Evolution of Dimethylsulfoniopropionate Metabolism in Marine Phytoplankton and Bacteria

Genomic analysis of Alteromonas sp. M12 isolated from the Mariana Trench reveals its role in dimethylsulfoniopropionate cycling

Dimethylsulfoniopropionate (DMSP) is a ubiquitous organosulfur molecule in marine environments with important roles in stress tolerance, global carbon and sulfur cycling, and chemotaxis. It is the main precursor of the climate active gas dimethyl sulfide (DMS), which is the greatest natural source of bio‑sulfur transferred from ocean to atmosphere. Alteromonas sp. M12, a Gram-negative and aerobic bacterium, was isolated from the seawater samples collected from the Mariana Trench at the depth of 2500 m. Here, we report the complete genome sequence of strain M12 and its genomic characteristics to import and utilize DMSP. The genome of strain M12 contains one circular chromosome (5,012,782 bp) with the GC content of 40.88%. Alteromonas sp. M12 can grow with DMSP as a sole carbon source, and produced DMS with DMSP as a precursor. Genomic analysis showed that strain M12 contained a set of genes involved in the downstream steps of DMSP cleavage, but no known genes encoding DMSP transporters or DMSP lyases. The results indicated that this strain contained novel DMSP transport and cleavage genes in its genome which warrants further investigation. The import of DMSP into cells may be a strategy of strain M12 to adapt the hydrostatic pressure environment in the Mariana Trench, as DMSP can be used as a hydrostatic pressure protectant. This study sheds light on the catabolism of DMSP by deep-sea bacteria.

Morphology, behavior, and phylogenomics of Oxytoxum lohmannii, Dinoflagellata

Dinoflagellates are an abundant and diverse group of protists representing a wealth of unique biology and ecology. While many dinoflagellates are photosynthetic or mixotrophic, many taxa are heterotrophs, often with complex feeding strategies. Compared to their photosynthetic counterparts, heterotrophic dinoflagellates remain understudied, as they are difficult to culture. One exception, a long-cultured isolate originally classified as Amphidinium but recently reclassified as Oxytoxum, has been the subject of a number of feeding, growth, and chemosensory studies. This lineage was recently determined to be closely related to Prorocentrum using phylogenetics of ribosomal RNA gene sequences, but the exact nature of this relationship remains unresolved. Using transcriptomes sequenced from culture and three single cells from the environment, we produce a robust phylogeny of 242 genes, revealing Oxytoxum is likely sister to the Prorocentrum clade, rather than nested within it. Molecular investigations uncover evidence of a reduced, nonphotosynthetic plastid and proteorhodopsin, a photoactive proton pump acquired horizontally from bacteria. We describe the ultrastructure of O. lohmannii, including densely packed trichocysts, and a new type of mucocyst. We observe that O. lohmannii feeds preferentially on cryptophytes using myzocytosis, but can also feed on various phytoflagellates using conventional phagocytosis. O. lohmannii is amenable to culture, providing an opportunity to better study heterotrophic dinoflagellate biology and feeding ecology.

Microbial community diversity from nearshore to offshore in the East China Sea

The Pollution Nagasaki (PN) section of the East China Sea (ECS) is a typical area for studying the complex hydrographic dynamics between Changjiang River discharge and Kuroshio, displaying intense variations of environmental gradients from nearshore to offshore. However, the temporal and spatial changes of microbial communities along the PN section have long been overlooked. In this study, we performed a comprehensive investigation into the abundance, diversity and ecology of free-living (FL) and particle-associated (PA) microbial communities in seawater samples along the PN section during both summer and winter. Distinct hydrological conditions and resulting environmental gradients were observed between summer and winter, with clear features of intrusive Kuroshio subsurface water in summer and strong vertical mixing of seawater in winter. Bacterial abundance along the PN section was higher in summer (1.11 × 108 copies·L-1 - 7.37 × 108 copies·L-1) than in winter (1.83 × 106 copies·L-1 - 1.34 × 108 copies·L-1). Microbial diversity, as indicated by α-diversity indices, remained at relatively stable levels in summer, while a clear decreasing trend was observed in winter along the PN section. Additionally, the winter communities exhibited a more evident spatial shift along the PN section compared to the summer communities. 16S rRNA gene amplicon sequencing showed that microbial community composition varied considerably between different seasons (summer and winter) and lifestyles (FL and PA), with a notable dominance of Ralstonia species. in winter. Regarding the assembly of microbial communities, the stochastic process represented by dispersal limitation was the dominant process in summer, while the deterministic homogeneous selection was the most important process in winter. Correspondingly, distinct topological properties of the microbial co-occurrence networks were shown between different seasons and along the PN section. These results enhance our understanding of how hydrological conditions influence dynamic changes of microbial communities along the PN section, providing new insights for the microbial community assembly and interactions in such a complex environment.

Microbiome composition and function within the Kellet's whelk perivitelline fluid

Microbiomes have gained significant attention in ecological research, owing to their diverse interactions and essential roles within different organismal ecosystems. Microorganisms, such as bacteria, archaea, and viruses, have profound impact on host health, influencing digestion, metabolism, immune function, tissue development, and behavior. This study investigates the microbiome diversity and function of Kellet's whelk (Kelletia kelletii) perivitelline fluid (PVF), which sustains thousands of developing K. kelletii embryos within a polysaccharide and protein matrix. Our core microbiome analysis reveals a diverse range of bacteria, with the Roseobacter genus being the most abundant. Additionally, genes related to host-microbe interactions, symbiosis, and quorum sensing were detected, indicating a potential symbiotic relationship between the microbiome and Kellet's whelk embryos. Furthermore, the microbiome exhibits gene expression related to antibiotic biosynthesis, suggesting a defensive role against pathogenic bacteria and potential discovery of novel antibiotics. Overall, this study sheds light on the microbiome's role in Kellet's whelk development, emphasizing the significance of host-microbe interactions in vulnerable life history stages. To our knowledge, ours is the first study to use 16S sequencing coupled with RNA sequencing (RNA-seq) to profile the microbiome of an invertebrate PVF.IMPORTANCEThis study provides novel insight to an encapsulated system with strong evidence of symbiosis between the microbial inhabitants and developing host embryos. The Kellet's whelk perivitelline fluid (PVF) contains microbial organisms of interest that may be providing symbiotic functions and potential antimicrobial properties during this vulnerable life history stage. This study, the first to utilize a comprehensive approach to investigating Kellet's whelk PVF microbiome, couples 16S rRNA gene long-read sequencing with RNA-seq. This research contributes to and expands our knowledge on the roles of beneficial host-associated microbes.

Quorum Sensing Regulates the Production of Methanethiol in Vibrio harveyi

Methanethiol (MeSH) and dimethyl sulfide (DMS) are important volatile organic sulfur compounds involved in atmospheric chemistry and climate regulation. However, little is known about the metabolism of these compounds in the ubiquitous marine vibrios. Here, we investigated MeSH/DMS production and whether these processes were regulated by quorum-sensing (QS) systems in Vibrio harveyi BB120. V. harveyi BB120 exhibited strong MeSH production from methionine (Met) (465 nmol mg total protein-1) and weak DMS production from dimethylsulfoniopropionate (DMSP) cleavage. The homologs of MegL responsible for MeSH production from L-Met widely existed in vibrio genomes. Using BB120 and its nine QS mutants, we found that the MeSH production was regulated by HAI-1, AI-2 and CAI-1 QS pathways, as well as the luxO gene located in the center of this QS cascade. The regulation role of HAI-1 and AI-2 QS systems in MeSH production was further confirmed by applying quorum-quenching enzyme MomL and exogenous autoinducer AI-2. By contrast, the DMS production from DMSP cleavage showed no significant difference between BB120 and its QS mutants. Such QS-regulated MeSH production may help to remove excess Met that can be harmful for vibrio growth. These results emphasize the importance of QS systems and the MeSH production process in vibrios.

Abundant production of dimethylsulfoniopropionate as a cryoprotectant by freshwater phytoplanktonic dinoflagellates in ice-covered Lake Baikal

Phytoplanktonic dinoflagellates form colonies between vertical ice crystals during the ice-melting season in Lake Baikal, but how the plankton survive the freezing conditions is not known. Here we show that the phytoplankton produces large amounts of dimethylsulfoniopropionate (DMSP), which is best-known as a marine compound. Lake-water DMSP concentrations in the spring season are comparable with those in the oceans, and colony water in ice exhibits extremely high concentrations. DMSP concentration of surface water correlates with plankton density and reaches a maximum in mid-April, with temperature-dependent fluctuations. DMSP is released from plankton cells into water in warm days. DMSP is a characteristic osmolyte of marine algae; our results demonstrate that freshwater plankton, Gymnodinium baicalense, has DMSP-producing ability, and efficiently uses the limited sulfur resource (only 1/500 of sea sulfate) to survive in freshwater ice. Plankton in Lake Baikal do not need an osmolyte, and our results clearly indicate that DMSP plays a cryoprotective role. DMSP, although a characteristic marine compound, could also be an important zwitterion for algae of other boreal lakes, alpine snow, and glaciers.

Bacterial networks in Atlantic salmon with Piscirickettsiosis

An unbalanced composition of gut microbiota in fish is hypothesized to play a role in promoting bacterial infections, but the synergistic or antagonistic interactions between bacterial groups in relation to fish health are not well understood. We report that pathogenic species in the Piscirickettsia, Aeromonas, Renibacterium and Tenacibaculum genera were all detected in the digesta and gut mucosa of healthy Atlantic salmon without clinical signs of disease. Although Piscirickettsia salmonis (and other pathogens) occurred in greater frequencies of fish with clinical Salmonid Rickettsial Septicemia (SRS), the relative abundance was about the same as that observed in healthy fish. Remarkably, the SRS-positive fish presented with a generalized mid-gut dysbiosis and positive growth associations between Piscirickettsiaceae and members of other taxonomic families containing known pathogens. The reconstruction of metabolic phenotypes based on the bacterial networks detected in the gut and mucosa indicated the synthesis of Gram-negative virulence factors such as colanic acid and O-antigen were over-represented in SRS positive fish. This evidence indicates that cooperative interactions between organisms of different taxonomic families within localized bacterial networks might promote an opportunity for P. salmonis to cause clinical SRS in the farm environment.

Phylogeny and biogeography of the algal DMS-releasing enzyme in the global ocean

Phytoplankton produce the volatile dimethyl sulfide (DMS), an important infochemical mediating microbial interactions, which is also emitted to the atmosphere and affecting the global climate. Albeit the enzymatic source for DMS in eukaryotes was elucidated, namely a DMSP lyase (DL) called Alma1, we still lack basic knowledge regarding its taxonomic distribution. We defined unique sequence motifs which enable the identification of DL homologs (DLHs) in model systems and environmental populations. We used these motifs to predict DLHs in diverse algae by analyzing hundreds of genomic and transcriptomic sequences from model systems under stress conditions and from environmental samples. Our findings show that the DL enzyme is more taxonomically widespread than previously thought, as it is encoded by known algal taxa as haptophytes and dinoflagellates, but also by chlorophytes, pelagophytes and diatoms, which were conventionally considered to lack the DL enzyme. By exploring the Tara Oceans database, we showed that DLHs are widespread across the oceans and are predominantly expressed by dinoflagellates. Certain dinoflagellate DLHs were differentially expressed between the euphotic and mesopelagic zones, suggesting a functional specialization and an involvement in the metabolic plasticity of mixotrophic dinoflagellates. In specific regions as the Southern Ocean, DLH expression by haptophytes and diatoms was correlated with environmental drivers such as nutrient availability. The expanded repertoire of putative DL enzymes from diverse microbial origins and geographic niches suggests new potential players in the marine sulfur cycle and provides a foundation to study the cellular function of the DL enzyme in marine microbes.

Molecular discoveries in microbial DMSP synthesis

Dimethylsulfoniopropionate (DMSP) is one of the Earth's most abundant organosulfur compounds because many marine algae, bacteria, corals and some plants produce it to high mM intracellular concentrations. In these organisms, DMSP acts an anti-stress molecule with purported roles to protect against salinity, temperature, oxidative stress and hydrostatic pressure, amongst many other reported functions. However, DMSP is best known for being a major precursor of the climate-active gases and signalling molecules dimethylsulfide (DMS), methanethiol (MeSH) and, potentially, methane, through microbial DMSP catabolism. DMSP catabolism has been extensively studied and the microbes, pathways and enzymes involved have largely been elucidated through the application of molecular research over the last 17 years. In contrast, the molecular biology of DMSP synthesis is a much newer field, with the first DMSP synthesis enzymes only being identified in the last 5 years. In this review, we discuss how the elucidation of key DMSP synthesis enzymes has greatly expanded our knowledge of the diversity of DMSP-producing organisms, the pathways used, and what environmental factors regulate production, as well as to inform on the physiological roles of DMSP. Importantly, the identification of key DMSP synthesis enzymes in the major groups of DMSP producers has allowed scientists to study the distribution and predict the importance of different DMSP-producing organisms to global DMSP production in diverse marine and sediment environments. Finally, we highlight key challenges for future molecular research into DMSP synthesis that need addressing to better understand the cycling of this important marine organosulfur compound, and its magnitude in the environment.

A bacterial symbiont in the gill of the marine scallop Argopecten irradians irradians metabolizes dimethylsulfoniopropionate

Microbial lysis of dimethylsulfoniopropionate (DMSP) is a key step in marine organic sulfur cycling and has been recently demonstrated to play an important role in mediating interactions between bacteria, algae, and zooplankton. To date, microbes that have been found to lyse DMSP are largely confined to free-living and surface-attached bacteria. In this study, we report for the first time that a symbiont (termed "Rhodobiaceae bacterium HWgs001") in the gill of the marine scallop Argopecten irradians irradians can lyse and metabolize DMSP. Analysis of 16S rRNA gene sequences suggested that HWgs001 accounted for up to 93% of the gill microbiota. Microscopic observations suggested that HWgs001 lived within the gill tissue. Unlike symbionts of other bivalves, HWgs001 belongs to Alphaproteobacteria rather than Gammaproteobacteria, and no genes for carbon fixation were identified in its small genome. Moreover, HWgs001 was found to possess a dddP gene, responsible for the lysis of DMSP to acrylate. The enzymatic activity of dddP was confirmed using the heterologous expression, and in situ transcription of the gene in scallop gill tissues was demonstrated using reverse-transcription PCR. Together, these results revealed a taxonomically and functionally unique symbiont, which represents the first-documented DMSP-metabolizing symbiont likely to play significant roles in coastal marine ecosystems.

Light stress induced DMS(P) production in Skeletonema costatum: An experimental approach and field observation

Dimethylsulphide is a dominant biogenic sulphur anti-greenhouse gas produced by marine phytoplankton. A non-axenic culture of Skeletonema costatum was studied to comprehend the effects of different growth stages and light stress on DMSP/DMS production. The intracellular DMSP concentration increased during late exponential to mid-stationary phase and attained a maximum (0.59 pg S cell^-1) during the stationary phase, indicating more contribution from actively dividing smaller cells. Likewise, exposure to first light after a 12-hour dark phase caused stress, invariably leading to elevated levels of DMS (~9 fold). These observations were upheld by additional laboratory and field experiments, and a field time-series observation, which recorded higher DMS concentrations during exposure to first light after a dark cycle and during early mornings, respectively. While our study depicts the variable DMSP and DMS concentrations during different growth stages of S. costatum, it gives new information on the effect of light stress on DMS production.

Impact of the Dimethyl Sulfoxide Reductase Superfamily on the Evolution of Biogeochemical Cycles

The dimethyl sulfoxide reductase (or MopB) family is a diverse assemblage of enzymes found throughout Bacteria and Archaea. Many of these enzymes are believed to have been present in the last universal common ancestor (LUCA) of all cellular lineages. However, gaps in knowledge remain about how MopB enzymes evolved and how this diversification of functions impacted global biogeochemical cycles through geologic time. In this study, we perform maximum likelihood phylogenetic analyses on manually curated comparative genomic and metagenomic data sets containing over 47,000 distinct MopB homologs. We demonstrate that these enzymes constitute a catalytically and mechanistically diverse superfamily defined not by the molybdopterin- or tungstopterin-containing [molybdopterin or tungstopterin bis(pyranopterin guanine dinucleotide) (Mo/W-bisPGD)] cofactor but rather by the structural fold that binds it in the protein. Our results suggest that major metabolic innovations were the result of the loss of the metal cofactor or the gain or loss of protein domains. Phylogenetic analyses also demonstrated that formate oxidation and CO2 reduction were the ancestral functions of the superfamily, traits that have been vertically inherited from the LUCA. Nearly all of the other families, which drive all other biogeochemical cycles mediated by this superfamily, originated in the bacterial domain. Thus, organisms from Bacteria have been the key drivers of catalytic and biogeochemical innovations within the superfamily. The relative ordination of MopB families and their associated catalytic activities emphasize fundamental mechanisms of evolution in this superfamily. Furthermore, it underscores the importance of prokaryotic adaptability in response to the transition from an anoxic to an oxidized atmosphere. IMPORTANCE The MopB superfamily constitutes a repertoire of metalloenzymes that are central to enduring mysteries in microbiology, from the origin of life and how microorganisms and biogeochemical cycles have coevolved over deep time to how anaerobic life adapted to increasing concentrations of O2 during the transition from an anoxic to an oxic world. Our work emphasizes that phylogenetic analyses can reveal how domain gain or loss events, the acquisition of novel partner subunits, and the loss of metal cofactors can stimulate novel radiations of enzymes that dramatically increase the catalytic versatility of superfamilies. We also contend that the superfamily concept in protein evolution can uncover surprising kinships between enzymes that have remarkably different catalytic and physiological functions.

Characterization of a bloom-associated alphaproteobacterial lineage, 'Candidatus Phycosocius': insights into freshwater algal-bacterial interactions

Marine bacterial lineages associated with algal blooms, such as the Roseobacter clade, have been well characterized in ecological and genomic contexts, yet such lineages have rarely been explored in freshwater blooms. This study performed phenotypic and genomic analyses of an alphaproteobacterial lineage 'Candidatus Phycosocius' (denoted the CaP clade), one of the few lineages ubiquitously associated with freshwater algal blooms, and described a novel species: 'Ca. Phycosocius spiralis.' Phylogenomic analyses indicated that the CaP clade is a deeply branching lineage in the Caulobacterales. Pangenome analyses revealed characteristic features of the CaP clade: aerobic anoxygenic photosynthesis and essential vitamin B auxotrophy. Genome size varies widely among members of the CaP clade (2.5-3.7 Mb), likely a result of independent genome reductions at each lineage. This includes a loss of tight adherence pilus genes (tad) in 'Ca. P. spiralis' that may reflect its adoption of a unique spiral cell shape and corkscrew-like burrowing activity at the algal surface. Notably, quorum sensing (QS) proteins showed incongruent phylogenies, suggesting that horizontal transfers of QS genes and QS-involved interactions with specific algal partners might drive CaP clade diversification. This study elucidates the ecophysiology and evolution of proteobacteria associated with freshwater algal blooms.

Oleaginous Heterotrophic Dinoflagellates—Crypthecodiniaceae

The heterotrophic Crypthecodinium cohnii is a major model for dinoflagellate cell biology, and a major industrial producer of docosahexaenoic acid, a key nutraceutical and added pharmaceutical compound. Despite these factors, the family Crypthecodiniaceae is not fully described, which is partly attributable to their degenerative thecal plates, as well as the lack of ribotype-referred morphological description in many taxons. We report here significant genetic distances and phylogenetic cladding that support inter-specific variations within the Crypthecodiniaceae. We describe Crypthecodinium croucheri sp. nov. Kwok, Law and Wong, that have different genome sizes, ribotypes, and amplification fragment length polymorphism profiles when compared to the C. cohnii. The interspecific ribotypes were supported by distinctive truncation-insertion at the ITS regions that were conserved at intraspecific level. The long genetic distances between Crypthecodiniaceae and other dinoflagellate orders support the separation of the group, which includes related taxons with high oil content and degenerative thecal plates, to be ratified to the order level. The current study provides the basis for future specific demarcation-differentiation, which is an important facet in food safety, biosecurity, sustainable agriculture feeds, and biotechnology licensing of new oleaginous models.

Highly active bacterial DMSP metabolism in the surface microlayer of the eastern China marginal seas

The microbial cycling of dimethylsulfoniopropionate (DMSP) and the resulting gaseous catabolites dimethylsulfide (DMS) or methylmercaptan (MeSH) play key roles in the global sulfur cycle and potentially climate regulation. As the ocean-atmosphere boundary, the sea surface microlayer (SML) is important for the generation and emission of DMS and MeSH. However, understanding of the microbial DMSP metabolism remains limited in the SML. Here, we studied the spatiotemporal differences for DMS/DMSP, bacterial community structure and the key bacterial DMSP metabolic genes between SML and subsurface seawater (SSW) samples in the eastern China marginal seas (the East China Sea and Yellow Sea). In general, DMSP_d and DMSP_t concentrations, and the abundance of total, free-living and particle-associated bacteria were higher in SML than that in SSW. DMSP synthesis (~7.81-fold for dsyB, ~2.93-fold for mmtN) and degradation genes (~5.38-fold for dmdA, ~6.27-fold for dddP) detected in SML were more abundant compared with SSW samples. Free-living bacteria were the main DMSP producers and consumers in eastern Chinese marginal sea. Regionally, the bacterial community structure was distinct between the East China Sea and the Yellow Sea. The abundance of DMSP metabolic genes (dsyB, dmdA, and dddP) and genera in the East China Sea were higher than those of the Yellow Sea. Seasonally, DMSP/DMS level and DMSP metabolic genes and bacteria were more abundant in SML of the East China Sea in summer than in spring. Different from those in spring, Ruegeria was the dominant DMSP metabolic bacteria. In conclusion, the DMSP synthesis and degradation showed significant spatiotemporal differences in the SML of the eastern China marginal seas, and were consistently more active in the SML than in the SSW.

Oxidative Stress Regulates a Pivotal Metabolic Switch in Dimethylsulfoniopropionate Degradation by the Marine Bacterium Ruegeria pomeroyi

Dimethylsulfoniopropionate (DMSP) is an abundant organic compound in marine surface water and source of dimethyl sulfide (DMS), the largest natural sulfur source to the upper atmosphere. Marine bacteria either mineralize DMSP through the demethylation pathway or transform it to DMS through the cleavage pathway. Factors that regulate which pathway is utilized are not fully understood. In chemostat experiments, the marine Roseobacter Ruegeria pomeroyi DSS-3 was exposed to oxidative stress either during growth with H2O2 or by mutation of the gene encoding catalase. Oxidative stress reduced expression of the genes in the demethylation pathway and increased expression of those encoding the cleavage pathway. These results are contrary to the sulfur demand hypothesis, which theorizes that DMSP metabolism is driven by sulfur requirements of bacterial cells. Instead, we find strong evidence consistent with oxidative stress control over the switch in DMSP metabolism from demethylation to DMS production in an ecologically relevant marine bacterium. IMPORTANCE Dimethylsulfoniopropionate (DMSP) is the most abundant low-molecular-weight organic compound in marine surface water and source of dimethyl sulfide (DMS), a climatically active gas that connects the marine and terrestrial sulfur cycles. Marine bacteria are the major DMSP consumers, either generating DMS or consuming DMSP as a source of reduced carbon and sulfur. However, the factors regulating the DMSP catabolism in bacteria are not well understood. Marine bacteria are also exposed to oxidative stress. RNA sequencing (RNA-seq) experiments showed that oxidative stress induced in the laboratory reduced expression of the genes encoding the consumption of DMSP via the demethylation pathway and increased the expression of genes encoding DMS production via the cleavage pathway in the marine bacterium Ruegeria pomeroyi. These results support a model where DMS production in the ocean is regulated in part by oxidative stress.

Dynamic Diatom-Bacteria Consortia in Synthetic Plankton Communities

Microalgae that form phytoplankton live and die in a complex microbial consortium in which they co-exist with bacteria and other microorganisms. The dynamics of species succession in the plankton depends on the interplay of these partners. Bacteria utilize substrates produced by the phototrophic algae, while algal growth can be supported by bacterial exudates. Bacteria might also use chemical mediators with algicidal properties to attack algae. To elucidate whether specific bacteria play universal or context-specific roles in the interaction with phytoplankton, we investigated the effect of cocultured bacteria on the growth of 8 microalgae. An interaction matrix revealed that the function of a given bacterium is highly dependent on the cocultured partner. We observed no universally algicidal or universally growth-promoting bacteria. The activity of bacteria can even change during the aging of an algal culture from inhibitory to stimulatory or vice versa. We further established a synthetic phytoplankton/bacteria community with the centric diatom, Coscinodiscus radiatus, and 4 phylogenetically distinctive bacterial isolates, Mameliella sp., Roseovarius sp., Croceibacter sp., and Marinobacter sp. Supported by a Lotka-Volterra model, we show that interactions within the consortium are specific and that the sum of the pairwise interactions can explain algal and bacterial growth in the community. No synergistic effects between bacteria in the presence of the diatom was observed. Our survey documents highly species-specific interactions that are dependent on algal fitness, bacterial metabolism, and community composition. This species specificity may underly the high complexity of the multi-species plankton communities observed in nature. IMPORTANCE The marine food web is fueled by phototrophic phytoplankton. These algae are central primary producers responsible for the fixation of ca. 40% of the global CO2. Phytoplankton always co-occur with a diverse bacterial community in nature. This diversity suggests the existence of ecological niches for the associated bacteria. We show that the interaction between algae and bacteria is highly species-specific. Furthermore, both, the fitness stage of the algae and the community composition are relevant in determining the effect of bacteria on algal growth. We conclude that bacteria should not be sorted into algicidal or growth supporting categories; instead, a context-specific function of the bacteria in the plankton must be considered. This functional diversity of single players within a consortium may underly the observed diversity in the plankton.

A central arctic extreme aerosol event triggered by a warm air-mass intrusion

Frequency and intensity of warm and moist air-mass intrusions into the Arctic have increased over the past decades and have been related to sea ice melt. During our year-long expedition in the remote central Arctic Ocean, a record-breaking increase in temperature, moisture and downwelling-longwave radiation was observed in mid-April 2020, during an air-mass intrusion carrying air pollutants from northern Eurasia. The two-day intrusion, caused drastic changes in the aerosol size distribution, chemical composition and particle hygroscopicity. Here we show how the intrusion transformed the Arctic from a remote low-particle environment to an area comparable to a central-European urban setting. Additionally, the intrusion resulted in an explosive increase in cloud condensation nuclei, which can have direct effects on Arctic clouds' radiation, their precipitation patterns, and their lifetime. Thus, unless prompt actions to significantly reduce emissions in the source regions are taken, such intrusion events are expected to continue to affect the Arctic climate.

Phytoplankton Sources and Sinks of Dimethylsulphoniopropionate (DMSP) in Temperate Coastal Waters of Australia

The ecologically important organic sulfur compound, dimethylsulfoniopropionate (DMSP), is ubiquitous in marine environments. Produced by some species of phytoplankton and bacteria, it plays a key role in cellular responses to environmental change. Recently, uptake of DMSP by non-DMSP-producing phytoplankton species has been demonstrated, highlighting knowledge gaps concerning DMSP distribution through the marine microbial food web. In this study, we traced the uptake and distribution of DMSP through a natural marine microbial community collected from off the eastern coastline Australia. We found a diverse phytoplankton community representing six major taxonomic groups and conducted DMSP-enrichment experiments both on the whole community, and the community separated into large (≥8.0 µm), medium (3.0−8.0 µm), and small (0.2−3.0 µm) size fractions. Our results revealed active uptake of DMSP in all three size fractions of the community, with the largest fraction (>8 µm) forming the major DMSP sink, where enrichment resulted in an increase of DMSPp by 144%. We observed evidence for DMSP catabolism in all size fractions with DMSP enrichment, highlighting loss from the system via MeSH or DMS production. Based on taxonomic diversity, we postulate the sources of DMSP were the dinoflagellates, Phaeocystis sp., and Trichodesmium sp., which were present in a relatively high abundance, and the sinks for DMSP were the diatoms and picoeucaryotes in this temperate community. These findings corroborate the role of hitherto disregarded phytoplankton taxa as potentially important players in the cycling of DMSP in coastal waters of Australia and emphasize the need to better understand the fate of accumulated DMSP and its significance in cellular metabolism of non-DMSP producers.

Organic matter availability drives the spatial variation in the community composition and activity of Antarctic marine bacterioplankton

Carbon cycling by Antarctic microbial plankton is poorly understood but it plays a major role in CO₂ sequestration in the Southern Ocean. We investigated the summer bacterioplankton community in the largely understudied Weddell Sea, applying Illumina amplicon sequencing, measurements of bacterial production and chemical analyses of organic matter. The results revealed that the patchy distribution of productive coastal polynyas and less productive, mostly ice-covered sites was the major driver of the spatial changes in the taxonomic composition and activity of bacterioplankton. Gradients in organic matter availability induced by phytoplankton blooms were reflected in the concentrations and composition of dissolved carbohydrates and proteins. Bacterial production at bloom stations was, on average, 2.7 times higher than at less productive sites. Abundant bloom-responsive lineages were predominately affiliated with ubiquitous marine taxa, including Polaribacter, Yoonia-Loktanella, Sulfitobacter, the SAR92 clade, and Ulvibacter, suggesting a widespread genetic potential for adaptation to sub-zero seawater temperatures. A co-occurrence network analysis showed that dominant taxa at stations with low phytoplankton productivity were highly connected, indicating beneficial interactions. Overall, our study demonstrates that heterotrophic bacterial communities along Weddell Sea ice shelves were primarily constrained by the availability of labile organic matter rather than low seawater temperature. This article is protected by copyright. All rights reserved.

Recent insights into oceanic dimethylsulfoniopropionate biosynthesis and catabolism

Dimethylsulfoniopropionate (DMSP), a globally important organosulfur compound is produced in prodigious amounts (2.0 Pg sulfur) annually in the marine environment by phytoplankton, macroalgae, heterotrophic bacteria, some corals and certain higher plants. It is an important marine osmolyte and a major precursor molecule for the production of climate-active volatile gas dimethyl sulfide (DMS). DMSP synthesis take place via three pathways: a transamination 'pathway-' in some marine bacteria and algae, a Met-methylation 'pathway-' in angiosperms and bacteria and a decarboxylation 'pathway-' in the dinoflagellate, Crypthecodinium. The enzymes DSYB and TpMMT are involved in the DMSP biosynthesis in eukaryotes while marine heterotrophic bacteria engage key enzymes such as DsyB and MmtN. Several marine bacterial communities import DMSP and degrade it via cleavage or demethylation pathways or oxidation pathway, thereby generating DMS, methanethiol, and dimethylsulfoxonium propionate, respectively. DMSP is cleaved through diverse DMSP lyase enzymes in bacteria and via Alma1 enzyme in phytoplankton. The demethylation pathway involves four different enzymes, namely DmdA, DmdB, DmdC and DmdD/AcuH. However, enzymes involved in the oxidation pathway have not been yet identified. We reviewed the recent advances on the synthesis and catabolism of DMSP and enzymes that are involved in these processes.

Biochemical Mapping of Pyrodinium bahamense Unveils Molecular Underpinnings behind Organismal Processes

Proteins, lipids, and carbohydrates from the harmful algal bloom (HAB)-causing organism Pyrodinium bahamense were characterized to obtain insights into the biochemical processes in this environmentally relevant dinoflagellate. Shotgun proteomics using label-free quantitation followed by proteome mapping using the P. bahamense transcriptome and translated protein databases of Marinovum algicola, Alexandrium sp., Cylindrospermopsis raciborskii, and Symbiodinium kawagutii for annotation enabled the characterization of the proteins in P. bahamense. The highest number of annotated hits were obtained from M. algicola and highlighted the contribution of microorganisms associated with P. bahamense. Proteins involved in dimethylsulfoniopropionate (DMSP) degradation such as propionyl CoA synthethase and acryloyl-CoA reductase were identified, suggesting the DMSP cleavage pathway as the preferred route in this dinoflagellate. Most of the annotated proteins were involved in amino acid biosynthesis and carbohydrate degradation and metabolism, indicating the active roles of these molecules in the vegetative stage of P. bahamense. This characterization provides baseline information on the cellular machinery and the molecular basis of the ecophysiology of P. bahamense.

Substrate specificity of the 3-methylmercaptopropionyl-CoA (DmdC1) dehydrogenase from Ruegeria pomeroyi DSS-3

The acyl-CoA dehydrogenase family enzyme DmdC catalyzes the third step in the dimethylsulfoniopropionate (DMSP) demethylation pathway, the oxidation of 3-methylmercaptopropionyl-CoA (MMPA-CoA) to 3-methylthioacryloyl-CoA (MTA-CoA). To study its substrate specificity, the recombinant DmdC1 from Ruegeria pomeroyi was characterized. In addition to MMPA-CoA, the enzyme was highly active with short chain acyl-CoAs, with K_m values for MMPA-CoA, butyryl-CoA, valeryl-CoA, caproyl-CoA, heptanoyl-CoA, caprylyl-CoA and isobutyryl-CoA of 36, 19, 7, 11, 14, 10, and 149 μM, respectively, and k_cat values of 1.48, 0.40, 0.48, 0.73, 0.46, 0.23 and 0.01 sec^-1, respectively. Among these compounds, MMPA-CoA was the best substrate. The high affinity of DmdC1 for its substrate supports the model for kinetic regulation of the demethylation pathway. In contrast to DmdB, which catalyzes the formation of MMPA-CoA from MMPA, CoA and ATP, DmdC1 was not affected by physiological concentrations of potential effectors, such as DMSP, MMPA, ATP and ADP. Thus, compared to the other enzymes of the DMSP demethylation pathway, DmdC1 has only minimal adaptations for DMSP metabolism compared to other enzymes in the same family with similar substrates, supporting the hypothesis that it evolved relatively recently from a short chain acyl-CoA dehydrogenase involved in fatty acid oxidation. Importance We report the kinetic properties of DmdC1 from the model organism R. pomeroyi and close an important gap in the literature. While the crystal structure of this enzyme was recently solved and its mechanism of action described (X. Shao, H. Y. Cao, F. Zhao, M. Peng, et al., Mol Microbiol 111:1057-1073, 2019, https://doi.org/10.1111/mmi.14211), its substrate specificity and sensitivity to potential effectors was never examined. We show that DmdC1 has a high affinity for other short chain acyl-CoAs in addition to MMPA-CoA, which is the natural substrate in DMSP metabolism and is not affected by the potential effectors tested. This evidence supports the hypothesis that DmdC1 possesses few adaptations to DMSP metabolism and likely evolved relatively recently from a short chain acyl-CoA dehydrogenase involved in fatty acid oxidation. This work is important because it expands our understanding about the adaptation of marine bacteria to the increased availability of DMSP about 250 million years ago.

Synergistic effects of temperature and light affect the relationship between Taonia atomaria and its epibacterial community: a controlled conditions study

In the context of global warming, this study aimed to assess the effect of temperature and irradiance on the macroalgal Taonia atomaria holobiont dynamics. We developed an experimental set-up using aquaria supplied by natural seawater with three temperatures combined with three irradiances. The holobiont response was monitored over 14 days using a multi-omics approach coupling algal surface metabolomics and metabarcoding. Both temperature and irradiance appeared to shape the microbiota and the surface metabolome, but with a distinct temporality. Epibacterial community first changed according to temperature, and later in relation to irradiance, while the opposite occurred for the surface metabolome. An increased temperature revealed a decreasing richness of the epiphytic community together with an increase of several bacterial taxa. Irradiance changes appeared to quickly impact surface metabolites production linked with the algal host photosynthesis (e.g. mannitol, fucoxanthin, dimethylsulfoniopropionate), which was hypothesized to explain modifications of the structure of the epiphytic community. Algal host may also directly adapt its surface metabolome to changing temperature with time (e.g. lipids content) and also in response to changing microbiota (e.g. chemical defences). Finally, this study brought new insights highlighting complex direct and indirect responses of seaweeds and their associated microbiota under changing environments.

Dimethyl sulfide mediates microbial predator-prey interactions between zooplankton and algae in the ocean

Phytoplankton are key components of the oceanic carbon and sulfur cycles¹. During bloom events, some species can emit large amounts of the organosulfur volatile dimethyl sulfide (DMS) into the ocean and consequently the atmosphere, where it can modulate aerosol formation and affect climate^2,3. In aquatic environments, DMS plays an important role as a chemical signal mediating diverse trophic interactions. Yet, its role in microbial predator-prey interactions remains elusive with contradicting evidence for its role in either algal chemical defence or in the chemo-attraction of grazers to prey cells^4,5. Here we investigated the signalling role of DMS during zooplankton-algae interactions by genetic and biochemical manipulation of the algal DMS-generating enzyme dimethylsulfoniopropionate lyase (DL) in the bloom-forming alga Emiliania huxleyi⁶. We inhibited DL activity in E. huxleyi cells in vivo using the selective DL-inhibitor 2-bromo-3-(dimethylsulfonio)-propionate⁷ and overexpressed the DL-encoding gene in the model diatom Thalassiosira pseudonana. We showed that algal DL activity did not serve as an anti-grazing chemical defence but paradoxically enhanced predation by the grazer Oxyrrhis marina and other microzooplankton and mesozooplankton, including ciliates and copepods. Consumption of algal prey with induced DL activity also promoted O. marina growth. Overall, our results demonstrate that DMS-mediated grazing may be ecologically important and prevalent during prey-predator dynamics in aquatic ecosystems. The role of algal DMS revealed here, acting as an eat-me signal for grazers, raises fundamental questions regarding the retention of its biosynthetic enzyme through the evolution of dominant bloom-forming phytoplankton in the ocean.

Acrylate protects a marine bacterium from grazing by a ciliate predator

Cleavage of dimethylsulfoniopropionate (DMSP) can deter herbivores in DMSP-producing eukaryotic algae; however, it is unclear whether a parallel defence mechanism operates in marine bacteria. Here we demonstrate that the marine bacterium Puniceibacterium antarcticum SM1211, which does not use DMSP as a carbon source, has a membrane-associated DMSP lyase, DddL. At high concentrations of DMSP, DddL causes an accumulation of acrylate around cells through the degradation of DMSP, which protects against predation by the marine ciliate Uronema marinum. The presence of acrylate can alter the grazing preference of U. marinum to other bacteria in the community, thereby influencing community structure.

Phylogenomics of SAR116 Clade Reveals Two Subclades with Different Evolutionary Trajectories and an Important Role in the Ocean Sulfur Cycle

The SAR116 clade within the class Alphaproteobacteria represents one of the most abundant groups of heterotrophic bacteria inhabiting the surface of the ocean. The small number of cultured representatives of SAR116 (only two to date) is a major bottleneck that has prevented an in-depth study at the genomic level to understand the relationship between genome diversity and its role in the marine environment. In this study, we use all publicly available genomes to provide a genomic overview of the phylogeny, metabolism, and biogeography within the SAR116 clade. This increased genomic diversity has led to the discovery of two subclades that, despite coexisting in the same environment, display different properties in their genomic makeup. One represents a novel subclade for which no pure cultures have been isolated and is composed mainly of single-amplified genomes (SAGs). Genomes within this subclade showed convergent evolutionary trajectories with more streamlined features, such as low GC content (ca. 30%), short intergenic spacers (<22 bp), and strong purifying selection (low ratio of nonsynonymous to synonymous polymorphisms [dN/dS]). Besides, they were more abundant in metagenomic databases recruiting at the deep chlorophyll maximum. Less abundant and restricted to the upper photic layers of the global ocean, the other subclade of SAR116, enriched in metagenome-assembled genomes (MAGs), included the only two pure cultures. Genomic analysis suggested that both clades have a significant role in the sulfur cycle with differences in the way both clades can metabolize dimethylsulfoniopropionate (DMSP). IMPORTANCE The SAR116 clade of Alphaproteobacteria is a ubiquitous group of heterotrophic bacteria inhabiting the surface of the ocean, but the information about their ecology and population genomic diversity is scarce due to the difficulty of getting pure culture isolates. The combination of single-cell genomics and metagenomics has become an alternative approach to study these kinds of microbes. Our results expand the understanding of the genomic diversity, distribution, and lifestyles within this clade and provide evidence of different evolutionary trajectories in the genomic makeup of the two subclades that could serve to illustrate how evolutionary pressure can drive different adaptations to the same environment. Therefore, the SAR116 clade represents an ideal model organism for the study of the evolutionary streamlining of genomes in microbes that have relatively close relatedness to each other.

Spatiotemporal distribution of bacterial dimethylsulfoniopropionate producing and catabolic genes in the Changjiang Estuary

The osmolyte dimethylsulfoniopropionate (DMSP) is produced in petagram amounts by marine microorganisms. Estuaries provide natural gradients in salinity and nutrients, factors known to regulate DMSP production; yet there have been no molecular studies of DMSP production and cycling across these gradients. Here, we study the abundance, distribution and transcription of key DMSP synthesis (e.g. dsyB and mmtN) and catabolic (e.g. dddP and dmdA) genes along the salinity gradient of the Changjiang Estuary. DMSP levels did not correlate with Chl a across the salinity gradient. In contrast, DMSP concentration, abundance of bacterial DMSP producers and their dsyB and mmtN transcripts were lowest in the freshwater samples and increased abruptly with salinity in the transitional and seawater samples. Metagenomics analysis suggests bacterial DMSP-producers were more abundant than their algal equivalents and were more prominent in summer than winter samples. Bacterial DMSP catabolic genes and their transcripts followed the same trend of being greatly enhanced in transitional and seawater samples with higher DMSP levels than freshwater samples. DMSP cleavage was likely the dominant catabolic pathway, with DMSP lyase genes being ~4.3-fold more abundant than the demethylase gene dmdA. This is an exemplar study for future research on microbial DMSP cycling in estuary environments.

Biogeographic traits of dimethyl sulfide and dimethylsulfoniopropionate cycling in polar oceans

BACKGROUND

Dimethyl sulfide (DMS) is the dominant volatile organic sulfur in global oceans. The predominant source of oceanic DMS is the cleavage of dimethylsulfoniopropionate (DMSP), which can be produced by marine bacteria and phytoplankton. Polar oceans, which represent about one fifth of Earth's surface, contribute significantly to the global oceanic DMS sea-air flux. However, a global overview of DMS and DMSP cycling in polar oceans is still lacking and the key genes and the microbial assemblages involved in DMSP/DMS transformation remain to be fully unveiled.

RESULTS

Here, we systematically investigated the biogeographic traits of 16 key microbial enzymes involved in DMS/DMSP cycling in 60 metagenomic samples from polar waters, together with 174 metagenome and 151 metatranscriptomes from non-polar Tara Ocean dataset. Our analyses suggest that intense DMS/DMSP cycling occurs in the polar oceans. DMSP demethylase (DmdA), DMSP lyases (DddD, DddP, and DddK), and trimethylamine monooxygenase (Tmm, which oxidizes DMS to dimethylsulfoxide) were the most prevalent bacterial genes involved in global DMS/DMSP cycling. Alphaproteobacteria (Pelagibacterales) and Gammaproteobacteria appear to play prominent roles in DMS/DMSP cycling in polar oceans. The phenomenon that multiple DMS/DMSP cycling genes co-occurred in the same bacterial genome was also observed in metagenome assembled genomes (MAGs) from polar oceans. The microbial assemblages from the polar oceans were significantly correlated with water depth rather than geographic distance, suggesting the differences of habitats between surface and deep waters rather than dispersal limitation are the key factors shaping microbial assemblages involved in DMS/DMSP cycling in polar oceans.

CONCLUSIONS

Overall, this study provides a global overview of the biogeographic traits of known bacterial genes involved in DMS/DMSP cycling from the Arctic and Antarctic oceans, laying a solid foundation for further studies of DMS/DMSP cycling in polar ocean microbiome at the enzymatic, metabolic, and processual levels. Video Abstract.

Integration of spatio-temporal variations of surface metabolomes and epibacterial communities highlights the importance of copper stress as a major factor shaping host-microbiota interactions within a Mediterranean seaweed holobiont

BACKGROUND

Although considered as holobionts, macroalgae and their surface microbiota share intimate interactions that are still poorly understood. Little is known on the effect of environmental parameters on the close relationships between the host and its surface-associated microbiota, and even more in a context of coastal pollutions. Therefore, the main objective of this study was to decipher the impact of local environmental parameters, especially trace metal concentrations, on an algal holobiont dynamics using the Phaeophyta Taonia atomaria as a model. Through a multidisciplinary multi-omics approach combining metabarcoding and untargeted LC-MS-based metabolomics, the epibacterial communities and the surface metabolome of T. atomaria were monitored along a spatio-temporal gradient in the bay of Toulon (Northwestern Mediterranean coast) and its surrounding. Indeed, this geographical area displays a well-described trace metal gradient particularly relevant to investigate the effect of such pollutants on marine organisms.

RESULTS

Epibacterial communities of T. atomaria exhibited a high specificity whatever the five environmentally contrasted collecting sites investigated on the NW Mediterranean coast. By integrating metabarcoding and metabolomics analyses, the holobiont dynamics varied as a whole. During the occurrence period of T. atomaria, epibacterial densities and α-diversity increased while the relative proportion of core communities decreased. Pioneer bacterial colonizers constituted a large part of the specific and core taxa, and their decrease might be linked to biofilm maturation through time. Then, the temporal increase of the Roseobacter was proposed to result from the higher temperature conditions, but also the increased production of dimethylsulfoniopropionate (DMSP) at the algal surface which could constitute of the source of carbon and sulfur for the catabolism pathways of these taxa. Finally, as a major result of this study, copper concentration constituted a key factor shaping the holobiont system. Thus, the higher expression of carotenoids suggested an oxidative stress which might result from an adaptation of the algal surface metabolome to high copper levels. In turn, this change in the surface metabolome composition could result in the selection of particular epibacterial taxa.

CONCLUSION

We showed that associated epibacterial communities were highly specific to the algal host and that the holobiont dynamics varied as a whole. While temperature increase was confirmed to be one of the main parameters associated to Taonia dynamics, the originality of this study was highlighting copper-stress as a major driver of seaweed-epibacterial interactions. In a context of global change, this study brought new insights on the dynamics of a Mediterranean algal holobiont submitted to heavy anthropic pressures. Video abstract.

A new family of globally distributed lytic roseophages with unusual deoxythymidine to deoxyuridine substitution

Marine bacterial viruses (bacteriophages) are abundant biological entities that are vital for shaping microbial diversity, impacting marine ecosystem function, and driving host evolution.1, 2, 3 The marine roseobacter clade (MRC) is a ubiquitous group of heterotrophic bacteria^4,5 that are important in the elemental cycling of various nitrogen, sulfur, carbon, and phosphorus compounds.6, 7, 8, 9, 10 Bacteriophages infecting MRC (roseophages) have thus attracted much attention and more than 30 roseophages have been isolated,11, 12, 13 the majority of which belong to the N4-like group (Podoviridae family) or the Chi-like group (Siphoviridae family), although ssDNA-containing roseophages are also known.¹⁴ In our attempts to isolate lytic roseophages, we obtained two new phages (DSS3_VP1 and DSS3_PM1) infecting the model MRC strain Ruegeria pomeroyi DSS-3. Here, we show that not only do these phages have unusual substitution of deoxythymidine with deoxyuridine (dU) in their DNA, but they are also phylogenetically distinct from any currently known double-stranded DNA bacteriophages, supporting the establishment of a novel family (“Naomiviridae”). These dU-containing phages possess DNA that is resistant to the commonly used library preparation method for metagenome sequencing, which may have caused significant underestimation of their presence in the environment. Nevertheless, our analysis of Tara Ocean metagenome datasets suggests that these unusual bacteriophages are of global importance and more diverse than other well-known bacteriophages, e.g., the Podoviridae in the oceans, pointing to an overlooked role for these novel phages in the environment.

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Two new roseophages isolated from the marine environment

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They have an unusual deoxythymidine to deoxyuridine substitution in their genomes

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These dU genomes are resistant to a common method of metagenome library preparation

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These phages represent a new family and are globally distributed in the oceans

A novel ATP dependent dimethylsulfoniopropionate lyase in bacteria that releases dimethyl sulfide and acryloyl-CoA

Dimethylsulfoniopropionate (DMSP) is an abundant and ubiquitous organosulfur molecule in marine environments with important roles in global sulfur and nutrient cycling. Diverse DMSP lyases in some algae, bacteria, and fungi cleave DMSP to yield gaseous dimethyl sulfide (DMS), an infochemical with important roles in atmospheric chemistry. Here, we identified a novel ATP-dependent DMSP lyase, DddX. DddX belongs to the acyl-CoA synthetase superfamily and is distinct from the eight other known DMSP lyases. DddX catalyses the conversion of DMSP to DMS via a two-step reaction: the ligation of DMSP with CoA to form the intermediate DMSP-CoA, which is then cleaved to DMS and acryloyl-CoA. The novel catalytic mechanism was elucidated by structural and biochemical analyses. DddX is found in several Alphaproteobacteria, Gammaproteobacteria, and Firmicutes, suggesting that this new DMSP lyase may play an overlooked role in DMSP/DMS cycles.

The global sulfur cycle is a collection of geological and biological processes that circulate sulfur-containing compounds through the oceans, rocks and atmosphere. Sulfur itself is essential for life and important for plant growth, hence its widespread use in fertilizers.

Marine organisms such as bacteria, algae and phytoplankton produce one particular sulfur compound, called dimethylsulfoniopropionate, or DMSP, in massive amounts. DMSP made in the oceans gets readily converted into a gas called dimethyl sulfide (DMS), which is the largest natural source of sulfur entering the atmosphere. In the air, DMS is converted to sulfate and other by-products that can act as cloud condensation nuclei, which, as the name suggests, are involved in cloud formation. In this way, DMS can influence weather and climate, so it is often referred to as ‘climate-active’ gas.

At least eight enzymes are known to cleave DMSP into DMS gas with a few by-products. These enzymes are found in algae, bacteria and fungi, and are referred to as lyases, for the way they breakdown their target compounds (DMSP, in this case). Recently, researchers have identified some bacteria that produce DMS from DMSP without using known DMSP lyases. This suggests there are other, unidentified enzymes that act on DMSP in nature, and likely contribute to global sulfur cycling.

Li, Wang et al. set out to uncover new enzymes responsible for converting the DMSP that marine bacteria produce into gaseous DMS. One new enzyme called DddX was identified and found to belong to a superfamily of enzymes quite separate to other known DMSP lyases. Li, Wang et al. also showed how DddX drives the conversion of DMSP to DMS in a two-step reaction, and that the enzyme is found across several classes of bacteria. Further experiments to characterise the protein structure of DddX also revealed the molecular mechanism for its catalytic action.

This study offers important insights into how marine bacteria generate the climatically important gas DMS from DMSP, leading to a better understanding of the global sulfur cycle. It gives microbial ecologists a more comprehensive perspective of these environmental processes, and provides biochemists with data on a family of enzymes not previously known to act on sulfur-containing compounds.

A New Protocol Using Acidification for Preserving DMSP in Macroalgae and Comparison with Existing Protocols

Dimethylsulfoniopropionate (DMSP) plays many important physiological and ecological roles in macroalgae. The most common method to measure DMSP is by gas chromatography analysis of the dimethylsulfide (DMS) produced after NaOH hydrolysis (pH > 12). Storage of DMS, however, is not recommended for more than a week. We investigated if acidification can be a suitable method to preserve DMSP in macroalgal samples over three months of storage, compared to widely used protocols such as drying and freezing at -20°C. The DMSP content of green (Ulva sp. and Ulva compressa), red (Chondrus crispus), and brown (Bifurcaria bifurcata) macroalgae were analyzed: 24 h after NaOH addition (control values); and after acidification (0.2 mol · L HCl^-1 ) for 24 h of fresh material, followed by NaOH addition for 24 h. These values were compared to measurements after 3-month storage of samples that had been either dried in a heater (60°C for a night, and storage at room temperature), or frozen at -20°C, or kept in 0.2 mol · L HCl^-1 . There was no significant difference between DMSP measurements on freshly collected material and after acidification of the samples, whether 24 h later or after 3 months of storage. This was in contrast to 3-month storage protocols involving overnight drying at 60°C (75-98% DMSP loss), and to a lesser degree freezing at -20°C (37-80% DMSP loss). We thus advise to acidify macroalgal samples for preservation over long periods of time rather than drying or freezing, when assaying DMSP content.

Stressed out: Bacterial response to high salinity using compatible solute biosynthesis and uptake systems, lessons from Vibrionaceae

Bacteria have evolved mechanisms that allow them to adapt to changes in osmolarity and some species have adapted to live optimally in high salinity environments such as in the marine ecosystem. Most bacteria that live in high salinity do so by the biosynthesis and/or uptake of compatible solutes, small organic molecules that maintain the turgor pressure of the cell. Osmotic stress response mechanisms and their regulation among marine heterotrophic bacteria are poorly understood. In this review, we discuss what is known about compatible solute metabolism and transport and new insights gained from studying marine bacteria belonging to the family Vibrionaceae.

DMSP synthesis genes distinguish two types of DMSP producer phenotypes

Dimethylsulfoniopropionate (DMSP) is an important organic carbon and sulfur source in the surface ocean that fuels microbial activity and significantly impacts Earth's climate. After three decades of research, the cellular role(s) of DMSP and environmental drivers of production remain enigmatic. Recent work suggests that cellular DMSP concentrations, and changes in these concentrations in response to environmental stressors, define two major groups of DMSP producers: high DMSP producers that contain ≥ 50 mM intracellular DMSP and low DMSP producers that contain < 50 mM. Here we show that two recently described DMSP synthesis genes (DSYB and TpMT2) may differentiate these two DMSP phenotypes. A survey of prokaryotic and eukaryotic isolates found a significant correlation between the presence of DSYB and TpMT2 genes and previous measurements of high and low DMSP concentrations, respectively. Phylogenetic analysis demonstrated that DSYB and TpMT2 form two distinct clades. DSYB and TpMT2 were also found to be globally abundant in in situ surface communities, and their taxonomic annotations were similar to those observed for isolates. The strong correlation of the DSYB and TpMT2 synthesis genes with high and low producer phenotypes establishes a foundation for direct quantification of DMSP producers, enabling significantly improved predictions of DMSP in situ.

Evidence of Interdomain Ammonium Cross-Feeding From Methylamine- and Glycine Betaine-Degrading Rhodobacteraceae to Diatoms as a Widespread Interaction in the Marine Phycosphere

Dissolved organic nitrogen (DON) compounds such as methylamines (MAs) and glycine betaine (GBT) occur at detectable concentrations in marine habitats and are also produced and released by microalgae. For many marine bacteria, these DON compounds can serve as carbon, energy, and nitrogen sources, but microalgae usually cannot metabolize them. Interestingly though, it was previously shown that Donghicola sp. strain KarMa—a member of the marine Rhodobacteraceae—can cross-feed ammonium such that the ammonium it produces upon degrading monomethylamine (MMA) then serves as nitrogen source for the diatom Phaeodactylum tricornutum; thus, these organisms form a mutual metabolic interaction under photoautotrophic conditions. In the present study, we investigated whether this interaction plays a broader role in bacteria–diatom interactions in general. Results showed that cross-feeding between strain KarMa and P. tricornutum was also possible with di- and trimethylamine as well as with GBT. Further, cross-feeding of strain KarMa was also observed in cocultures with the diatoms Amphora coffeaeformis and Thalassiosira pseudonana with MMA as the sole nitrogen source. Regarding cross-feeding involving other Rhodobacteraceae strains, the in silico analysis of MA and GBT degradation pathways indicated that algae-associated Rhodobacteraceae-type strains likely interact with P. tricornutum in a similar manner as the strain KarMa does. For these types of strains (such as Celeribacter halophilus, Roseobacter denitrificans, Roseovarius indicus, Ruegeria pomeroyi, and Sulfitobacter noctilucicola), ammonium cross-feeding after methylamine degradation showed species-specific patterns, whereas bacterial GBT degradation always led to diatom growth. Overall, the degradation of DON compounds by the Rhodobacteraceae family and the subsequent cross-feeding of ammonium may represent a widespread, organism-specific, and regulated metabolic interaction for establishing and stabilizing associations with photoautotrophic diatoms in the oceans.

Evolutionary history of dimethylsulfoniopropionate (DMSP) demethylation enzyme DmdA in marine bacteria

Dimethylsulfoniopropionate (DMSP), an osmolyte produced by oceanic phytoplankton and bacteria, is primarily degraded by bacteria belonging to the Roseobacter lineage and other marine Alphaproteobacteria via DMSP-dependent demethylase A protein (DmdA). To date, the evolutionary history of DmdA gene family is unclear. Some studies indicate a common ancestry between DmdA and GcvT gene families and a co-evolution between Roseobacter and the DMSP-producing-phytoplankton around 250 million years ago (Mya). In this work, we analyzed the evolution of DmdA under three possible evolutionary scenarios: (1) a recent common ancestor of DmdA and GcvT, (2) a coevolution between Roseobacter and the DMSP-producing-phytoplankton, and (3) an enzymatic adaptation for utilizing DMSP in marine bacteria prior to Roseobacter origin. Our analyses indicate that DmdA is a new gene family originated from GcvT genes by duplication and functional divergence driven by positive selection before a coevolution between Roseobacter and phytoplankton. Our data suggest that Roseobacter acquired dmdA by horizontal gene transfer prior to an environment with higher DMSP. Here, we propose that the ancestor that carried the DMSP demethylation pathway genes evolved in the Archean, and was exposed to a higher concentration of DMSP in a sulfur-rich atmosphere and anoxic ocean, compared to recent Roseobacter eco-orthologs (orthologs performing the same function under different conditions), which should be adapted to lower concentrations of DMSP.

Large Diversity in Nitrogen- and Sulfur-Containing Compatible Solute Profiles in Polar and Temperate Diatoms

Intense bottom-ice algal blooms, often dominated by diatoms, are an important source of food for grazers, organic matter for export during sea ice melt, and dissolved organic carbon. Sea-ice diatoms have a number of adaptations, including accumulation of compatible solutes, that allows them to inhabit this highly variable environment characterized by extremes in temperature, salinity, and light. In addition to protecting them from extreme conditions, these compounds present a labile, nutrient-rich source of organic matter, and include precursors to climate active compounds (e.g., dimethyl sulfide [DMS]), which are likely regulated with environmental change. Here, intracellular concentrations of 45 metabolites were quantified in three sea-ice diatom species and were compared to two temperate diatom species, with a focus on compatible solutes and free amino acid pools. There was a large diversity of metabolite concentrations between diatoms with no clear pattern identifiable for sea-ice species. Concentrations of some compatible solutes (isethionic acid, homarine) approached 1 M in the sea-ice diatoms, Fragilariopsis cylindrus and Navicula cf. perminuta, but not in the larger sea-ice diatom, Nitzschia lecointei or in the temperate diatom species. The differential use of compatible solutes in sea-ice diatoms suggests different adaptive strategies and highlights which small organic compounds may be important in polar biogeochemical cycles.

Cell death associated release of volatile organic sulphur compounds with antioxidant properties in chemical-challenged tobacco BY-2 suspension cultured cells

The production of volatile organic compounds (VOCs) during programmed cell death (PCD) is still insufficiently studied and their implication in the process is not well understood. The present study demonstrates that the release of VOSCs with presumed antioxidant capacity (methanethiol, dimethylsulfide and dimethyldisulfide) accompanies the cell death in chemical-stressed tobacco BY-2 suspension cultured cells. The cells were exposed to cell death inducers of biotic nature mastoparan (MP, wasp venom) and camptothecin (CPT, alkaloid), and to the abiotic stress agent CdSO4. The VOCs emission was monitored by proton-transfer reaction mass spectrometry (PTR-MS). The three chemicals induced PCD expressing apoptotic-like phenotype. The identified VOSCs were emitted in response to MP and CPT but not in presence of Cd. The VOSCs production occurred within few hours after the administration of the elicitors, peaked up when 20-50 % of the cells were dead and further levelled off with cell death advancement. This suggests that VOSCs with antioxidant activity may contribute to alleviation of cell death-associated oxidative stress at medium severity of cell death in response to the stress factors of biotic origin. The findings provide novel information about cell death defence mechanisms in chemical-challenged BY-2 cells and show that PCD related VOSCs synthesis depends on the type of inducer.

DMSP-Producing Bacteria Are More Abundant in the Surface Microlayer than Subsurface Seawater of the East China Sea

Microbial production and catabolism of dimethylsulfoniopropionate (DMSP), generating the climatically active gases dimethyl sulfide (DMS) and methanethiol (MeSH), have key roles in global carbon and sulfur cycling, chemotaxis, and atmospheric chemistry. Microorganisms in the sea surface microlayer (SML), the interface between seawater and atmosphere, likely play an important role in the generation of DMS and MeSH and their exchange to the atmosphere, but little is known about these SML microorganisms. Here, we investigated the differences between bacterial community structure and the distribution and transcription profiles of the key bacterial DMSP synthesis (dsyB and mmtN) and catabolic (dmdA and dddP) genes in East China Sea SML and subsurface seawater (SSW) samples. Per equivalent volume, bacteria were far more abundant (~ 7.5-fold) in SML than SSW, as were those genera predicted to produce DMSP. Indeed, dsyB (~ 7-fold) and mmtN (~ 4-fold), robust reporters for bacterial DMSP production, were also far more abundant in SML than SSW. In addition, the SML had higher dsyB transcripts (~ 3-fold) than SSW samples, which may contribute to the significantly higher DMSP level observed in SML compared with SSW. Furthermore, the abundance of bacteria with dmdA and their transcription were higher in SML than SSW samples. Bacteria with dddP and transcripts were also prominent, but less than dmdA and presented at similar levels in both layers. These data indicate that the SML might be an important hotspot for bacterial DMSP production as well as generating the climatically active gases DMS and MeSH, a portion of which are likely transferred to the atmosphere.

Identification of a functional dddD-Rh for dimethyl sulfide production in the Antarctic Rhodococcus sp. NJ-530

Dimethylsulfoniopropionate (DMSP) is widespread in the oceans, and its biological metabolite, dimethyl sulfide (DMS), plays an important role in the atmosphere. The Antarctic region has become a hotspot in DMS studies due to the high spatial and temporal variability in DMS(P) concentration, but the level of bacterial DMS production remains unclear. In this study, a bacterium isolated from Antarctic floating ice, Rhodococcus sp. NJ-530, was found to metabolize DMSP into DMS, and the rate of DMS production was measured as 3.96 pmol·mg protein^-1 ·h^-1 . Rhodococcus sp. NJ-530 had a DddD-Rh enzyme containing two CaiB domains, which belonged to the CoA-transferase III superfamily. However, the DddD-Rh had a molecular weight of 73.21 kDa, which was very different from previously characterized DddD enzymes in sequence and evolution. In vitro assays showed that DddD-Rh was functional in the presence of acetyl-CoA. This was the first functional DddD from Gram-positive Actinobacteria. Moreover, a quantitative real-time polymerase chain reaction revealed that high temperature facilitated the expression of dddD-Rh, and changes of salinity had little effect on it. This study adds new evidence to the bacterial DMS production in the Southern Ocean and provides a basis for investigating the metabolic mechanism of DMSP in extreme environments.

Comparative genomics: Dominant coral-bacterium Endozoicomonas acroporae metabolizes dimethylsulfoniopropionate (DMSP)

Dominant coral-associated Endozoicomonas bacteria species are hypothesized to play a role in the coral sulfur cycle by metabolizing dimethylsulfoniopropionate (DMSP) into dimethylsulfide (DMS); however, no sequenced genome to date harbors genes for this process. In this study, we assembled high-quality (>95% complete) draft genomes of strains of the recently added species Endozoicomonas acroporae (Acr-14T, Acr-1, and Acr-5) isolated from the coral Acropora sp. and performed a comparative genomic analysis on the genus Endozoicomonas. We identified DMSP CoA-transferase/lyase-a dddD gene homolog in all sequenced genomes of E. acroporae strains-and functionally characterized bacteria capable of metabolizing DMSP into DMS via the DddD cleavage pathway using RT-qPCR and gas chromatography (GC). Furthermore, we demonstrated that E. acroporae strains can use DMSP as a carbon source and have genes arranged in an operon-like manner to link DMSP metabolism to the central carbon cycle. This study confirms the role of Endozoicomonas in the coral sulfur cycle.

Dimethylsulfoniopropionate Sulfur and Methyl Carbon Assimilation in Ruegeria Species

Dimethylsulfoniopropionate (DMSP) is abundant in marine environments and an important source of reduced carbon and sulfur for marine bacteria. While both Ruegeria pomeroyi and Ruegeria lacuscaerulensis possessed genes encoding the DMSP demethylation and cleavage pathways, their responses to DMSP differed. A glucose-fed, chemostat culture of R. pomeroyi consumed 99% of the DMSP even when fed a high concentration of 5 mM. At the same time, cultures released 19% and 7.1% of the DMSP as dimethylsulfide (DMS) and methanethiol, respectively. Under the same conditions, R. lacuscaerulensis consumed only 28% of the DMSP and formed one-third of the amount of gases. To examine the pathways of sulfur and methyl C assimilation, glucose-fed chemostats of both species were fed 100 μM mixtures of unlabeled and doubly labeled [dimethyl-¹³C, ³⁴S]DMSP. Both species derived nearly all of their sulfur from DMSP despite high sulfate availability. In addition, only 33% and 50% of the methionine was biosynthesized from the direct capture of methanethiol in R. pomeroyi and R. lacuscaerulensis, respectively. The remaining methionine was biosynthesized by the random assembly of free sulfide and methyl-tetrahydrofolate derived from DMSP. Thus, although the two species possessed similar genes encoding DMSP metabolism, their growth responses were very different.IMPORTANCE Dimethylsulfoniopropionate (DMSP) is abundant in marine environments and an important source of reduced carbon and sulfur for marine bacteria. DMSP is the precursor for the majority of atmospheric dimethylsulfide (DMS), a climatically active gas that connects the marine and terrestrial sulfur cycles. Although research into the assimilation of DMSP has been conducted for over 20 years, the fate of DMSP in microbial biomass is not well understood. In particular, the biosynthesis of methionine from DMSP has been a focal point, and it has been widely believed that most methionine was synthesized via the direct capture of methanethiol. Using an isotopic labeling strategy, we have demonstrated that the direct capture of methanethiol is not the primary pathway used for methionine biosynthesis in two Ruegeria species, a genus comprised primarily of globally abundant marine bacteria. Furthermore, although the catabolism of DMSP by these species varied greatly, the anabolic pathways were highly conserved.

Transcriptome reconstruction and functional analysis of eukaryotic marine plankton communities via high-throughput metagenomics and metatranscriptomics

Large-scale metagenomic and metatranscriptomic data analyses are often restricted by their gene-centric approach, limiting the ability to understand organismal and community biology. De novo assembly of large and mosaic eukaryotic genomes from complex meta-omics data remains a challenging task, especially in comparison with more straightforward bacterial and archaeal systems. Here, we use a transcriptome reconstruction method based on clustering co-abundant genes across a series of metagenomic samples. We investigated the co-abundance patterns of ∼37 million eukaryotic unigenes across 365 metagenomic samples collected during the Tara Oceans expeditions to assess the diversity and functional profiles of marine plankton. We identified ∼12,000 co-abundant gene groups (CAGs), encompassing ∼7 million unigenes, including 924 metagenomics-based transcriptomes (MGTs, CAGs larger than 500 unigenes). We demonstrated the biological validity of the MGT collection by comparing individual MGTs with available references. We identified several key eukaryotic organisms involved in dimethylsulfoniopropionate (DMSP) biosynthesis and catabolism in different oceanic provinces, thus demonstrating the potential of the MGT collection to provide functional insights on eukaryotic plankton. We established the ability of the MGT approach to capture interspecies associations through the analysis of a nitrogen-fixing haptophyte-cyanobacterial symbiotic association. This MGT collection provides a valuable resource for analyses of eukaryotic plankton in the open ocean by giving access to the genomic content and functional potential of many ecologically relevant eukaryotic species.