddK protein from Pelagibacter ubique strain HTCC1062 and determined the crystal structures of wild-type DddK and its Y64A and Y122A mutants (bearing a change of Y to A at position 64 or 122, respectively), where the Y122A mutant is complexed with DMSP. The structural and mutational analyses largely support the catalytic role of Tyr64, but not the method of its deprotonation. Our data indicate that an active water molecule in the active site of DddK plays an important role in the deprotonation of Tyr64 and that this is far more likely than coordination to the metal or His96. Sequence alignment and phylogenetic analysis suggest that the proposed catalytic mechanism of DddK has universal significance. Our results provide new mechanistic insights into DddK and enrich our understanding of DMS generation by SAR11 bacteria.IMPORTANCE The climate-active gas dimethyl sulfide (DMS) plays an important role in global sulfur cycling and atmospheric chemistry. DMS is mainly produced through the bacterial cleavage of marine dimethylsulfoniopropionate (DMSP). When released into the atmosphere from the oceans, DMS can be photochemically oxidized into DMSO or sulfate aerosols, which form cloud condensation nuclei that influence the reflectivity of clouds and, thereby, global temperature. SAR11 bacteria are the most abundant marine heterotrophic bacteria, and many of them contain DMSP lyase DddK to cleave DMSP, generating DMS. In this study, based on structural analyses and mutational assays, we revealed the catalytic mechanism of DddK, which has universal significance in SAR11 bacteria. This study provides new insights into the catalytic mechanism of DddK, leading to a better understanding of how SAR11 bacteria generate DMS.

Structural and Biochemical Insights into Dimethylsulfoniopropionate Cleavage by Cofactor-Bound DddK from the Prolific Marine Bacterium Pelagibacter.

Enormous amounts of the organic osmolyte dimethylsulfoniopropionate (DMSP) are produced in marine environments where bacterial DMSP lyases cleave it, yielding acrylate and the climate-active gas dimethyl sulfide (DMS). SAR11 bacteria are the most abundant clade of heterotrophic bacteria in the oceans and play a key role in DMSP catabolism. An important environmental factor affecting DMS generation via DMSP lyases is the availability of metal ions because they are essential cofactors for many of these enzymes. Here we examine the structure and activity of DddK in the presence of various metal ions. We have established that DddK containing a double-stranded β-helical motif utilizes various divalent metal ions as cofactors for catalytic activity. However, nickel, an abundant metal ion in marine environments, adopts a distorted octahedral coordination environment and conferred the highest DMSP lyase activity. Crystal structures of cofactor-bound DddK reveal key metal ion binding and catalytic residues and provide the first rationalization for varying activities with different metal ions. The structures of DddK along with site-directed mutagenesis and ultraviolet-visible studies are consistent with Tyr 64 acting as a base to initiate the β-elimination reaction of DMSP. Our biochemical and structural studies provide a detailed understanding of DMS generation by one of the ocean's most prolific bacteria.

Towards a revised climatology of summertime dimethylsulfide concentrations and sea–air fluxes in the Southern Ocean

Environmental context The trace gas dimethylsulfide (DMS) is emitted from surface ocean waters to the overlying atmosphere, where it forms aerosols that promote cloud formation and influence Earth’s climate. We present an updated climatology of DMS emissions from the vast Southern Ocean, demonstrating how the inclusion of new data yields higher regional sources compared with previously derived values. Our work provides an important step towards better quantifying the oceanic emissions of an important climate-active gas. Abstract The Southern Ocean is a dominant source of the climate-active gas dimethylsulfide (DMS) to the atmosphere. Despite significant improvements in data coverage over the past decade, the most recent global DMS climatology does not include a growing number of high-resolution surface measurements in Southern Ocean waters. Here, we incorporate these high resolution data (~700000 measurements) into an updated Southern Ocean climatology of summertime DMS concentrations and sea–air fluxes. Owing to sparse monthly data coverage, we derive a single summertime climatology based on December through February means. DMS frequency distributions and oceanographic properties (mixed-layer depth and chlorophyll-a) show good general coherence across these months, providing justification for the use of summertime mean values. The revised climatology shows notable differences with the existing global climatology. In particular, we find increased DMS concentrations and sea–air fluxes south of the Polar Frontal zone (between ~60 and 70°S), and increased sea–air fluxes in mid-latitude waters (40–50°S). These changes are attributable to both the inclusion of new data and the use of region-specific parameters (e.g. data cut-off thresholds and interpolation radius) in our objective analysis. DMS concentrations in the Southern Ocean exhibit weak though statistically significant correlations with several oceanographic variables, including ice cover, mixed-layer depth and chlorophyll-a, but no apparent relationship with satellite-derived measures of phytoplankton photophysiology or taxonomic group abundance. Our analysis highlights the importance of using regional parameters in constructing climatological DMS fields, and identifies regions where additional observations are most needed.

A remote sensing algorithm for planktonic dimethylsulfoniopropionate (DMSP) and an analysis of global patterns

Abstract Dimethylsulfoniopropionate (DMSP) is a ubiquitous phytoplankton metabolite and the main precursor of the climate-active gas dimethylsulfide (DMS) in the oceans' surface. Here we use total DMSP (DMSPt) and ancillary measurements from a global database to develop a remote sensing algorithm for DMSPt in the upper mixed layer (UML). Over 55% of total DMSPt variability (log10 scale) is explained by in situ chlorophyll a (Chl) after dividing the database into two subsets, according to “stratified” and “mixed” water column criteria, based on the ratio between euphotic layer depth (Zeu) and mixed layer depth (MLD). Up to 70% of the variability is explained when adding sea surface temperature (SST) and log10(Zeu/MLD) as predictors for the stratified and mixed subsets, respectively. Independent validation on satellite Chl match-ups indicates that the algorithm predicts DMSPt across three orders of magnitude with a root-mean-squared error spanning from 0.20 to 0.26 (log10 space) and mean absolute error typically around 45% (linear space). An additional submodel based on remotely sensed particulate inorganic carbon (PIC) is used to predict DMSPt in coccolithophore blooms if satellite Chl is not available. We use the algorithm to produce a monthly global DMSPt climatology, and estimate that DMSP synthesis amounts to 5–9% of oceanic phytoplankton gross carbon production. Our algorithm provides a new remote sensing tool for resolving temporal and spatial variations in DMSPt concentration, and represents a step forward toward improved diagnosis of contemporary DMS emission based on satellite Earth observation.

High concentrations and turnover rates of DMS, DMSP and DMSO in Antarctic sea ice

[1] The vast Antarctic sea-ice zone (SIZ) is a potentially significant source of the climate-active gas dimethylsulfide (DMS), yet few data are available on the concentrations and turnover rates of DMS and the related compounds dimethylsulfoniopropionate (DMSP) and dimethylsulfoxide (DMSO) in sea ice environments. Here we present new measurements characterizing the spatial variability of DMS, DMSP, and DMSO concentrations across the Antarctic SIZ, and results from tracer experiments quantifying the production rates of DMS from various sources. We observed extremely high concentrations (>200 nM) and turnover rates (>100 nM d−1) of DMS in sea-ice brines, indicating intense cycling of DMS/P/O. Our results demonstrate a previously unrecognized role for DMSO reduction as a major pathway of DMS production in Antarctic sea ice.

The analysis of dimethylsulfide and dimethylsulfoniopropionate in sea ice: Dry-crushing and melting using stable isotope additions

Sea ice is thought to be an important source of the climate-active gas dimethylsulfide (DMS), since extremely high concentrations of its precursor dimethylsulfoniopropionate (DMSP) have been found associated with high algal biomass. Accurate measurements of DMS and associated compounds in sea ice were until now not possible due to difficulties associated with the unavoidable melting process before analysis. Here we present and evaluate two methods to analyze DMS and DMSP in sea-ice cores accurately. The first, describes the dry-crushing method, which has its focus on the volatile compound DMS. A sub-sample of deeply frozen (<−30 °C) ice is crushed in a stainless steel vessel and the released gas phase is analyzed directly for DMS. The remaining ice is subsequently analyzed for its total DMSP content. With this method, DMS and DMSP profiles can be resolved even in ice cores stored deeply frozen for two years. The second method, involves a melting procedure, during which the conversion of compounds is monitored by adding differently deuterated isotopes of DMS and DMSP. Natural concentrations and stable isotopes of DMS and DMSP are simultaneously analyzed on a Proton-Transfer-Reaction Mass Spectrometer (PTR-MS). Loss and conversion rates of the artificial isotopes are used to reconstruct the original concentrations of DMS and DMSP in ice and give important information on potential dynamical processes in sea-ice communities. It is concluded that in stored cores, the dry-crushing method provides the best results when the aim of the study is to differentiate between DMS and DMSP. When direct processing and analysis of the samples is possible, the isotope-addition method has the potential of providing concentrations of all S-compounds, including dissolved and particulate fractions. Moreover, it is suitable for the determination of process rates within the S-cycle.

Analysis of sulfur‐related transcription by Roseobacter communities using a taxon‐specific functional gene microarray

The fraction of dissolved dimethylsulfoniopropionate (DMSPd) converted by marine bacterioplankton into the climate-active gas dimethylsulfide (DMS) varies widely in the ocean, with the factors that determine this value still largely unknown. One current hypothesis is that the ratio of DMS formation: DMSP demethylation is determined by DMSP availability, with 'availability' in both an absolute sense (i.e. concentration in seawater) and in a relative sense (i.e. proportionally to other labile organic S compounds) proposed as the critical factor. We investigated these models during an experimentally induced phytoplankton bloom using a taxon-specific microarray targeting DMSP-related gene transcription in members of the Roseobacter clade, a group hypothesized to play an important role in the surface ocean sulfur cycle and well represented by genome sequences. The array consisted of 1578 probes to 431 genes and was designed to target diverse Roseobacter communities in natural seawater by using hierarchical probe design based on 13 genome sequences. The prevailing pattern of Roseobacter gene transcription showed relative depletion of DMSP-related transcripts during the peak of the bloom, despite increasing absolute concentrations and flux of DMSP-related compounds. DMSPd thus appeared to be assimilated by Roseobacter populations in proportion to its relative abundance in the organic matter pool (the 'relative sense' hypothesis), rather than assimilated in preference to other labile organic sulfur or carbon compounds produced during the bloom. The relative investment of the Roseobacter community in DMSP demethylation was not useful for predicting the formation of DMS, however, suggesting a complex regulatory process that may involve multiple taxa and alternative fates of DMSPd.

Transcriptomic analysis of a marine bacterial community enriched with dimethylsulfoniopropionate

Dimethylsulfoniopropionate (DMSP) is an important source of reduced sulfur and carbon for marine microbial communities, as well as the precursor of the climate-active gas dimethylsulfide (DMS). In this study, we used metatranscriptomic sequencing to analyze gene expression profiles of a bacterial assemblage from surface waters at the Bermuda Atlantic Time-series Study (BATS) station with and without a short-term enrichment of DMSP (25 nM for 30 min). An average of 303 143 reads were obtained per treatment using 454 pyrosequencing technology, of which 51% were potential protein-encoding sequences. Transcripts from Gammaproteobacteria and Bacteroidetes increased in relative abundance on DMSP addition, yet there was little change in the contribution of two bacterioplankton groups whose cultured members harbor known DMSP degradation genes, Roseobacter and SAR11. The DMSP addition led to an enrichment of transcripts supporting heterotrophic activity, and a depletion of those encoding light-related energy generation. Genes for the degradation of C3 compounds were significantly overrepresented after DMSP addition, likely reflecting the metabolism of the C3 component of DMSP. Mapping these transcripts to known biochemical pathways indicated that both acetyl-CoA and succinyl-CoA may be common entry points of this moiety into the tricarboxylic acid cycle. In a short time frame (30 min) in the extremely oligotrophic Sargasso Sea, different gene expression patterns suggest the use of DMSP by a diversity of marine bacterioplankton as both carbon and sulfur sources.

Iron-induced alterations of bacterial DMSP metabolism in the western subarctic Pacific during SEEDS-II

Abstract The effect of added iron on bacterial cycling of the climate-active gas dimethylsulfide (DMS) and its precursor dimethylsulfoniopropionate (DMSP) was tested during the second Subarctic Pacific Iron Experiment for Ecosystem Dynamics Study (SEEDS II) from 19 July to 21 August 2004 aboard the R/V Hakuho-Maru. The study area in the northwest Pacific Ocean (48°N 165°E) was enriched with Fe and the conservative tracer, SF6, allowing the fertilized patch to be tracked. Microbial DMSP cycling rates were determined in the surface mixed layer (5 m) during incubations using the 35S-DMSP technique. The addition of iron resulted in a 4-fold increase in concentrations of chlorophyll a (chl a) within the surface mixed layer (5 m depth), and the length of the sampling period allowed the observation of both bloom and post-bloom conditions. Inside the fertilized patch, the alleviation of resource limitation gave rise to the concurrent increase in bacterial abundance and production. Changes in the phytoplankton community within the Fe-enriched patch translated into a sustained decrease in chl a-normalized particulate DMSP (DMSPp) concentrations, suggesting a preferential stimulation of the growth of DMSPp-poor phytoplankton species. Despite short-lived peaks of DMSPp within the Fe-enriched area, concentrations of DMSPp generally remained stable during the entire sampling period inside and outside the fertilized patch. During the Fe-induced bloom, microbial DMSP-sulfur (DMSP-S) assimilation efficiency increased 2.6-fold inside the Fe-enriched area, which indicated that as bacterial production increased, a greater proportion of DMSP-S was assimilated and possibly diverted away from the bacterial cleavage pathway (i.e. production of DMS). Our results suggest that iron-induced stimulation of weak DMSPp-producers and DMSP-assimilating bacteria may diminish the potential production of DMS and thus limit its flux towards the atmosphere over the subarctic Pacific Ocean.

Abundant and diverse bacteria involved in DMSP degradation in marine surface waters

An expanded analysis of oceanic metagenomic data indicates that the majority of prokaryotic cells in marine surface waters have the genetic capability to demethylate dimethylsulfoniopropionate (DMSP). The 1701 homologues of the DMSP demethylase gene, dmdA, identified in the (2007) Global Ocean Sampling (GOS) metagenome, are sufficient for 58% (+/-9%) of sampled cells to participate in this critical step in the marine sulfur cycle. This remarkable frequency of DMSP-demethylating cells is in accordance with biogeochemical data indicating that marine phytoplankton direct up to 10% of fixed carbon to DMSP synthesis, and that most of this DMSP is subsequently degraded by bacteria via demethylation. The GOS metagenomic data also revealed a new cluster of dmdA sequences (designated Clade E) that implicates marine gammaproteobacteria in DMSP demethylation, along with previously recognized alphaproteobacterial groups Roseobacter and SAR11. Analyses of G+C content and gene order indicate that lateral gene transfer is likely responsible for the wide distribution of dmdA among diverse taxa, contributing to the homogenization of biogeochemical roles among heterotrophic marine bacterioplankton. Candidate genes for the competing bacterial degradation process that converts DMSP to the climate-active gas dimethylsulfide (DMS) (dddD and dddL) occur infrequently in the (2007) GOS metagenome, suggesting either that the key DMS-producing bacterial genes are yet to be identified or that DMS formation by free-living bacterioplankton is insignificant relative to their demethylation activity.