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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.

Key Points The anti-stress molecule dimethylsulphoniopropionate (DMSP) is made in vast quantities — about 1 billion tonnes per year — by many single-celled plankton and some algal seaweeds; when it is released by these organisms into the oceans, it is a food source for many marine bacteria. The importance of the associated catabolic biotransformations in the global sulphur cycle is all the more great because one of the products, the volatile dimethyl sulphide (DMS), has several environmental effects, ranging from the initiation of cloud cover by some of its oxidation products to its ability to act as a chemoattractant for many marine animals. Recent genetic and genomic analyses of several marine bacteria have provided many insights into the mechanisms of DMSP catabolism. These insights include an unexpected amount of diversity in the enzymatic mechanisms and the regulation involved, and in the identities of the microorganisms that can degrade DMSP. The dmd genes that encode enzymes of the demethylation pathway for DMSP catabolism occur in many strains of abundant marine alphaproteobacteria known as the roseobacters and also in the world's most populous group of marine bacteria, the SAR11 clade. These genes are therefore widespread in metagenomic data sets from marine environments. The demethylation pathway that was revealed by molecular genetics differed from that which had been previously predicted. Another series of catabolic pathways involves the cleavage of DMSP by enzymes known generically as DMSP lyases, which generate dimethyl sulphide (DMS) as a primary product. A total of six enzymes, encoded by their corresponding ddd genes, were identified in different bacteria, and these differ with regard to their polypeptide families, their subcellular locations (one of them, DddY, is in the periplasm) and the identities of their catabolites. DddD generates 3-hydroxypropionate (3HP), whereas the other five — DddL, DddP, DddQ, DddW and DddY — give rise to acrylate. Several ddd genes that encode different DMSP lyases are subject to horizontal gene transfer, in some cases between taxonomically diverse organisms. For example, DddP occurs not only in roseobacters, but also sporadically in other distantly related marine bacteria and, more remarkably, in some fungal pathogens. Some individual bacteria have multiple ways of catabolizing DMSP. This feature is most prevalent in the roseobacters, several strains of which contain the DMSP demethylase and one or more different DMSP lyases. These different mechanisms may be adapted to particular environmental conditions. In several bacteria, the regulation of DMSP cleavage is unusual, as the catabolic products, acrylate or 3HP, can act as co-inducers of the ddd genes and, hence, of the DMS-producing phenotype. Although the substrate DMSP may seem to be an effective co-inducer in some species, it must first be converted to one of the bona fide inducer molecules. The compatible solute dimethylsulphoniopropionate (DMSP) has important roles in the ecology and biogeochemistry of marine environments, as do some of its breakdown products. In this Review, Johnston and colleagues describe the recent advances in our understanding of the microorganisms, enzymes and genes involved in DMSP catabolism. The compatible solute dimethylsulphoniopropionate (DMSP) has important roles in marine environments. It is an anti-stress compound made by many single-celled plankton, some seaweeds and a few land plants that live by the shore. Furthermore, in the oceans it is a major source of carbon and sulphur for marine bacteria that break it down to products such as dimethyl sulphide, which are important in their own right and have wide-ranging effects, from altering animal behaviour to seeding cloud formation. In this Review, we describe how recent genetic and genomic work on the ways in which several different bacteria, and some fungi, catabolize DMSP has provided new and surprising insights into the mechanisms, regulation and possible evolution of DMSP catabolism in microorganisms.

Dimethylsulfide (DMS) is the major biosulfur source emitted to the atmosphere with key roles in global sulfur cycling and potentially climate regulation. The main precursor of DMS is thought to be dimethylsulfoniopropionate. However, hydrogen sulfide (H 2 S), a widely distributed and abundant volatile in natural environments, can be methylated to DMS. The microorganisms and the enzymes that convert H 2 S to DMS, and their importance in global sulfur cycling were unknown. Here we demonstrate that the bacterial MddA enzyme, previously known as a methanethiol S -methyltransferase, could methylate inorganic H 2 S to DMS. We determine key residues involved in MddA catalysis and propose the mechanism for H 2 S S -methylation. These results enabled subsequent identification of functional MddA enzymes in abundant haloarchaea and a diverse range of algae, thus expanding the significance of MddA mediated H 2 S methylation to other domains of life. Furthermore, we provide evidence for H 2 S S -methylation being a detoxification strategy in microorganisms. The mddA gene was abundant in diverse environments including marine sediments, lake sediments, hydrothermal vents and soils. Thus, the significance of MddA-driven methylation of inorganic H 2 S to global DMS production and sulfur cycling has likely been considerably underestimated.

Phylogenetic analysis, homology modelling and biochemical methods have been employed to characterize a phytase from a Gram-negative soil bacterium. Acinetobacter sp. AC1-2 phytase belongs to clade 2 of the histidine (acid) phytases, to the Multiple Inositol Polyphosphate Phosphatase (MINPP) subclass. The enzyme was extraordinarily stable in solution both at room temperature and 4°C, retaining near 100% activity over 755 days. It showed a broad pH activity profile from 2–8.5 with maxima at 3, 4.5–5 and 6. The enzyme showed Michaelis-Menten kinetics and substrate inhibition (V max , K m , and K i , 228 U/mg, 0.65 mM and 2.23 mM, respectively). Homology modelling using the crystal structure of a homologous MINPP from a human gut commensal bacterium indicated the presence of a potentially stabilising polypeptide loop (a U-loop) straddling the active site. By employ of the enantiospecificity of Arabidopsis inositol tris/tetrakisphosphate kinase 1 for inositol pentakisphosphates, we show AC1-2 MINPP to possess D6-phytase activity, which allowed modelling of active site specificity pockets for InsP 6 substrate. While phytase gene transcription was unaltered in rich media, it was repressed in minimal media with phytic acid and orthophosphate as phosphate sources. The results of this study reveal AC1-2 MINPP to possess desirable attributes relevant to biotechnological use.

Background The Mariana Trench is the deepest known site in the Earth’s oceans, reaching a depth of ~ 11,000 m at the Challenger Deep. Recent studies reveal that hadal waters harbor distinctive microbial planktonic communities. However, the genetic potential of microbial communities within the hadal zone is poorly understood. Results Here, implementing both culture-dependent and culture-independent methods, we perform extensive analysis of microbial populations and their genetic potential at different depths in the Mariana Trench. Unexpectedly, we observed an abrupt increase in the abundance of hydrocarbon-degrading bacteria at depths > 10,400 m in the Challenger Deep. Indeed, the proportion of hydrocarbon-degrading bacteria at > 10,400 m is the highest observed in any natural environment on Earth. These bacteria were mainly Oleibacter , Thalassolituus , and Alcanivorax genera, all of which include species known to consume aliphatic hydrocarbons. This community shift towards hydrocarbon degraders was accompanied by increased abundance and transcription of genes involved in alkane degradation. Correspondingly, three Alcanivorax species that were isolated from 10,400 m water supplemented with hexadecane were able to efficiently degrade n -alkanes under conditions simulating the deep sea, as did a reference Oleibacter strain cultured at atmospheric pressure. Abundant n- alkanes were observed in sinking particles at 2000, 4000, and 6000 m (averaged 23.5 μg/gdw) and hadal surface sediments at depths of 10,908, 10,909, and 10,911 m (averaged 2.3 μg/gdw). The δ 2 H values of n- C 16/18 alkanes that dominated surface sediments at near 11,000-m depths ranged from − 79 to − 93‰, suggesting that these sedimentary alkanes may have been derived from an unknown heterotrophic source. Conclusions These results reveal that hydrocarbon-degrading microorganisms are present in great abundance in the deepest seawater on Earth and shed a new light on potential biological processes in this extreme environment.

The balance between the uptake of CO2 by phytoplankton photosynthesis and the production of CO2 from prokaryoplankton, zooplankton and phytoplankton respiration controls how much carbon can be stored in the ocean and hence how much remains in the atmosphere to affect climate. Yet, despite its crucial role, knowledge on the respiration of plankton groups is severely limited because traditional methods cannot differentiate the respiration of constituent groups within the plankton community. The reduction of the iodonitrotetrazolium salt (INT) to formazan, which when converted to oxygen consumption (O2C) using an appropriate conversion equation, provides a proxy for both total and size fractionated plankton respiration. However, the method has not been thoroughly tested with prokaryoplankton. Here we present respiration rates, as O2C and formazan formation (INTR), for a wide range of relevant marine prokaryoplankton including the gammaproteobacteria Halomonas venusta, the alphaproteobacteria Ruegeria pomeroyi and Candidatus Pelagibacter ubique (SAR11), the actinobacteria Agrococcus lahaulensis, and the cyanobacteria Synechococcus marinus and Prochlorococcus marinus. All species imported and reduced INT, but the relationship between the rate of O2C and INTR was not constant between oligotrophs and copiotrophs. The range of measured O2C / INTR conversion equations equates to an up to 40-fold difference in derived O2C. These results suggest that when using the INT method in natural waters, a constant O2C / INTR relationship cannot be assumed, but must be determined for each plankton community studied.

Background Marine Group I (MGI) Thaumarchaeota , which play key roles in the global biogeochemical cycling of nitrogen and carbon (ammonia oxidizers), thrive in the aphotic deep sea with massive populations. Recent studies have revealed that MGI Thaumarchaeota were present in the deepest part of oceans—the hadal zone (depth > 6000 m, consisting almost entirely of trenches), with the predominant phylotype being distinct from that in the “shallower” deep sea. However, little is known about the metabolism and distribution of these ammonia oxidizers in the hadal water. Results In this study, metagenomic data were obtained from 0–10,500 m deep seawater samples from the Mariana Trench. The distribution patterns of Thaumarchaeota derived from metagenomics and 16S rRNA gene sequencing were in line with that reported in previous studies: abundance of Thaumarchaeota peaked in bathypelagic zone (depth 1000–4000 m) and the predominant clade shifted in the hadal zone. Several metagenome-assembled thaumarchaeotal genomes were recovered, including a near-complete one representing the dominant hadal phylotype of MGI. Using comparative genomics, we predict that unexpected genes involved in bioenergetics, including two distinct ATP synthase genes (predicted to be coupled with H + and Na + respectively), and genes horizontally transferred from other extremophiles, such as those encoding putative di-myo-inositol-phosphate (DIP) synthases, might significantly contribute to the success of this hadal clade under the extreme condition. We also found that hadal MGI have the genetic potential to import a far higher range of organic compounds than their shallower water counterparts. Despite this trait, hadal MDI ammonia oxidation and carbon fixation genes are highly transcribed providing evidence they are likely autotrophic, contributing to the primary production in the aphotic deep sea. Conclusions Our study reveals potentially novel adaptation mechanisms of deep-sea thaumarchaeotal clades and suggests key functions of deep-sea Thaumarchaeota in carbon and nitrogen cycling. En6fqpb_2L47ybAR2Rb-e_ Video Abstract

Dimethylsulfoniopropionate (DMSP) is an important marine anti-stress compound, with key roles in global nutrient cycling, chemotaxis and, potentially, climate regulation. Recently, diverse marine Actinobacteria , α- and γ-proteobacteria were shown to initiate DMSP synthesis via the methionine (Met) S -methyltransferase enzyme (MmtN), generating S -methyl-Met (SMM). Here we characterize a roseobacterial MmtN, providing structural and mechanistic insights into this DMSP synthesis enzyme. We propose that MmtN uses the proximity and desolvation mechanism for Met S -methylation with two adjacent MmtN monomers comprising the Met binding site. We also identify diverse functional MmtN enzymes in potentially symbiotic archaeal Candidatus Woesearchaeota and Candidate Phyla Radiation (CPR) bacteria, and the animalcule Adineta steineri , not anticipated to produce SMM and/or DMSP. These diverse MmtN enzymes, alongside the larger plant MMT enzyme with an N-terminus homologous to MmtN, likely utilize the same proximity and desolvation mechanism. This study provides important insights into the catalytic mechanism of SMM and/or DMSP production, and proposes roles for these compounds in secondary metabolite production, and SMM cycling in diverse organisms and environments. S-methyl methionine (SMM) is a key molecule in production of dimethylsulfoniopropionate (DMSP), an important marine anti-stress compound, with roles in global nutrient cycling. Here, the authors determine the mechanism of SMM synthesis and uncover unexpected roles for SMM in archaea, CPR bacteria and animals.

Dimethylsulfide (DMS) is an environmentally important trace gas with roles in sulfur cycling, signalling to higher organisms and in atmospheric chemistry. DMS is believed to be predominantly produced in marine environments via microbial degradation of the osmolyte dimethylsulfoniopropionate (DMSP). However, significant amounts of DMS are also generated from terrestrial environments, for example, peat bogs can emit ~6 μmol DMS m −2 per day, likely via the methylation of methanethiol (MeSH). A methyltransferase enzyme termed ‘MddA’, which catalyses the methylation of MeSH, generating DMS, in a wide range of bacteria and some cyanobacteria, may mediate this process, as the mddA gene is abundant in terrestrial metagenomes. This is the first study investigating the functionality of MeSH-dependent DMS production (Mdd) in a wide range of aerobic environments. All soils and marine sediment samples tested produced DMS when incubated with MeSH. Cultivation-dependent and cultivation-independent methods were used to assess microbial community changes in response to MeSH addition in a grassland soil where 35.9% of the bacteria were predicted to contain mddA . Bacteria of the genus Methylotenera were enriched in the presence of MeSH. Furthermore, many novel Mdd + bacterial strains were isolated. Despite the abundance of mddA in the grassland soil, the Mdd pathway may not be a significant source of DMS in this environment as MeSH addition was required to detect DMS at only very low conversion rates.

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. Invasive Spartina grasses accumulate high levels of intracellular dimethylsulfoniopropionate (DMSP). Here, the authors report the isolation and characterization of the genes involved in DMSP biosynthesis and show that administration of DMSP by root uptake or overexpression of the DMSP biosynthesis genes results in salinity and drought tolerance in Arabidopsis.