Novel Insights Into Bacterial Dimethylsulfoniopropionate Catabolism in the East China Sea

Diversity and potential functional role of phyllosphere-associated actinomycetota isolated from cupuassu (Theobroma grandiflorum) leaves: implications for ecosystem dynamics and plant defense strategies

Exploring the intricate relationships between plants and their resident microorganisms is crucial not only for developing new methods to improve disease resistance and crop yields but also for understanding their co-evolutionary dynamics. Our research delves into the role of the phyllosphere-associated microbiome, especially Actinomycetota species, in enhancing pathogen resistance in Theobroma grandiflorum, or cupuassu, an agriculturally valuable Amazonian fruit tree vulnerable to witches' broom disease caused by Moniliophthora perniciosa. While breeding resistant cupuassu genotypes is a possible solution, the capacity of the Actinomycetota phylum to produce beneficial metabolites offers an alternative approach yet to be explored in this context. Utilizing advanced long-read sequencing and metagenomic analysis, we examined Actinomycetota from the phyllosphere of a disease-resistant cupuassu genotype, identifying 11 Metagenome-Assembled Genomes across eight genera. Our comparative genomic analysis uncovered 54 Biosynthetic Gene Clusters related to antitumor, antimicrobial, and plant growth-promoting activities, alongside cutinases and type VII secretion system-associated genes. These results indicate the potential of phyllosphere-associated Actinomycetota in cupuassu for inducing resistance or antagonism against pathogens. By integrating our genomic discoveries with the existing knowledge of cupuassu's defense mechanisms, we developed a model hypothesizing the synergistic or antagonistic interactions between plant and identified Actinomycetota during plant-pathogen interactions. This model offers a framework for understanding the intricate dynamics of microbial influence on plant health. In conclusion, this study underscores the significance of the phyllosphere microbiome, particularly Actinomycetota, in the broader context of harnessing microbial interactions for plant health. These findings offer valuable insights for enhancing agricultural productivity and sustainability.

Novel insights into dimethylsulfoniopropionate cleavage by deep subseafloor fungi

Dimethylsulfoniopropionate (DMSP), a key organic sulfur compound in marine and subseafloor sediments, is degraded by phytoplankton and bacteria, resulting in the release of the climate-active volatile gas dimethylsulfide (DMS). However, it remains unclear if dominant eukaryotic fungi in subseafloor sediments possess specific abilities and metabolic mechanisms for DMSP degradation and DMS formation. Our study provides the first evidence that fungi from coal-bearing sediments ∼2 km below the seafloor, such as Aspergillus spp., Chaetomium globosum, Cladosporium sphaerospermum, and Penicillium funiculosum, can degrade DMSP and produce DMS. In Aspergillus sydowii 29R-4-F02, which exhibited the highest DMSP-dependent DMS production rate (16.95 pmol/μg protein/min), two DMSP lyase genes, dddP and dddW, were identified. Remarkably, the dddW gene, previously observed only in bacteria, was found to be crucial for fungal DMSP cleavage. These findings not only extend the list of fungi capable of degrading DMSP, but also enhance our understanding of DMSP lyase diversity and the role of fungi in DMSP decomposition in subseafloor sedimentary ecosystems.

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.

Interaction between phytoplankton and heterotrophic bacteria in Arctic fjords during the glacial melting season as revealed by eDNA metabarcoding

The hydrographic variability in the fjords of Svalbard significantly influences water mass properties, causing distinct patterns of microbial diversity and community composition between surface and subsurface layers. However, surveys on the phytoplankton-associated bacterial communities, pivotal to ecosystem functioning in Arctic fjords, are limited. This study investigated the interactions between phytoplankton and heterotrophic bacterial communities in Svalbard fjord waters through comprehensive eDNA metabarcoding with 16S and 18S rRNA genes. The 16S rRNA sequencing results revealed a homogenous community composition including a few dominant heterotrophic bacteria across fjord waters, whereas 18S rRNA results suggested a spatially diverse eukaryotic plankton distribution. The relative abundances of heterotrophic bacteria showed a depth-wise distribution. By contrast, the dominant phytoplankton populations exhibited variable distributions in surface waters. In the network model, the linkage of phytoplankton (Prasinophytae and Dinophyceae) to heterotrophic bacteria, particularly Actinobacteria, suggested the direct or indirect influence of bacterial contributions on the fate of phytoplankton-derived organic matter. Our prediction of the metabolic pathways for bacterial activity related to phytoplankton-derived organic matter suggested competitive advantages and symbiotic relationships between phytoplankton and heterotrophic bacteria. Our findings provide valuable insights into the response of phytoplankton-bacterial interactions to environmental changes in Arctic fjords.

High dimethylsulfoniopropionate concentrations in the surface seawater over the marginal seas of China and the Northwest Pacific Ocean during May-July of 2021 following La Niña

The total dimethylsulfoniopropionate (DMSPt) concentrations over the surface seawater of China's marginal seas and the northwest Pacific Ocean (NWPO) in May-July 2021 (during the recessional period of La Niña) were analysed. The results showed that the DMSPt concentrations in the marginal seas of China varied from 4.73 to 775.96 nmol L-1, with an average value of 111.42 ± 129.30 nmol L-1 (average ± standard deviation). It was 2-12 times higher than those previously measured in the same seas and in the NWPO in this study. Significant positive correlations between DMSPt, chlorophyll-a and surface seawater temperature (SST) were observed in the SYS, the ECS and the NWPO. Moreover, their abnormally high SST was related to La Niña. These results suggested that high phytoplankton abundance was caused by abnormally high SST following La Niña, which further promoted DMSPt concentration increases. However, the increase of DMSPt was also related to other factors such as nutrients.

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

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

A new dimethylsulfoniopropionate lyase of the cupin superfamily in marine bacteria

Dimethylsulfoniopropionate (DMSP) is a marine organosulfur compound with important roles in stress protection, marine biogeochemical cycling, chemical signalling and atmospheric chemistry. Diverse marine microorganisms catabolize DMSP via DMSP lyases to generate the climate-cooling gas and info-chemical dimethyl sulphide. Abundant marine heterotrophs of the Roseobacter group (MRG) are well known for their ability to catabolize DMSP via diverse DMSP lyases. Here, a new DMSP lyase DddU within the MRG strain Amylibacter cionae H-12 and other related bacteria was identified. DddU is a cupin superfamily DMSP lyase like DddL, DddQ, DddW, DddK and DddY, but shares <15% amino acid sequence identity with these enzymes. Moreover, DddU proteins forms a distinct clade from these other cupin-containing DMSP lyases. Structural prediction and mutational analyses suggested that a conserved tyrosine residue is the key catalytic amino acid residue in DddU. Bioinformatic analysis indicated that the dddU gene, mainly from Alphaproteobacteria, is widely distributed in the Atlantic, Pacific, Indian and polar oceans. For reference, dddU is less abundant than dddP, dddQ and dddK, but much more frequent than dddW, dddY and dddL in marine environments. This study broadens our knowledge on the diversity of DMSP lyases, and enhances our understanding of marine DMSP biotransformation.

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

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

Comparison of prokaryotes between Mount Everest and the Mariana Trench

BACKGROUND

Mount Everest and the Mariana Trench represent the highest and deepest places on Earth, respectively. They are geographically separated, with distinct extreme environmental parameters that provide unique habitats for prokaryotes. Comparison of prokaryotes between Mount Everest and the Mariana Trench will provide a unique perspective to understanding the composition and distribution of environmental microbiomes on Earth.

RESULTS

Here, we compared prokaryotic communities between Mount Everest and the Mariana Trench based on shotgun metagenomic analysis. Analyzing 25 metagenomes and 1176 metagenome-assembled genomes showed distinct taxonomic compositions between Mount Everest and the Mariana Trench, with little taxa overlap, and significant differences in genome size, GC content, and predicted optimal growth temperature. However, community metabolic capabilities exhibited striking commonality, with > 90% of metabolic modules overlapping among samples of Mount Everest and the Mariana Trench, with the only exception for CO₂ fixations (photoautotrophy in Mount Everest but chemoautotrophy in the Mariana Trench). Most metabolic pathways were common but performed by distinct taxa in the two extreme habitats, even including some specialized metabolic pathways, such as the versatile degradation of various refractory organic matters, heavy metal metabolism (e.g., As and Se), stress resistance, and antioxidation. The metabolic commonality indicated the overall consistent roles of prokaryotes in elemental cycling and common adaptation strategies to overcome the distinct stress conditions despite the intuitively huge differences in Mount Everest and the Mariana Trench.

CONCLUSION

Our results, the first comparison between prokaryotes in the highest and the deepest habitats on Earth, may highlight the principles of prokaryotic diversity: although taxa are habitat-specific, primary metabolic functions could be always conserved. Video abstract.

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.

Acrylate protects a marine bacterium from grazing by a ciliate predator

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

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

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

Uptake of Dimethylsulfoniopropionate (DMSP) by Natural Microbial Communities of the Great Barrier Reef (GBR), Australia

Dimethylsulfoniopropionate (DMSP) is a key organic sulfur compound that is produced by many phytoplankton and macrophytes and is ubiquitous in marine environments. Following its release into the water column, DMSP is primarily metabolised by heterotrophic bacterioplankton, but recent evidence indicates that non-DMSP producing phytoplankton can also assimilate DMSP from the surrounding environment. In this study, we examined the uptake of DMSP by communities of bacteria and phytoplankton within the waters of the Great Barrier Reef (GBR), Australia. We incubated natural GBR seawater with DMSP and quantified the uptake of DMSP by different fractions of the microbial community (>8 µm, 3-8 µm, <3 µm). We also evaluated how microbial community composition and the abundances of DMSP degrading genes are influenced by elevated dissolved DMSP levels. Our results showed uptake and accumulation of DMSP in all size fractions of the microbial community, with the largest fraction (>8 µm) forming the dominant sink, increasing in particulate DMSP by 44-115% upon DMSP enrichment. Longer-term incubations showed however, that DMSP retention was short lived (<24 h) and microbial responses to DMSP enrichment differed depending on the community carbon and sulfur demand. The response of the microbial communities from inside the reef indicated a preference towards cleaving DMSP into the climatically active aerosol dimethyl sulfide (DMS), whereas communities from the outer reef were sulfur and carbon limited, resulting in more DMSP being utilised by the cells. Our results show that DMSP uptake is shared across members of the microbial community, highlighting larger phytoplankton taxa as potentially relevant DMSP reservoirs and provide new information on sulfur cycling as a function of community metabolism in deeper, oligotrophic GBR waters.

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.

Bacterial Dimethylsulfoniopropionate Biosynthesis in the East China Sea

Dimethylsulfoniopropionate (DMSP) is one of Earth's most abundant organosulfur molecules. Recently, many marine heterotrophic bacteria were shown to produce DMSP, but few studies have combined culture-dependent and independent techniques to study their abundance, distribution, diversity and activity in seawater or sediment environments. Here we investigate bacterial DMSP production potential in East China Sea (ECS) samples. Total DMSP (DMSPt) concentration in ECS seawater was highest in surface waters (SW) where phytoplankton were most abundant, and it decreased with depth to near bottom waters. However, the percentage of DMSPt mainly apportioned to bacteria increased from the surface to the near bottom water. The highest DMSP concentration was detected in ECS oxic surface sediment (OSS) where phytoplankton were not abundant. Bacteria with the genetic potential to produce DMSP and relevant biosynthesis gene transcripts were prominent in all ECS seawater and sediment samples. Their abundance also increased with depth and was highest in the OSS samples. Microbial enrichments for DMSP-producing bacteria from sediment and seawater identified many novel taxonomic groups of DMSP-producing bacteria. Different profiles of DMSP-producing bacteria existed between seawater and sediment samples and there are still novel DMSP-producing bacterial groups to be discovered in these environments. This study shows that heterotrophic bacteria significantly contribute to the marine DMSP pool and that their contribution increases with water depth and is highest in seabed surface sediment where DMSP catabolic potential is lowest. Furthermore, distinct bacterial groups likely produce DMSP in seawater and sediment samples, and many novel producing taxa exist, especially in the sediment.

Metagenomic Insights Into the Microbial Assemblage Capable of Quorum Sensing and Quorum Quenching in Particulate Organic Matter in the Yellow Sea

Quorum sensing (QS) is a density-dependent communicating mechanism that allows bacteria to regulate a wide range of biogeochemical important processes and could be inhibited by quorum quenching (QQ). Increasing researches have demonstrated that QS can affect the degradation of particulate organic matter (POM) in the photic zone. However, knowledge of the diversity and variation of microbial QS and QQ systems in sinking POM is scarce. Here, POM samples were collected from surface seawater (SW), bottom seawater (BW), and surficial sediment (SS) in the Yellow Sea of China. 16S rRNA gene amplicon and metagenome sequencing were performed to analyze the community structure of particle-associated microorganisms and distribution of QS genes [acylated homoserine lactone (AHL) synthesizing gene luxI and AHL sensing gene luxR] and QQ genes (genes encoding for AHL lactonase and acylase) in POM. Shifting community structures were observed at different sampling depths, with an increase of microbial abundance and diversity from SW to BW. Along with the variation of microbial communities, the abundances of luxI and luxR decreased slightly but were restored or even exceeded when POM arrived at SS. Comparatively, abundances of AHL lactonase and acylase remained constant during the transportation process from SW to BW but increased dramatically in SS. Correlation tests indicated that abundances of luxI and luxR were positively correlated with temperature, while those of AHL acylase were positively correlated with depth, SiO4 2-, PO4 3-, and NO3 -, but negatively correlated with temperature and pH. According to phylogenetic analyses, the retrieved QS and QQ genes are more diverse and distinctive than ever experimentally identified. Besides, the vertical transmission of QS and QQ genes along with POM sinking was observed, which could be one of the key factors leading to the prevalence of QS and QQ genes in marine ecosystems. Overall, our results increase the current knowledge of QS and QQ metabolic pathways in marine environment and shed light on the intertwined interspecies relationships to better investigate their dynamics and ecological roles in POM cycling.

Bacteria are important dimethylsulfoniopropionate producers in marine aphotic and high-pressure environments

Dimethylsulfoniopropionate (DMSP) is an important marine osmolyte. Aphotic environments are only recently being considered as potential contributors to global DMSP production. Here, our Mariana Trench study reveals a typical seawater DMSP/dimethylsulfide (DMS) profile, with highest concentrations in the euphotic zone and decreased but consistent levels below. The genetic potential for bacterial DMSP synthesis via the dsyB gene and its transcription is greater in the deep ocean, and is highest in the sediment.s DMSP catabolic potential is present throughout the trench waters, but is less prominent below 8000 m, perhaps indicating a preference to store DMSP in the deep for stress protection. Deep ocean bacterial isolates show enhanced DMSP production under increased hydrostatic pressure. Furthermore, bacterial dsyB mutants are less tolerant of deep ocean pressures than wild-type strains. Thus, we propose a physiological function for DMSP in hydrostatic pressure protection, and that bacteria are key DMSP producers in deep seawater and sediment.

Dimethylsulfoniopropionate (DMSP) is an osmolyte produced by marine microbes that plays an important role in nutrient cycling and atmospheric chemistry. Here the authors go to the Mariana Trench—the deepest point in the ocean—and find bacteria are key DMSP producers, and that DMSP has a role in protection against high pressure.

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

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

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

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

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.

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.

Role of RpoN from Labrenzia aggregata LZB033 (Rhodobacteraceae) in Formation of Flagella and Biofilms, Motility, and Environmental Adaptation

Labrenzia aggregata LZB033 (Rhodobacteraceae), which produces dimethylsulfoniopropionate (DMSP) and reduces nitrate to nitrogen, was isolated from seawater of the East China Sea. Its genome encodes a large number of transcriptional regulators which may be important for its adaptation to diverse marine environments. The alternative σ⁵⁴ factor (RpoN) is a central regulator of many bacteria, regulating the transcription of multiple genes and controlling important cellular functions. However, the exact role of RpoN in Labrenzia spp. is unknown. In this study, an in-frame rpoN deletion mutant was constructed in LZB033, and the function of RpoN was determined. To systematically identify RpoN-controlled genes, we performed a detailed analysis of gene expression differences between the wild-type strain and the ΔrpoN mutant using RNA sequencing. The expression of 175 genes was shown to be controlled by RpoN. Subsequent phenotypic assays showed that the ΔrpoN mutant was attenuated in flagellar biosynthesis and swimming motility, utilized up to 13 carbon substrates differently, lacked the ability to assimilate malic acid, and displayed markedly decreased biofilm formation. In addition, stress response assays showed that the ΔrpoN mutant was impaired in the ability to survive under different challenge conditions, including osmotic stress, oxidative stress, temperature changes, and acid stress. Moreover, both the DMSP synthesis and catabolism rates of LZB033 decreased after rpoN was knocked out. Our work provides essential insight into the regulatory function of RpoN, revealing that RpoN is a key determinant for LZB033 flagellar formation, motility, biofilm formation, and environmental fitness, as well as DMSP production and degradation.IMPORTANCE This study established an in-frame gene deletion method in the alphaproteobacterium Labrenzia aggregata LZB033 and generated an rpoN gene mutant. A comparison of the transcriptomes and phenotypic characteristics between the mutant and wild-type strains confirmed the role of RpoN in L. aggregata LZB033 flagellar formation, motility, biofilm formation, and carbon usage. Most importantly, RpoN is a key factor for survival under different environmental challenge conditions. Furthermore, the ability to synthesize and metabolize dimethylsulfoniopropionate (DMSP) was related to RpoN. These features revealed RpoN to be an important regulator of stress resistance and survival for L. aggregata LZB033 in marine environments.