Bacterial Catabolism of Dimethylsulfoniopropionate (DMSP)

Comprehensive profiles of sulfur cycling microbial communities along a mangrove sediment depth

The sulfur (S) cycle is an important biogeochemical cycle with profound implications for both cellular- and ecosystem-level processes by diverse microorganisms. Mangrove sediments are a hotspot of biogeochemical cycling, especially for the S cycle with high concentrations of S compounds. Previous studies have mainly focused on some specific inorganic S cycling processes without paying specific attention to the overall S-cycling communities and processes as well as organic S metabolism. In this study, we comprehensively analyzed the distribution, ecological network and assembly mechanisms of S cycling microbial communities and their changes with sediment depths using metagenome sequencing data. The results showed that the abundance of gene families involved in sulfur oxidation, assimilatory sulfate reduction, and dimethylsulfoniopropionate (DMSP) cleavage and demethylation decreased with sediment depths, while those involved in S reduction and dimethyl sulfide (DMS) transformation showed an opposite trend. Specifically, glpE, responsible for converting S2O32- to SO32-, showed the highest abundance in the surface sediment and decreased with sediment depths; in contrast, high abundances of dmsA, responsible for converting dimethyl sulfoxide (DMSO) to DMS, were identified and increased with sediment depths. We identified Pseudomonas and Streptomyces as the main S-cycling microorganisms, while Thermococcus could play an import role in microbial network connections in the S-cycling microbial community. Our statistical analysis showed that both taxonomical and functional compositions were generally shaped by stochastic processes, while the functional composition of organic S metabolism showed a transition from stochastic to deterministic processes. This study provides a novel perspective of diversity distribution of S-cycling functions and taxa as well as their potential assembly mechanisms, which has important implications for maintaining mangrove ecosystem functions.

Influence of the community assemblage on sulfur distributions in the South China sea

Marine distribution of dimethylsulfoniopropionate (DMSP) and its cleavage product dimethyl sulfide (DMS) is greatly affected by the community structures of bacteria, phytoplankton, and zooplankton. Spatial distributions of dissolved and particulate DMSP (DMSPd,p), and DMS were measured and their relationships with DMSP lyase activity (DLA), abundance of DMSP-consuming bacteria (DCB), and the community structures of phytoplankton, zooplankton, and bacteria were determined during summer in the South China Sea (SCS). The depth distributions of DMSPd,p exhibited a similar trend with Chl a, reaching their maxima in the mixing layer. The DMS concentration was positively correlated with DCB abundance and DLA, indicating that DCB and DMSP lyase had a significant effect on DMS production. High DMS concentrations in the horizontal distribution coincided with high DCB abundance and DLA and may be due to the rapid growth of phytoplankton resulting from the high dissolved inorganic nitrogen concentration brought by the cold vortices. Moreover, the highest copepod abundance at station G3 coincided with the highest DMS concentrations there among stations B4, F2, and G3. These results suggest that copepod may play an important role in DMS production. The bacterial SAR11 clade was positively correlated with DLA, indicating its significant contribution to DMSP degradation in the SCS. These findings contribute to the understanding of the effect of the community assemblage on DMSP/DMS distributions in the SCS dominated by mesoscale vortices.

Rhodobacteraceae methanethiol oxidases catalyze methanethiol degradation to produce sulfane sulfur other than hydrogen sulfide

Methanethiol (MT) is a sulfur-containing compound produced during dimethylsulfoniopropionate (DMSP) degradation by marine bacteria. The C-S bond of MT can be cleaved by methanethiol oxidases (MTOs) to release a sulfur atom. However, the cleaving process remains unclear, and the species of sulfur product is uncertain. It has long been assumed that MTOs produce hydrogen sulfide (H2S) from MT. Herein, we studied the MTOs in the Rhodobacteraceae family-whose members are important DMSP degraders ubiquitous in marine environments. We identified 57 MTOs from 1,904 Rhodobacteraceae genomes. These MTOs were grouped into two major clusters. Cluster 1 members share three conserved cysteine residues, while cluster 2 members contain one conserved cysteine residue. We examined the products of three representative MTOs both in vitro and in vivo. All of them produced sulfane sulfur other than H2S from MT. Their conserved cysteines are substrate-binding sites in which the MTO-S-S-CH3 complex is formed. This finding clarified the sulfur product of MTOs and enlightened the MTO-catalyzing process. Moreover, this study connected DMSP degradation with sulfane sulfur metabolism, filling a critical gap in the DMSP degradation pathway and representing new knowledge in the marine sulfur cycle field.

IMPORTANCE

This study overthrows a long-time assumption that methanethiol oxidases (MTOs) cleave the C-S bond of methanethiol to produce both H2S and H2O2-the former is a strong reductant and the latter is a strong oxidant. From a chemistry viewpoint, this reaction is difficult to happen. Investigations on three representative MTOs indicated that sulfane sulfur (S0) was the direct product, and no H2O2 was produced. Finally, the products of MTOs were corrected to be S0 and H2O. This finding connected dimethylsulfoniopropionate (DMSP) degradation with sulfane sulfur metabolism, filling a critical gap in the DMSP degradation pathway and representing new knowledge in the marine sulfur cycle field.

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.

Dynamic changes in bacterial communities in three species of corals during the 2017 bleaching event in subtropical Hong Kong waters

Bacteria play important roles in coral health, yet little is known about the dynamics of coral-associated bacterial communities during coral bleaching. Here, we reported the dynamic changes of bacterial communities in three scleractinian corals (Montipora peltiformis, Pavona decussata and Platygyra carnosa) during and after bleaching through amplicon sequencing. Our results revealed that the bacterial composition and dominant bacteria varied among the three coral species. The higher susceptibility of M. peltiformis to bleaching corresponded to a lower bacterial community diversity, and the dominant Synechococcus shifted in abundance during the bleaching and coral recovery phases. The resilient P. decussata and P. carnosa had higher bacterial diversity and a more similar bacterial composition between the healthy and bleached conditions. Overall, our study reveals the dynamic changes in coral-associated microbial diversity under different conditions, contributing to explaining the differential susceptibility of corals to extreme climate conditions.

DMSOP-cleaving enzymes are diverse and widely distributed in marine microorganisms

Dimethylsulfoxonium propionate (DMSOP) is a recently identified and abundant marine organosulfur compound with roles in oxidative stress protection, global carbon and sulfur cycling and, as shown here, potentially in osmotolerance. Microbial DMSOP cleavage yields dimethyl sulfoxide, a ubiquitous marine metabolite, and acrylate, but the enzymes responsible, and their environmental importance, were unknown. Here we report DMSOP cleavage mechanisms in diverse heterotrophic bacteria, fungi and phototrophic algae not previously known to have this activity, and highlight the unappreciated importance of this process in marine sediment environments. These diverse organisms, including Roseobacter, SAR11 bacteria and Emiliania huxleyi, utilized their dimethylsulfoniopropionate lyase 'Ddd' or 'Alma' enzymes to cleave DMSOP via similar catalytic mechanisms to those for dimethylsulfoniopropionate. Given the annual teragram predictions for DMSOP production and its prevalence in marine sediments, our results highlight that DMSOP cleavage is likely a globally significant process influencing carbon and sulfur fluxes and ecological interactions.

Metagenome-assembled genomes reveal greatly expanded taxonomic and functional diversification of the abundant marine Roseobacter RCA cluster

BACKGROUND

The RCA (Roseobacter clade affiliated) cluster belongs to the family Roseobacteracea and represents a major Roseobacter lineage in temperate to polar oceans. Despite its prevalence and abundance, only a few genomes and one described species, Planktomarina temperata, exist. To gain more insights into our limited understanding of this cluster and its taxonomic and functional diversity and biogeography, we screened metagenomic datasets from the global oceans and reconstructed metagenome-assembled genomes (MAG) affiliated to this cluster.

RESULTS

The total of 82 MAGs, plus five genomes of isolates, reveal an unexpected diversity and novel insights into the genomic features, the functional diversity, and greatly refined biogeographic patterns of the RCA cluster. This cluster is subdivided into three genera: Planktomarina, Pseudoplanktomarina, and the most deeply branching Candidatus Paraplanktomarina. Six of the eight Planktomarina species have larger genome sizes (2.44-3.12 Mbp) and higher G + C contents (46.36-53.70%) than the four Pseudoplanktomarina species (2.26-2.72 Mbp, 42.22-43.72 G + C%). Cand. Paraplanktomarina is represented only by one species with a genome size of 2.40 Mbp and a G + C content of 45.85%. Three novel species of the genera Planktomarina and Pseudoplanktomarina are validly described according to the SeqCode nomenclature for prokaryotic genomes. Aerobic anoxygenic photosynthesis (AAP) is encoded in three Planktomarina species. Unexpectedly, proteorhodopsin (PR) is encoded in the other Planktomarina and all Pseudoplanktomarina species, suggesting that this light-driven proton pump is the most important mode of acquiring complementary energy of the RCA cluster. The Pseudoplanktomarina species exhibit differences in functional traits compared to Planktomarina species and adaptations to more resource-limited conditions. An assessment of the global biogeography of the different species greatly expands the range of occurrence and shows that the different species exhibit distinct biogeographic patterns. They partially reflect the genomic features of the species.

CONCLUSIONS

Our detailed MAG-based analyses shed new light on the diversification, environmental adaptation, and global biogeography of a major lineage of pelagic bacteria. The taxonomic delineation and validation by the SeqCode nomenclature of prominent genera and species of the RCA cluster may be a promising way for a refined taxonomic identification of major prokaryotic lineages and sublineages in marine and other prokaryotic communities assessed by metagenomics approaches. Video Abstract.

Similar but different: Characterization of dddD gene-mediated DMSP metabolism among coral-associated Endozoicomonas

Endozoicomonas are often predominant bacteria and prominently important in coral health. Their role in dimethylsulfoniopropionate (DMSP) degradation has been a subject of discussion for over a decade. A previous study found that Endozoicomonas degraded DMSP through the dddD pathway. This process releases dimethyl sulfide, which is vital for corals coping with thermal stress. However, little is known about the related gene regulation and metabolic abilities of DMSP metabolism in Endozoicomonadaceae. In this study, we isolated a novel Endozoicomonas DMSP degrader and observed a distinct DMSP metabolic trend in two phylogenetically close dddD-harboring Endozoicomonas species, confirmed genetically by comparative transcriptomic profiling and visualization of the change of DMSP stable isotopes in bacterial cells using nanoscale secondary ion spectrometry. Furthermore, we found that DMSP cleavage enzymes are ubiquitous in coral Endozoicomonas with a preference for having DddD lyase. We speculate that harboring DMSP degrading genes enables Endozoicomonas to successfully colonize various coral species across the globe.

SAR92 clade bacteria are potentially important DMSP degraders and sources of climate-active gases in marine environments

Dimethylsulfoniopropionate (DMSP) is one of Earth's most abundant organosulfur molecules, which can be catabolized by marine bacteria to release climate-active gases through the cleavage and/or demethylation pathways. The marine SAR92 clade is an abundant oligotrophic group of Gammaproteobacteria in coastal seawater, but their ability to catabolize DMSP is untested. Three SAR92 clade strains isolated from coastal seawater in this study and the SAR92 representative strain HTCC2207 were all shown to catabolize DMSP as a carbon source. All the SAR92 clade strains exhibited DMSP lyase activity producing dimethylsulfide (DMS) and their genomes encoded a ratified DddD DMSP lyase. In contrast, only HTCC2207 and two isolated strains contained the DMSP demethylase dmdA gene and potentially simultaneously demethylated and cleaved DMSP to produce methanethiol (MeSH) and DMS. In SAR92 clade strains with dddD and dmdA, transcription of these genes was inducible by DMSP substrate. Bioinformatic analysis indicated that SAR92 clade bacteria containing and transcribing DddD and DmdA were widely distributed in global oceans, especially in polar regions. This study highlights the SAR92 clade of oligotrophic bacteria as potentially important catabolizers of DMSP and sources of the climate-active gases MeSH and DMS in marine environments, particularly in polar regions.IMPORTANCECatabolism of dimethylsulfoniopropionate (DMSP) by marine bacteria has important impacts on the global sulfur cycle and climate. However, whether and how members of most oligotrophic bacterial groups participate in DMSP metabolism in marine environments remains largely unknown. In this study, by characterizing culturable strains, we have revealed that bacteria of the SAR92 clade, an abundant oligotrophic group of Gammaproteobacteria in coastal seawater, can catabolize DMSP through the DMSP lyase DddD-mediated cleavage pathway and/or the DMSP demethylase DmdA-mediated demethylation pathway to produce climate-active gases dimethylsulfide and methanethiol. Additionally, we found that SAR92 clade bacteria capable of catabolizing DMSP are widely distributed in global oceans. These results indicate that SAR92 clade bacteria are potentially important DMSP degraders and sources of climate-active gases in marine environments that have been overlooked, contributing to a better understanding of the roles and mechanisms of the oligotrophic bacteria in oceanic DMSP degradation.

Genome analysis of a coral-associated bacterial consortium highlights complementary hydrocarbon degradation ability and other beneficial mechanisms for the host

Here we report the oil degradation genetic potential of six oil-degrading bacteria (ODB), previously used as a bioremediation consortium, isolated from the hydrocoral Millepora alcicornis and seawater. The strains were identified as Halomonas sp. (LC_1), Cobetia sp. (LC_6), Pseudoalteromonas shioyasakiensis (LC_2), Halopseudomonas aestusnigri (LC_3), Shewanella algae (LC_4), and Brucella intermedia (LC_5). The taxonomic identification differed from that of the original paper when we used whole genome gene markers instead of just 16S rRNA gene. Genes responsible for the degradation of aromatic hydrocarbons and n-alkanes were found in all genomes, although different (and complementary) steps of the metabolic pathways were unique to each strain. Genes for naphthalene and toluene degradation were found in various strains. We annotated quinate degradation genes in LC_6, while LC_3 and LC_5 presented genes for biosurfactant and rhamnolipid biosynthesis. We also annotated genes related to beneficial mechanisms for corals, such as genes involved in nitrogen and DMSP metabolism, cobalamin biosynthesis and antimicrobial compounds production. Our findings reinforce the importance of using bacterial consortia for bioremediation approaches instead of single strains, due to their complementary genomic arsenals. We also propose a genome-based framework to select complementary ODB that can provide additional benefits to coral health.

Degradation of high-strength acrylic acid wastewater with anaerobic granulation technology: A mini-review

The anaerobic granulation technology has been successfully applied full-scale for treating high-strength recalcitrant acrylic acid wastewater. This mini-review highlighted the recalcitrance of acrylic acid and its biological degradation pathways. And then, the full-scale practices using anaerobic granulation technology for acrylic wastewater treatment were outlined. The granules are proposed to provide barriers for high-concentration acrylic acid to the embedded anaerobic microbes, maintaining its high degradation rate without apparent substrate inhibition. Based on this proposal, the prospects of applying anaerobic granulation technology to handle a wide range of high-strength recalcitrant wastewaters, to improve the current process performances, and to recover renewable resources were delineated. The anaerobic granulation for high-strength recalcitrant wastewater treatment is an emergent technology that can assist in fulfilling the appeals of the circular bioeconomy of modern society.

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.

You Exude What You Eat: How Carbon-, Nitrogen-, and Sulfur-Rich Organic Substrates Shape Microbial Community Composition and the Dissolved Organic Matter Pool

Phytoplankton is the major source of labile organic matter in the sunlit ocean, and they are therefore key players in most biogeochemical cycles. However, studies examining the heterotrophic bacterial cycling of specific phytoplankton-derived nitrogen (N)- and sulfur (S)-containing organic compounds are currently lacking at the molecular level. Therefore, the present study investigated how the addition of N-containing (glycine betaine [GBT]) and S-containing (dimethylsulfoniopropionate [DMSP]) organic compounds, as well as glucose, influenced the microbial production of new organic molecules and the microbial community composition. The chemical composition of microbial-produced dissolved organic matter (DOM) was analyzed by ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) demonstrating that CHO-, CHON-, and CHOS-containing molecules were enriched in the glucose, GBT, and DMSP experiments, respectively. High-throughput sequencing showed that Alteromonadales was the dominant group in the glucose, while Rhodobacterales was the most abundant group in both the GBT and DMSP experiments. Cooccurrence network analysis furthermore indicated more complex linkages between the microbial community and organic molecules in the GBT compared with the other two experiments. Our results shed light on how different microbial communities respond to distinct organic compounds and mediate the cycling of ecologically relevant compounds. IMPORTANCE Nitrogen (N)- and sulfur (S)-containing compounds are normally considered part of the labile organic matter pool that fuels heterotrophic bacterial activity in the ocean. Both glycine betaine (GBT) and dimethylsulfoniopropionate (DMSP) are representative N- and S-containing organic compounds, respectively, that are important phytoplankton cellular compounds. The present study therefore examined how the microbial community and the organic matter they produce are influenced by the addition of carbohydrate-containing (glucose), N-containing (GBT), and S-containing (DMSP) organic compounds. The results demonstrate that when these carbon-, N-, and S-rich compounds are added separately, the organic molecules produced by the bacteria growing on them are enriched in the same elements. Similarly, the microbial community composition was also distinct when different compounds were added as the substrate. Overall, this study demonstrates how the microbial communities metabolize and transform different substrates thereby, expanding our understanding of the complexity of links between microbes and substrates in the ocean.

Ecology of Methanonatronarchaeia

Methanonatronarchaeia represents a deep-branching phylogenetic lineage of extremely halo(alkali)philic and moderately thermophilic methyl-reducing methanogens belonging to the phylum Halobacteriota. It includes two genera, the alkaliphilic Methanonatronarchaeum and the neutrophilic Ca. Methanohalarchaeum. The former is represented by multiple closely related pure culture isolates from hypersaline soda lakes, while the knowledge about the latter is limited to a few mixed cultures with anaerobic haloarchaea. To get more insight into the distribution and ecophysiology of this enigmatic group of extremophilic methanogens, potential activity tests and enrichment cultivation with different substrates and at different conditions were performed with anaerobic sediment slurries from various hypersaline lakes in Russia. Methanonatronarchaeum proliferated exclusively in hypersaline soda lake samples mostly at elevated temperature, while at mesophilic conditions it coexisted with the extremely salt-tolerant methylotroph Methanosalsum natronophilum. Methanonatronarchaeum was also able to serve as a methylotrophic or hydrogenotrophic partner in several thermophilic enrichment cultures with fermentative bacteria. Ca. Methanohalarchaeum did not proliferate at mesophilic conditions and at thermophilic conditions it competed with extremely halophilic and moderately thermophilic methylotroph Methanohalobium, which it outcompeted at a combination of elevated temperature and methyl-reducing conditions. Overall, the results demonstrated that Methanonatronarchaeia are specialized extremophiles specifically proliferating in conditions of elevated temperature coupled with extreme salinity and simultaneous availability of a wide range of C₁ -methylated compounds and H₂ /formate.

Dynamic Diatom-Bacteria Consortia in Synthetic Plankton Communities

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 CO 2 .

GC-MS profiling of volatile metabolites produced by Klebsiella pneumoniae

Currently used methods for diagnosing ventilator-associated pneumonia (VAP) are complex, time-consuming and require invasive procedures while empirical antibacterial therapy applies broad spectrum antibiotics that may promote antimicrobial resistance. Hence, novel and fast methods based on alternative markers are needed for VAP detection and differentiation of causative pathogens. Pathogenic bacteria produce a broad range of volatile organic compounds (VOCs), some of which may potentially serve as biomarkers for microorganism identification. Additionally, monitoring of dynamically changing VOCs concentration profiles may indicate emerging pneumonia and allow timely implementation of appropriate antimicrobial treatment. This study substantially extends the knowledge on bacterial metabolites providing the unambiguous identification of volatile metabolites produced by carbapenem-resistant and susceptible strains of Klebsiella pneumoniae (confirmed with pure standards in addition to mass spectra match) but also revealing their temporary concentration profiles (along the course of pathogen proliferation) and dependence on the addition of antibiotic (imipenem) to bacteria. Furthermore, the clinical strains of K. pneumoniae isolated from bronchoalveolar lavage specimens collected from mechanically ventilated patients were investigated to reveal, whether bacterial metabolites observed in model experiments with reference strains could be relevant for wild pathogens as well. In all experiments, the headspace samples from bacteria cultures were collected on multibed sorption tubes and analyzed by GC-MS. Sampling was done under strictly controlled conditions at seven time points (up to 24 h after bacteria inoculation) to follow the dynamic changes in VOC concentrations, revealing three profiles: release proportional to bacteria load, temporary maximum and uptake. Altogether 32 VOCs were released by susceptible and 25 VOCs by resistant strain, amongst which 2-pentanone, 2-heptanone, and 2-nonanone were significantly higher for carbapenem-resistant KPN. Considerably more metabolites (n = 64) were produced by clinical isolates and in higher diversity compared to reference KPN strains.

A tripartite model system for Southern Ocean diatom-bacterial interactions reveals the coexistence of competing symbiotic strategies

Southern Ocean (SO) diatoms play an important role in global carbon flux, and their influence on carbon export is directly linked to interactions with epiphytic bacteria. Bacterial symbionts that increase diatom growth promote atmospheric carbon uptake, while bacterial degraders divert diatom biomass into the microbial loop where it can then be released as carbon dioxide through respiration. To further explore SO diatom-bacterial associations, a natural model system is needed that is representative of these diverse and important interactions. Here, we use concurrent cultivation to isolate a species of the ecologically-important SO diatom, Pseudo-nitzschia subcurvata, and its co-occurring bacteria. Although vitamin-depleted, axenic Pseudo-nitzschia grew poorly in culture, addition of a co-isolated Roseobacter promoted diatom growth, while addition of a co-isolated Flavobacterium negatively impacted diatom growth. Microscopy revealed both bacterial isolates are physically associated with diatom cells and genome sequencing identified important predicted functions including vitamin synthesis, motility, cell attachment mechanisms, and diverse antimicrobial weapons that could be used for interbacterial competition. These findings revealed the natural coexistence of competing symbiotic strategies of diatom-associated bacteria in the SO, and the utility of this tripartite system, composed of a diatom and two bacterial strains, as a co-culture model to probe ecological-relevant interactions between diatoms and the bacteria that compete for access to the phycosphere.

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

BACKGROUND

Ubiquitous 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.

RESULTS

Here, 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.

CONCLUSIONS

This 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. Video abstract.

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.

Biogeographical and seasonal dynamics of the marine Roseobacter community and ecological links to DMSP-producing phytoplankton

Ecological interactions between marine bacteria and phytoplankton play a pivotal role in governing the ocean's major biogeochemical cycles. Among these, members of the marine Roseobacter Group (MRG) can establish mutualistic relationships with phytoplankton that are, in part, maintained by exchanges of the organosulfur compound, dimethylsulfoniopropionate (DMSP). Yet most of what is known about these interactions has been derived from culture-based laboratory studies. To investigate temporal and spatial co-occurrence patterns between members of the MRG and DMSP-producing phytoplankton we analysed 16S and 18S rRNA gene amplicon sequence variants (ASVs) derived from 5 years of monthly samples from seven environmentally distinct Australian oceanographic time-series. The MRG and DMSP-producer communities often displayed contemporaneous seasonality, which was greater in subtropical and temperate environments compared to tropical environments. The relative abundance of both groups varied latitudinally, displaying a poleward increase, peaking (MRG at 33% of total bacteria, DMSP producers at 42% of eukaryotic phototrophs) during recurrent spring-summer phytoplankton blooms in the most temperate site (Maria Island, Tasmania). Network analysis identified 20,140 significant positive correlations between MRG ASVs and DMSP producers and revealed that MRGs exhibit significantly stronger correlations to high DMSP producers relative to other DMSP-degrading bacteria (Pelagibacter, SAR86 and Actinobacteria). By utilising the power of a continental network of oceanographic time-series, this study provides in situ confirmation of interactions found in laboratory studies and demonstrates that the ecological dynamics of an important group of marine bacteria are shaped by the production of an abundant and biogeochemically significant organosulfur compound.

Quorum Sensing Bacteria in the Phycosphere of HAB Microalgae and Their Ecological Functions Related to Cross-Kingdom Interactions

It has been proven that the relationship between microalgae and bacteria affects the dynamic process of harmful algal blooms (HABs). Microalgae-associated microorganisms widely exist in the phycosphere and play an essential role in algae-bacteria cross-kingdom interactions. Among these processes, quorum sensing (QS), as a communication system of bacteria, is thought to participate in algae-bacteria interactions. However, the species of QS bacteria in the phycosphere and their ecological function are still unknown. In this study, microalgae-associated microorganisms with a QS system were screened by the biosensor method and identified based on 16S rRNA gene analysis. The types and number of acyl-L-homoserine lactone (AHL) signalling molecules produced by QS bacteria were analysed by thin layer chromatography (TLC) bioautography and gas chromatography-mass spectrometer (GC-MS). The film formation, β-dimethylmercaptopropionic (DMSP) degradation and algae growth effects of QS bacteria were investigated. The results showed that 113 QS bacteria were isolated from 842 microalgae-associated bacteria. Detection of AHL molecules in 10 different species of QS bacteria showed that most of them were N-(3-Oxodecanoyl)-L-homoserine lactone (OC10-HSL), N-Octanoyl-L-homoserine lactone (C8-HSL) and N-(3-Oxooctanoyl)-L-homoserine lactone (OC8-HSL). All 10 QS bacteria had film-forming ability, and they could degrade DMSP (except strain E26). The crude metabolic extracts of the 10 QS bacteria can inhibit or promote microalgae growth to different degrees. Our study is helpful to understand the role of microalgae-associated microorganisms with the QS system in algae-bacteria interactions and community succession of HAB microalgae.

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.

Naturally occurring fire coral clones demonstrate a genetic and environmental basis of microbiome composition

Coral microbiomes are critical to holobiont functioning, but much remains to be understood about how prevailing environment and host genotype affect microbial communities in ecosystems. Resembling human identical twin studies, we examined bacterial community differences of naturally occurring fire coral clones within and between contrasting reef habitats to assess the relative contribution of host genotype and environment to microbiome structure. Bacterial community composition of coral clones differed between reef habitats, highlighting the contribution of the environment. Similarly, but to a lesser extent, microbiomes varied across different genotypes in identical habitats, denoting the influence of host genotype. Predictions of genomic function based on taxonomic profiles suggest that environmentally determined taxa supported a functional restructuring of the microbial metabolic network. In contrast, bacteria determined by host genotype seemed to be functionally redundant. Our study suggests microbiome flexibility as a mechanism of environmental adaptation with association of different bacterial taxa partially dependent on host genotype.

Dimethylsulfoniopropionate Biosynthetic Bacteria in the Subseafloor Sediments of the South China Sea

Dimethylsulfoniopropionate (DMSP) is one of Earth’s most abundant organosulfur molecules, and bacteria in marine sediments have been considered significant producers. However, the vertical profiles of DMSP content and DMSP-producing bacteria in subseafloor sediment have not been described. Here, we used culture-dependent and -independent methods to investigate microbial DMSP production and cycling potential in South China Sea (SCS) sediment. The DMSP content of SCS sediment decreased from 11.25 to 20.90 nmol g^–1 in the surface to 0.56–2.08 nmol g^–1 in the bottom layers of 8-m-deep subseafloor sediment cores (n = 10). Very few eukaryotic plastid sequences were detected in the sediment, supporting bacteria and not algae as important sediment DMSP producers. Known bacterial DMSP biosynthesis genes (dsyB and mmtN) were only predicted to be in 0.0007–0.0195% of sediment bacteria, but novel DMSP-producing isolates with potentially unknown DMSP synthesis genes and/or pathways were identified in these sediments, including Marinobacter (Gammaproteobacteria) and Erythrobacter (Alphaproteobacteria) sp. The abundance of bacteria with the potential to produce DMSP decreased with sediment depth and was extremely low at 690 cm. Furthermore, distinct DMSP-producing bacterial groups existed in surface and subseafloor sediment samples, and their abundance increased when samples were incubated under conditions known to enrich for DMSP-producing bacteria. Bacterial DMSP catabolic genes were also most abundant in the surface oxic sediments with high DMSP concentrations. This study extends the current knowledge of bacterial DMSP biosynthesis in marine sediments and implies that DMSP biosynthesis is not only confined to the surface oxic sediment zones. It highlights the importance of future work to uncover the DMSP biosynthesis genes/pathways in novel DMSP-producing bacteria.

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.

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.

DiTing: A Pipeline to Infer and Compare Biogeochemical Pathways From Metagenomic and Metatranscriptomic Data

Metagenomics and metatranscriptomics are powerful methods to uncover key micro-organisms and processes driving biogeochemical cycling in natural ecosystems. Databases dedicated to depicting biogeochemical pathways (for example, metabolism of dimethylsulfoniopropionate (DMSP), which is an abundant organosulfur compound) from metagenomic/metatranscriptomic data are rarely seen. Additionally, a recognized normalization model to estimate the relative abundance and environmental importance of pathways from metagenomic and metatranscriptomic data has not been organized to date. These limitations impact the ability to accurately relate key microbial-driven biogeochemical processes to differences in environmental conditions. Thus, an easy-to-use, specialized tool that infers and visually compares the potential for biogeochemical processes, including DMSP cycling, is urgently required. To solve these issues, we developed DiTing, a tool wrapper to infer and compare biogeochemical pathways among a set of given metagenomic or metatranscriptomic reads in one step, based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) and a manually created DMSP cycling gene database. Accurate and specific formulae for over 100 pathways were developed to calculate their relative abundance. Output reports detail the relative abundance of biogeochemical pathways in both text and graphical format. DiTing was applied to simulated metagenomic data and resulted in consistent genetic features of simulated benchmark genomic data. Subsequently, when applied to natural metagenomic and metatranscriptomic data from hydrothermal vents and the Tara Ocean project, the functional profiles predicted by DiTing were correlated with environmental condition changes. DiTing can now be confidently applied to wider metagenomic and metatranscriptomic datasets, and it is available at https://github.com/xuechunxu/DiTing.

Divergent Genomic Adaptations in the Microbiomes of Arctic Subzero Sea-Ice and Cryopeg Brines

Subzero hypersaline brines are liquid microbial habitats within otherwise frozen environments, where concentrated dissolved salts prevent freezing. Such extreme conditions presumably require unique microbial adaptations, and possibly altered ecologies, but specific strategies remain largely unknown. Here we examined prokaryotic taxonomic and functional diversity in two seawater-derived subzero hypersaline brines: first-year sea ice, subject to seasonally fluctuating conditions; and ancient cryopeg, under relatively stable conditions geophysically isolated in permafrost. Overall, both taxonomic composition and functional potential were starkly different. Taxonomically, sea-ice brine communities (∼10⁵ cells mL^–1) had greater richness, more diversity and were dominated by bacterial genera, including Polaribacter, Paraglaciecola, Colwellia, and Glaciecola, whereas the more densely inhabited cryopeg brines (∼10⁸ cells mL^–1) lacked these genera and instead were dominated by Marinobacter. Functionally, however, sea ice encoded fewer accessory traits and lower average genomic copy numbers for shared traits, though DNA replication and repair were elevated; in contrast, microbes in cryopeg brines had greater genetic versatility with elevated abundances of accessory traits involved in sensing, responding to environmental cues, transport, mobile elements (transposases and plasmids), toxin-antitoxin systems, and type VI secretion systems. Together these genomic features suggest adaptations and capabilities of sea-ice communities manifesting at the community level through seasonal ecological succession, whereas the denser cryopeg communities appear adapted to intense bacterial competition, leaving fewer genera to dominate with brine-specific adaptations and social interactions that sacrifice some members for the benefit of others. Such cryopeg genomic traits provide insight into how long-term environmental stability may enable life to survive extreme conditions.

Roseobacters in a Sea of Poly- and Paraphyly: Whole Genome-Based Taxonomy of the Family Rhodobacteraceae and the Proposal for the Split of the "Roseobacter Clade" Into a Novel Family, Roseobacteraceae fam. nov

The family Rhodobacteraceae consists of alphaproteobacteria that are metabolically, phenotypically, and ecologically diverse. It includes the roseobacter clade, an informal designation, representing one of the most abundant groups of marine bacteria. The rapid pace of discovery of novel roseobacters in the last three decades meant that the best practice for taxonomic classification, a polyphasic approach utilizing phenotypic, genotypic, and phylogenetic characteristics, was not always followed. Early efforts for classification relied heavily on 16S rRNA gene sequence similarity and resulted in numerous taxonomic inconsistencies, with several poly- and paraphyletic genera within this family. Next-generation sequencing technologies have allowed whole-genome sequences to be obtained for most type strains, making a revision of their taxonomy possible. In this study, we performed whole-genome phylogenetic and genotypic analyses combined with a meta-analysis of phenotypic data to review taxonomic classifications of 331 type strains (under 119 genera) within the Rhodobacteraceae family. Representatives of the roseobacter clade not only have different environmental adaptions from other Rhodobacteraceae isolates but were also found to be distinct based on genomic, phylogenetic, and in silico-predicted phenotypic data. As such, we propose to move this group of bacteria into a new family, Roseobacteraceae fam. nov. In total, reclassifications resulted to 327 species and 128 genera, suggesting that misidentification is more problematic at the genus than species level. By resolving taxonomic inconsistencies of type strains within this family, we have established a set of coherent criteria based on whole-genome-based analyses that will help guide future taxonomic efforts and prevent the propagation of errors.

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.

Tritonibacter aquimaris sp. nov. and Tritonibacter litoralis sp. nov., two novel members of the Roseobacter group isolated from coastal seawater

Two Gram-stain-negative bacterial strains, SM1969^T and SM1979^T, were isolated from coastal surface seawater of Qingdao, China. They were taxonomically characterized by the phylogenetic, genomic, chemotaxonomic and phenotypic analyses. The two strains shared 97.0% 16S rRNA gene sequence similarity with each other and the highest similarity (96.8-97.5%) with type strains of six species in the genera Shimia, Tritonibacter and Tropicibacter in the Roseobacter group of the family Rhodobacteraceae. In the phylogenetic tree based on single-copy orthologous clusters (OCs), both strains clustered with known species of the genus Tritonibacter and together formed a separate branch adjacent to Tritonibacter ulvae. Although sharing many chemotaxonomic and phenotypic characteristics, the two strains could be differentiated from each other and closely related species by numerous traits. Particularly, strain SM1969^T was found to have a DMSP lyase coding gene dddW in its genome and have the ability to produce DMS from DMSP while strain SM1979^T was not. The average nucleotide identity and in silico DNA-DNA hybridization values between strains SM1969^T and SM1979^T and type strains of closely related species were all below the thresholds to discriminate bacterial species, demonstrating that they constitute two new species in the genus Tritonibacter. The names Tritonibacter aquimaris sp. nov. and Tritonibacter litoralis sp. nov. are proposed for the two new species, with type strains being SM1969^T (= MCCC 1K04320^T = KCTC 72843^T) and SM1979^T (= MCCC 1K04321^T = KCTC 72842^T), respectively.

Anaerobic microbial methanol conversion in marine sediments

Methanol is an ubiquitous compound that plays a role in microbial processes as a carbon and energy source, intermediate in metabolic processes or as end product in fermentation. In anoxic environments, methanol can act as the sole carbon and energy source for several guilds of microorganisms: sulfate-reducing microorganisms, nitrate-reducing microorganisms, acetogens and methanogens. In marine sediments, these guilds compete for methanol as their common substrate, employing different biochemical pathways. In this review, we will give an overview of current knowledge of the various ways in which methanol reaches marine sediments, the ecology of microorganisms capable of utilizing methanol and their metabolism. Furthermore, through a metagenomic analysis, we shed light on the unknown diversity of methanol utilizers in marine sediments which is yet to be explored.

The organosulfur compound dimethylsulfoniopropionate (DMSP) is utilized as an osmoprotectant by Vibrio species

Dimethylsulfoniopropionate (DMSP), a key component of the global geochemical sulfur cycle, is a secondary metabolite produced in large quantities by marine phytoplankton and utilized as an osmoprotectant, thermoprotectant and antioxidant. Marine bacteria can use two pathways to degrade and catabolize DMSP, a demethylation pathway and a cleavage pathway that produces the climate active gas dimethylsulfide (DMS). Whether marine bacteria can also accumulate DMSP as an osmoprotectant to maintain the turgor pressure of the cell in response to changes in external osmolarity has received little attention. The marine halophile Vibrio parahaemolyticus, contains at least six osmolyte transporters, four betaine carnitine choline transport (BCCT) carriers BccT1-BccT4 and two ABC-family ProU transporters. In this study, we showed that DMSP is used as an osmoprotectant by V. parahaemolyticus and several other Vibrio species including V. cholerae and V. vulnificus Using a V. parahaemolyticus proU double mutant, we demonstrated that these ABC transporters are not required for DMSP uptake. However, a bccT null mutant lacking all four BCCTs had a growth defect compared to wild type in high salinity media supplemented with DMSP. Using mutants possessing only one functional BCCT in growth pattern assays, we identified two BCCT-family transporters, BccT1 and BccT2, which are carriers of DMSP. The only V. parahaemolyticus BccT homolog that V. cholerae and V. vulnificus possess is BccT3 and functional complementation in Escherichia coli MKH13 showed V. cholerae VcBccT3 could transport DMSP. In V. vulnificus strains, we identified and characterized an additional BCCT family transporter, which we named BccT5 that was also a carrier for DMSP.Importance DMSP is present in the marine environment, produced in large quantities by marine phytoplankton as an osmoprotectant, and is an important component of the global geochemical sulfur cycle. This algal osmolyte has not been previously investigated for its role in marine heterotrophic bacterial osmotic stress response. Vibrionaceae are marine species, many of which are halophiles exemplified by V. parahaemolyticus, a species that possesses at least six transporters for the uptake of osmolytes. Here, we demonstrated that V. parahaemolyticus and other Vibrio species can accumulate DMSP as an osmoprotectant and show that several BCCT family transporters uptake DMSP. These studies suggest that DMSP is a significant bacterial osmoprotectant, which may be important for understanding the fate of DMSP in the environment. DMSP is produced and present in coral mucus and Vibrio species form part of the microbial communities associated with them. The function of DMSP in these interactions is unclear, but could be an important driver for these associations allowing Vibrio proliferation. This work suggests that DMSP likely has an important role in heterotrophic bacteria ecology than previously appreciated.

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.

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.

A Model Roseobacter, Ruegeria pomeroyi DSS-3, Employs a Diffusible Killing Mechanism To Eliminate Competitors

The Roseobacter clade is a group of alphaproteobacteria that have diverse metabolic and regulatory capabilities. They are abundant in marine environments and have a substantial role in marine ecology and biogeochemistry. However, interactions between roseobacters and other bacterioplankton have not been extensively explored. In this study, we identify a killing mechanism in the model roseobacter Ruegeria pomeroyi DSS-3 by coculturing it with a group of phylogenetically diverse bacteria. The killing mechanism is diffusible and occurs when cells are grown both on surfaces and in suspension and is dependent on cell density. A screen of random transposon mutants revealed that the killing phenotype, as well as resistance to killing, require genes within an ∼8-kb putative gamma-butyrolactone synthesis gene cluster, which resembles similar pheromone-sensing systems in actinomycetes that regulate secondary metabolite production, including antimicrobials. Transcriptomics revealed the gene cluster is highly upregulated in wild-type DSS-3 compared to a nonkiller mutant when grown in liquid coculture with a roseobacter target. Our findings show that R. pomeroyi has the capability to eliminate closely and distantly related competitors, providing a mechanism to alter the community structure and function in its native habitats.IMPORTANCE Bacteria carry out critical ecological and biogeochemical processes and form the foundations of ecosystems. Identifying the factors that influence microbial community composition and the functional capabilities encoded within them is key to predicting how microbes impact an ecosystem. Because microorganisms must compete for limited space and nutrients to promote their own propagation, they have evolved diverse mechanisms to outcompete or kill competitors. However, the genes and regulatory strategies that promote such competitive abilities are largely underexplored, particularly in free-living marine bacteria. Here, genetics and omics techniques are used to investigate how a model marine bacterium is capable of quickly eliminating natural competitors in coculture. We determined that a previously uncharacterized horizontally acquired gene cluster is required for this bacterium to kill diverse competitors. This work represents an important step toward understanding the mechanisms bacterial populations can use to become dominant members in marine microbial communities.

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.

DNA stable-isotope probing reveals potential key players for microbial decomposition and degradation of diatom-derived marine particulate matter

Microbially mediated decomposition of particulate organic carbon (POC) is a central component of the oceanic carbon cycle, controlling the flux of organic carbon from the surface ocean to the deep ocean. Yet, the specific microbial taxa responsible for POC decomposition and degradation in the deep ocean are still unknown. To target the active microbial lineages involved in these processes, ¹³ C-labeled particulate organic matter (POM) was used as a substrate to incubate particle-attached (PAM) and free-living microbial (FLM) assemblages from the epi- and bathypelagic zones of the New Britain Trench (NBT). By combining DNA stable-isotope probing and Illumina Miseq high-throughput sequencing of bacterial 16S rRNA gene, we identified 14 active bacterial taxonomic groups that implicated in the decomposition of ¹³ C-labeled POM at low and high pressures under the temperature of 15°C. Our results show that both PAM and FLM were able to decompose POC and assimilate the released DOC. However, similar bacterial taxa in both the PAM and FLM assemblages were involved in POC decomposition and DOC degradation, suggesting the decoupling between microbial lifestyles and ecological functions. Microbial decomposition of POC and degradation of DOC were accomplished primarily by particle-attached bacteria at atmospheric pressure and by free-living bacteria at high pressures. Overall, the POC degradation rates were higher at atmospheric pressure (0.1 MPa) than at high pressures (20 and 40 MPa) under 15°C. Our results provide direct evidence linking the specific particle-attached and free-living bacterial lineages to decomposition and degradation of diatomic detritus at low and high pressures and identified the potential mediators of POC fluxes in the epi- and bathypelagic zones.

Phytoplankton-derived zwitterionic gonyol and dimethylsulfonioacetate interfere with microbial dimethylsulfoniopropionate sulfur cycling

The marine sulfur cycle is substantially fueled by the phytoplankton osmolyte dimethylsulfoniopropionate (DMSP). This metabolite can be metabolized by bacteria, which results in the emission of the volatile sulfur species methanethiol (MeSH) and the climate‐cooling dimethylsulfide (DMS). It is generally accepted that bacteria contribute significantly to DMSP turnover. We show that the other low molecular weight zwitterionic dimethylsulfonio compounds dimethylsulfonioacetate (DMSA) and gonyol are also widely distributed in phytoplankton and can serve as alternative substrates for volatile production. DMSA was found in 11 of the 16 surveyed phytoplankton species, and gonyol was detected in all haptophytes and dinoflagellates. These prevalent zwitterions are also metabolized by marine bacteria. The patterns of bacterial MeSH and DMS release were dependent on the zwitterions present. Certain bacteria metabolize DMSA and gonyol and release MeSH, in others gonyol inhibited DMS‐producing enzymes. If added in addition to DMSP, gonyol entirely inhibited the formation of volatiles in Ruegeria pomeroyi. In contrast, no substantial effect of this compound was observed in the DMSP metabolism of Halomonas sp. We argue that the production of DMSA and gonyol and their inhibitory properties on the release of volatiles from DMSP has the potential to modulate planktonic sulfur cycling between species.

Metagenomic Insights Into the Cycling of Dimethylsulfoniopropionate and Related Molecules in the Eastern China Marginal Seas

The microbial cycling of dimethylsulfoniopropionate (DMSP) and its gaseous catabolites dimethylsulfide (DMS) and methanethiol (MeSH) are important processes in the global sulfur cycle, marine microbial food webs, signaling pathways, atmospheric chemistry, and potentially climate regulation. Many functional genes have been identified and used to study the genetic potential of microbes to produce and catabolize these organosulfur compounds in different marine environments. Here, we sampled seawater, marine sediment and hydrothermal sediment, and polymetallic sulfide in the eastern Chinese marginal seas and analyzed their microbial communities for the genetic potential to cycle DMSP, DMS, and MeSH using metagenomics. DMSP was abundant in all sediment samples, but was fivefold less prominent in those from hydrothermal samples. Indeed, Yellow Sea (YS) sediment samples had DMSP concentrations two orders of magnitude higher than in surface water samples. Bacterial genetic potential to synthesize DMSP (mainly in Rhodobacteraceae bacteria) was far higher than for phytoplankton in all samples, but particularly in the sediment where no algal DMSP synthesis genes were detected. Thus, we propose bacteria as important DMSP producers in these marine sediments. DMSP catabolic pathways mediated by the DMSP lyase DddP (prominent in Pseudomonas and Mesorhizobium bacteria) and DMSP demethylase DmdA enzymes (prominent in Rhodobacteraceae bacteria) and MddA-mediated MeSH S-methylation were very abundant in Bohai Sea and Yellow Sea sediments (BYSS) samples. In contrast, the genetic potential for DMSP degradation was very low in the hydrothermal sediment samples-dddP was the only catabolic gene detected and in only one sample. However, the potential for DMS production from MeSH (mddA) and DMS oxidation (dmoA and ddhA) was relatively abundant. This metagenomics study does not provide conclusive evidence for DMSP cycling; however, it does highlight the potential importance of bacteria in the synthesis and catabolism of DMSP and related compounds in diverse sediment environments.

Metabolic relationships of uncultured bacteria associated with the microalgae Gambierdiscus

Microbial communities inhabit algae cell surfaces and produce a variety of compounds that can impact the fitness of the host. These interactions have been studied via culturing, single-gene diversity and metagenomic read survey methods that are limited by culturing biases and fragmented genetic characterizations. Higher-resolution frameworks are needed to resolve the physiological interactions within these algal-bacterial communities. Here, we infer the encoded metabolic capabilities of four uncultured bacterial genomes (reconstructed using metagenomic assembly and binning) associated with the marine dinoflagellates Gambierdiscus carolinianus and G. caribaeus. Phylogenetic analyses revealed that two of the genomes belong to the commonly algae-associated families Rhodobacteraceae and Flavobacteriaceae. The other two genomes belong to the Phycisphaeraceae and include the first algae-associated representative within the uncultured SM1A02 group. Analyses of all four genomes suggest these bacteria are facultative aerobes, with some capable of metabolizing phytoplanktonic organosulfur compounds including dimethylsulfoniopropionate and sulfated polysaccharides. These communities may biosynthesize compounds beneficial to both the algal host and other bacteria, including iron chelators, B vitamins, methionine, lycopene, squalene and polyketides. These findings have implications for marine carbon and nutrient cycling and provide a greater depth of understanding regarding the genetic potential for complex physiological interactions between microalgae and their associated bacteria.

Seasonal dynamics of marine snow-associated and free-living demethylating bacterial communities in the coastal northern Adriatic Sea

The extent of DMSP demethylation has been hypothesized to depend on DMSP availability and bacterial sulfur demand, which might lead to niche differentiation of the demethylating bacterial community. In this study, we determined DMSP concentrations in marine snow and the ambient water over a seasonal cycle and linked DMSP concentrations to the abundance of bacteria harbouring the demethylation dmdA gene in the Adriatic Sea. In marine snow, DMSP concentrations were up to four times higher than in the ambient water and three times higher in marine snow in summer than in winter. The average dmdA:recA gene ratio over the sampling period was 0.40 ± 0.24 in marine snow and 0.48 ± 0.21 in the ambient water. However, at the subclade level, differences in the demethylating bacterial community of marine snow and the ambient water were apparent. Seasonal patterns of potentially demethylating bacteria were best visible at the oligotype level. In the ambient water, the SAR116 and the OM60/NOR5 clade were composed of oligotypes that correlated to high DMSP concentrations, while oligotypes of the Rhodospirillales correlated to low DMSP concentrations. Our results revealed a pronounced seasonal variability and spatial heterogeneity in DMSP concentrations and the associated demethylating bacterial community.

Sulfur metabolites in the pelagic ocean

Marine microorganisms play crucial roles in Earth's element cycles through the production and consumption of organic matter. One of the elements whose fate is governed by microbial activities is sulfur, an essential constituent of biomass and a crucial player in climate processes. With sulfur already being well studied in the ocean in its inorganic forms, organic sulfur compounds are emerging as important chemical links between marine phytoplankton and bacteria. The high concentration of inorganic sulfur in seawater, which can readily be reduced by phytoplankton, provides a freely available source of sulfur for biomolecule synthesis. Mechanisms such as exudation and cell lysis release these phytoplankton-derived sulfur metabolites into seawater, from which they are rapidly assimilated by marine bacteria and archaea. Energy-limited bacteria use scavenged sulfur metabolites as substrates or for the synthesis of vitamins, cofactors, signalling compounds and antibiotics. In this Review, we examine the current knowledge of sulfur metabolites released into and taken up from the marine dissolved organic matter pool by microorganisms, and the ecological links facilitated by their diversity in structures, oxidation states and chemistry.

Sulfonate-based networks between eukaryotic phytoplankton and heterotrophic bacteria in the surface ocean

In the surface ocean, phytoplankton transform inorganic substrates into organic matter that fuels the activity of heterotrophic microorganisms, creating intricate metabolic networks that determine the extent of carbon recycling and storage in the ocean. Yet, the diversity of organic molecules and interacting organisms has hindered detection of specific relationships that mediate this large flux of energy and matter. Here, we show that a tightly coupled microbial network based on organic sulfur compounds (sulfonates) exists among key lineages of eukaryotic phytoplankton producers and heterotrophic bacterial consumers in the North Pacific Subtropical Gyre. We find that cultured eukaryotic phytoplankton taxa produce sulfonates, often at millimolar internal concentrations. These same phytoplankton-derived sulfonates support growth requirements of an open-ocean isolate of the SAR11 clade, the most abundant group of marine heterotrophic bacteria. Expression of putative sulfonate biosynthesis genes and sulfonate abundances in natural plankton communities over the diel cycle link sulfonate production to light availability. Contemporaneous expression of sulfonate catabolism genes in heterotrophic bacteria highlights active cycling of sulfonates in situ. Our study provides evidence that sulfonates serve as an ecologically important currency for nutrient and energy exchange between microbial autotrophs and heterotrophs, highlighting the importance of organic sulfur compounds in regulating ecosystem function.