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

Community stability of free-living and particle-attached prokaryotes in coastal waters across four seasons: insights from 9.5 years of weekly sampling

Free-living (FL) and particle-attached (PA) prokaryotes, having distinct ecological niches, play significant roles in marine ecosystems. These communities respond rapidly to environmental changes and exhibit seasonal patterns. However, their temporal stability, crucial for maintaining microbial community structure and function, remains poorly understood. This study assessed community stability, particularly in terms of resistance to environmental perturbations, and inferred regulatory mechanisms using weekly collected samples over 9.5 years from FL and PA communities in coastal water. Short-read amplicon sequencing revealed habitat-specific microbial compositions, with Actinobacteria and Euryarchaeota dominating FL community, while Planctomycetes and Verrucomicrobia prevailed in PA community. Network analysis, constructed based on relative abundance, uncovered seasonal co-occurrence patterns and highlighted keystone taxa, such as Nitrosopumilus in FL and Synechococcus in PA community, as critical for maintaining stability within specific seasons and niches. Seasonal variations in community stability indices suggest that higher network complexity can enhance resistance; however, excessive interactions with greater complexity may also undermine it. Furthermore, it was found that FL community stability was primarily affected by abiotic factors, likely due to direct exposure to environmental changes, whereas PA community stability was more influenced by biotic factors, as their association with particles fosters localized interactions and biological processes. These findings reveal the intricate balance between network complexity and stability and the importance of niche-specific approaches in ecological research. Our results contribute to a deeper understanding of marine microbial niche partitioning and provide insights into ecosystem management and conservation strategies, particularly regarding keystone taxa.

Genomic analysis of Vibrio sp. D3 reveals its role in marine sulfur cycling

Dimethylsulfoniopropionate (DMSP) is an important organosulfur compound, with key roles in global carbon and sulfur cycling, stress tolerance, chemotaxis, and, potentially, climate regulation. The strain Vibrio sp. D3 was isolated from the surface seawater samples in Qingdao coastal area, which could grow on DMSP as sole carbon source. Here, we report the complete genome sequence of strain D3 and analyzed its genomic characteristics related to the sulfur metabolism, especially DMSP. The genome of strain D3 contains two circular chromosomes of total 5,104,020 bp with a mean GC content of 44.87 %. DMSP transporter gene bccT and acryloy-CoA reductase gene acuI, which is essential in DMSP cleavage, are identified in the genome of Vibrio sp. D3. Potential DMSP demethylase gene dmdA (26.07 %, amino acid sequence identity) and DMSP lyase gene dddX (26.32 %, amino acid sequence identity) are predicted in the genome of strain D3, whose functions need further experimental verification. Vibrio sp. D3 also contains L-Met gamma-lyase (MegL) to generate MeSH from L-Met and complete assimilatory sulfate reduction pathway. Together, the genome of strain D3 reveals the possible DMSP catabolic pathways and supports its role in sulfur cycling.

Vertical distributions of dimethyl sulfide and dimethylsulfoniopropionate and impacts of DMSP lyase and bacteria in the Yellow Sea and East China Sea

Dimethyl sulfide (DMS), a degradation product of dimethylsulfoniopropionate (DMSP), is a significant trace gas influencing global temperature. This study examined the distribution of DMSP lyase activity (DLA) and the degradation of DMSP and dimethyl sulfoxide (DMSO) by bacteria to elucidate the influences of DMSP lyase and bacteria on the distributions of DMS and DMSP in the Yellow Sea and the East China Sea during the summer. We observed that DMS and DMSP concentrations in transect B, located near the Yellow Sea Cold Water Mass, declined with deepening water depth, coinciding with the changing trend of the temperatures. A positive correlation between Chl a and dissolved and particulate dimethylsulfoniopropionate (DMSPd,p) concentrations in transects B, D, F, P, and T indicated that DMSPd,p primarily originated from phytoplankton. The phytoplankton in transects D, F, and P thrived under the nutrient-rich conditions brought by the Yangtze Diluted Water. A positive correlation between DMS concentrations and DMSPd,p concentrations was found, suggesting that DMS originated from the degradation of DMSPd,p. Additionally, we successfully isolated twenty-one DMSP-degrading bacteria and twelve DMSO-degrading bacteria capable of utilizing DMSP or DMSO as their sole carbon and sulfur sources. DMSP was consumed by DMSP-degrading bacteria, which simultaneously transformed it into DMS. The DMS production pathway accounted for 2.5%-47.1% of the total DMSP degradation process. Furthermore, the addition of glucose enhanced DMSO degradation by DMSO-degrading bacteria by a factor of 4.5-7.0 compared to conditions without glucose. These findings advance our understanding of the key factors influencing DMS and DMSP dynamics, as well as the roles of DMSP lyase and bacteria in the organic sulfur cycle.

Dimethylsulfoniopropionate (DMSP): From Biochemistry to Global Ecological Significance

Dimethylsulfoniopropionate (DMSP) is one of Earth's most abundant organosulfur compounds with important roles in stress tolerance, chemotaxis, global carbon and sulfur cycling, and climate-active gas production. Diverse marine prokaryotes and eukaryotes produce DMSP via three known pathways (methylation, transamination, and decarboxylation) and metabolize DMSP via three further pathways (demethylation, cleavage, and oxidation). Over 20 key enzymes from these pathways have been identified that demonstrate the biodiversity and importance of DMSP cycling. The last dozen years have seen significant changes in our understanding of the enzymology and molecular mechanisms of these DMSP cycling enzymes through the application of biochemistry and structural biology. This has yielded more than 10 crystal structures and, in many cases, detailed explanations as to how and why organisms synthesis and metabolize DMSP. In this review, we describe recent progress in biochemical and mechanistic understandings of DMSP synthesis and metabolism, highlighting the important knowledge gleaned and current challenges that warrant further exploration.

Elucidation of Spartina dimethylsulfoniopropionate synthesis genes enables engineering of stress tolerant plants

The organosulfur compound dimethylsulfoniopropionate (DMSP) has key roles in stress protection, global carbon and sulfur cycling, chemotaxis, and is a major source of climate-active gases. Saltmarshes are global hotspots for DMSP cycling due to Spartina cordgrasses that produce exceptionally high concentrations of DMSP. Here, in Spartina anglica, we identify the plant genes that underpin high-level DMSP synthesis: methionine S-methyltransferase (MMT), S-methylmethionine decarboxylase (SDC) and DMSP-amine oxidase (DOX). Homologs of these enzymes are common in plants, but differences in expression and catalytic efficiency explain why S. anglica accumulates such high DMSP concentrations and other plants only accumulate low concentrations. Furthermore, DMSP accumulation in S. anglica is consistent with DMSP having a role in oxidative and osmotic stress protection. Importantly, administration of DMSP by root uptake or over-expression of Spartina DMSP synthesis genes confers plant tolerance to salinity and drought offering a route for future bioengineering for sustainable crop production.

Algal methylated compounds shorten the lag phase of Phaeobacter inhibens bacteria

The lag phase is key in resuming bacterial growth, but it remains underexplored particularly in environmental bacteria. Here we use transcriptomics and 13C-labelled metabolomics to show that the lag phase of the model marine bacterium Phaeobacter inhibens is shortened by methylated compounds produced by the microalgal partner, Emiliania huxleyi. Methylated compounds are abundantly produced and released by microalgae, and we show that their methyl groups can be collected by bacteria and assimilated through the methionine cycle. Our findings underscore the significance of methyl groups as a limiting factor during the lag phase and highlight the adjustability of this growth phase. In addition, we show that methylated compounds, typical of photosynthetic organisms, prompt diverse reductions in lag times in bacteria associated with algae and plants, potentially favouring early growth in some bacteria. These findings suggest ways to accelerate bacterial growth and underscore the significance of studying bacteria within an environmental context.

Alternative dimethylsulfoniopropionate biosynthesis enzymes in diverse and abundant microorganisms

Dimethylsulfoniopropionate (DMSP) is an abundant marine organosulfur compound with roles in stress protection, chemotaxis, nutrient and sulfur cycling and climate regulation. Here we report the discovery of a bifunctional DMSP biosynthesis enzyme, DsyGD, in the transamination pathway of the rhizobacterium Gynuella sunshinyii and some filamentous cyanobacteria not previously known to produce DMSP. DsyGD produces DMSP through its N-terminal DsyG methylthiohydroxybutyrate S-methyltransferase and C-terminal DsyD dimethylsulfoniohydroxybutyrate decarboxylase domains. Phylogenetically distinct DsyG-like proteins, termed DSYE, with methylthiohydroxybutyrate S-methyltransferase activity were found in diverse and environmentally abundant algae, comprising a mix of low, high and previously unknown DMSP producers. Algae containing DSYE, particularly bloom-forming Pelagophyceae species, were globally more abundant DMSP producers than those with previously described DMSP synthesis genes. This work greatly increases the number and diversity of predicted DMSP-producing organisms and highlights the importance of Pelagophyceae and other DSYE-containing algae in global DMSP production and sulfur cycling.

Reducing the Bacterial Lag Phase Through Methylated Compounds: Insights from Algal-Bacterial Interactions

The bacterial lag phase is a key period for resuming growth. Despite its significance, the lag phase remains underexplored, particularly in environmental bacteria. Here, we explore the lag phase of the model marine bacterium Phaeobacter inhibens when it transitions from starvation to growth with a microalgal partner. Utilizing transcriptomics and 13 C-labeled metabolomics, our study reveals that methylated compounds, which are abundantly produced by microalgae, shorten the bacterial lag phase. Our findings underscore the significance of methyl groups as a limiting factor during the lag phase and demonstrate that methyl groups can be harvested from algal compounds and assimilated through the methionine cycle. Furthermore, we show that methylated compounds, characteristic of photosynthetic organisms, induce variable reductions in lag times among bacteria associated with algae and plants. These findings highlight the adjustability of the bacterial lag phase and emphasize the importance of studying bacteria in an environmental context.

One-Sentence Summary

Bacteria use algal compounds as a metabolic shortcut to transition from starvation to growth.

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

IMPORTANCE

Catabolism 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.

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.

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.

Genomic exploration of coral-associated bacteria: identifying probiotic candidates to increase coral bleaching resilience in Galaxea fascicularis

BACKGROUND

Reef-building corals are acutely threatened by ocean warming, calling for active interventions to reduce coral bleaching and mortality. Corals associate with a wide diversity of bacteria which can influence coral health, but knowledge of specific functions that may be beneficial for corals under thermal stress is scant. Under the oxidative stress theory of coral bleaching, bacteria that scavenge reactive oxygen (ROS) or nitrogen species (RNS) are expected to enhance coral thermal resilience. Further, bacterial carbon export might substitute the carbon supply from algal photosymbionts, enhance thermal resilience and facilitate bleaching recovery. To identify probiotic bacterial candidates, we sequenced the genomes of 82 pure-cultured bacteria that were isolated from the emerging coral model Galaxea fascicularis.

RESULTS

Genomic analyses showed bacterial isolates were affiliated with 37 genera. Isolates such as Ruegeria, Muricauda and Roseovarius were found to encode genes for the synthesis of the antioxidants mannitol, glutathione, dimethylsulfide, dimethylsulfoniopropionate, zeaxanthin and/or β-carotene. Genes involved in RNS-scavenging were found in many G. fascicularis-associated bacteria, which represents a novel finding for several genera (including Pseudophaeobacter). Transporters that are suggested to export carbon (semiSWEET) were detected in seven isolates, including Pseudovibrio and Roseibium. Further, a range of bacterial strains, including strains of Roseibium and Roseovarius, revealed genomic features that may enhance colonisation and association of bacteria with the coral host, such as secretion systems and eukaryote-like repeat proteins.

CONCLUSIONS

Our work provides an in-depth genomic analysis of the functional potential of G. fascicularis-associated bacteria and identifies novel combinations of traits that may enhance the coral's ability to withstand coral bleaching. Identifying and characterising bacteria that are beneficial for corals is critical for the development of effective probiotics that boost coral climate resilience. Video Abstract.