Environmental VOSCs--formation and degradation of dimethyl sulfide, methanethiol and related materials

Sulfur Development in the Water-Sediment System of the Algae Accumulation Embay Area in Lake Taihu

Sulfur development in water-sediment systems is closely related to eutrophication and harmful algae blooms (HABs). However, the development of sulfur in water-sediment systems during heavy algae accumulation still remains unclear, especially in hyper-eutrophic shallow lakes. In this study, a quarterly field investigation was carried out for a year in the algae accumulated embay area of Lake Taihu, accompanied by a short-term laboratory experiment on algae accumulation. The results show that hydrogen sulfide and methanethiol dominated the volatile sulfur compounds (VSCs) in the water during non-accumulation seasons, whereas the concentrations of dimethyl sulfides increased during heavy algae accumulation, both in the field and the laboratory. An increase in the acid volatile sulfide (AVS) in the surface sediments was also discovered together with the increase in dimethyl sulfides. The depletion of oxygen in the overlying water and sediment–water interface during the heavy algae accumulation and decomposition was found to be closely related to both the increase in VSCs in the overlying water and increase in AVS in the sediment. The increased concentrations of these reductive sulfocompounds might aggravate the eutrophication and HABs and should be given more consideration in future eutrophication control plans for lakes.

Surface flux and vertical profile of dimethyl sulfide in acid sulfate soils at Cudgen Lake, northern New South Wales, Australia

A dimethyl sulfide (DMS) vertical concentration profile and DMS surface emission flux were quantified in undisturbed acid sulfate soils (ASS) at Cudgen Lake on the north coast of New South Wales, Australia. A deuterated internal standard was used to account for soil adsorption characteristics. The DMS vertical concentration profile increased exponentially from 0.6 m depth to the surface layer. This profile reflected the adsorption properties of the ASS horizons present and the experimentally determined octanol/water partition coefficient for DMS of 1.36, suggesting that DMS would be mobilised in the soil water medium for upward translocation in time due to surface evaporation. The organic material in the oxidised ASS crustal layer had a chemically strong adsorption affinity for DMS, which appeared to restrain its emission from surface soil particles to the atmosphere. The seasonally averaged DMS surface flux estimate from the Cudgen Lake ASS was 9 ng S m^-2 min^-1, which is relatively low by comparison to DMS fluxes reported from other wetland soils such as salt-marshes and acidic peat bogs. The worldwide annual average DMS emission from ASS was estimated to be 1.14 × 10^-3 Tg S, which is globally insignificant by comparison to DMS emission from the world's oceans.

Soil carbonyl sulfide exchange in relation to microbial community composition: insights from a managed grassland soil amendment experiment

The viability of carbonyl sulfide (COS) measurements for partitioning ecosystem-scale net carbon dioxide (CO2) fluxes into photosynthesis and respiration critically depends on our knowledge of non-leaf sinks and sources of COS in ecosystems. We combined soil gas exchange measurements of COS and CO2 with next-generation sequencing technology (NGS) to investigate the role of soil microbiota for soil COS exchange. We applied different treatments (litter and glucose addition, enzyme inhibition and gamma sterilization) to soil samples from a temperate grassland to manipulate microbial composition and activity. While untreated soil was characterized by consistent COS uptake, other treatments reduced COS uptake and even turned the soil into a net COS source. Removing biotic processes through sterilization led to positive or zero fluxes. We used NGS to link changes in the COS response to alterations in the microbial community composition, with bacterial data having a higher explanatory power for the measured COS fluxes than fungal data. We found that the genera Arthrobacter and Streptomyces were particularly abundant in samples exhibiting high COS emissions. Our results indicate co-occurring abiotic production and biotic consumption of COS in untreated soil, the latter linked to carbonic anhydrase activity, and a strong dependency of the COS flux on the activity, identity, abundance of and substrate available to microorganisms.

Methanethiol and Dimethylsulfide Cycling in Stiffkey Saltmarsh

Methanethiol (MeSH) and dimethylsulfide (DMS) are volatile organic sulfur compounds (VOSCs) with important roles in sulfur cycling, signaling and atmospheric chemistry. DMS can be produced from MeSH through a reaction mediated by the methyltransferase MddA. The mddA gene is present in terrestrial and marine metagenomes, being most abundant in soil environments. The substrate for MddA, MeSH, can also be oxidized by bacteria with the MeSH oxidase (MTO) enzyme, encoded by the mtoX gene, found in marine, freshwater and soil metagenomes. Methanethiol-dependent DMS production (Mdd) pathways have been shown to function in soil and marine sediments, but have not been characterized in detail in the latter environments. In addition, few molecular studies have been conducted on MeSH consumption in the environment. Here, we performed process measurements to confirm that Mdd-dependent and Mdd-independent MeSH consumption pathways are active in tested surface saltmarsh sediment when MeSH is available. We noted that appreciable natural Mdd-independent MeSH and DMS consumption processes masked Mdd activity. 16S rRNA gene amplicon sequencing and metagenomics data showed that Methylophaga, a bacterial genus known to catabolise DMS and MeSH, was enriched by the presence of MeSH. Moreover, some MeSH and/or DMS-degrading bacteria isolated from this marine environment lacked known DMS and/or MeSH cycling genes and can be used as model organisms to potentially identify novel genes in these pathways. Thus, we are likely vastly underestimating the abundance of MeSH and DMS degraders in these marine sediment environments. The future discovery and characterization of novel enzymes involved in MeSH and/or DMS cycling is essential to better assess the role and contribution of microbes to global organosulfur cycling.

Volatile compounds released by microalgae-water phase from Taihu Lake in China

The spectrum of Volatile Organic Compounds (VOCs) released by the microalgae-water phase of Taihu Lake in China was examined, then release behaviors were studied using non-methane hydrocarbons (NMHC, including a few polar organics) to describe the total amount of the released VOCs. Coupled dynamic headspace sampling with on-line monitoring of methane and NMHC was used to reflect the quasi-realtime release behavior of methane and NMHC by the microalgae-water phase. Alkanes, alkenes, oxygenated VOCs (OVOCs) and volatile sulfide chemicals (VOSCs) were detected. Their relative contents over time varied markedly from the stationary to the apoptosis phase, with their release rates as described by NMHC estimated from 0.02 to 0.59 μgC/(h g). Methane was investigated simultaneously, and its release rate was found to be 0.05-3.96 μgC/(h g). The release rates of both NMHC and methane were found to relate to the culture phase of the microalgae.

Blackening and odorization of urban rivers: a bio-geochemical process

Urban rivers constitute a major part of urban drainage systems, and play critical roles in connecting other surface waters in urban areas. Black-odorous urban rivers are widely found in developing countries experiencing rapid urbanization, and the mismatch between urbanization and sewage treatment is thought to be the reason. The phenomena of blackening and odorization are likely complex bio-geochemical processes of which the microbial interactions with the environment are not fully understood. Here, we provide an overview of the major chemical compounds, such as iron and sulfur, and their bio-geochemical conversions during blackening and odorization of urban rivers. Scenarios explaining the formation of black-odorous urban rivers are proposed. Finally, we point out knowledge gaps in mechanisms and microbial ecology that need to be addressed to better understand the development of black-odorous urban rivers.

High sulfide production induced by algae decomposition and its potential stimulation to phosphorus mobility in sediment

This study is devoted to addressing the effects of algae blooms on sulfur cycle and the consequent phosphorus mobility in the sediments of freshwater lake ecosystems. A mesocosm experiment was conducted to investigate these effects through monitoring the dynamics of sulfur (S), iron (Fe) and phosphorus (P) in water and sediments, and their diffusion fluxes at the sediment-water interface (SWI). In addition, the abundance of sulfate-reducing bacteria (SRB) in the water column was also detected. The addition of the algae lead to an increase of SRB, a drastic decline of sulfate and a significant increase of total dissolved sulfide (ΣS^2-, the peak value of near 3.0 mmol/L on day 6) in the water column. These results suggest the sulfate reduction was dramatically promoted during algae decomposition. Indeed the ΣS^2- was 2 to 3 times of SO₄^2- initial concentration, and higher ΣS^2- was produced with higher algal biomass. Moreover, the diffusive flux of ΣS^2- at the SWI was negative, indicating that diffusion of ΣS^2- from water column toward sediment was occurring. These results indicated that algae decomposition might also be another important source of ΣS^2- (termed "algae-derived ΣS^2-") in addition to sulfate reduction. The increase of Fe(II) in surface sediment pore-water was slightly delayed compared to the ΣS^2- generation in the water column, which illustrated that Fe oxyhydroxides in sediments were transformed into Fe(II) through chemical reduction of ΣS^2-. Concomitantly, the vertical distribution of PO₄^3- in high amounts algae group suggested that desorption and release of iron oxides-bound PO₄^3- occurred in sediments. Collectively, algae bloom can boost the lake eutrophication not only through direct release of nutrients but also through the high production of ΣS^2-and indirect promotion of phosphorus mobility in sediment.

SfnR2 Regulates Dimethyl Sulfide-Related Utilization in Pseudomonas aeruginosa PAO1

Dimethyl sulfide (DMS) is a volatile sulfur compound produced mainly from the degradation of dimethylsulfoniopropionate (DMSP) in marine environments. DMS undergoes oxidation to form dimethyl sulfoxide (DMSO), dimethyl sulfone (DMSO₂), and methanesulfonate (MSA), all of which occur in terrestrial environments and are accessible for consumption by various microorganisms. The purpose of the present study was to determine how the enhancer-binding proteins SfnR1 and SfnR2 contribute to the utilization of DMS and its derivatives in Pseudomonas aeruginosa PAO1. First, results from cell growth experiments showed that deletion of either sfnR2 or sfnG, a gene encoding a DMSO₂-monooxygenase, significantly inhibits the ability of P. aeruginosa PAO1 to use DMSP, DMS, DMSO, and DMSO₂ as sulfur sources. Deletion of the sfnR1 or msuEDC genes, which encode a MSA desulfurization pathway, did not abolish the growth of P. aeruginosa PAO1 on any sulfur compound tested. Second, data collected from β-galactosidase assays revealed that the msuEDC-sfnR1 operon and the sfnG gene are induced in response to sulfur limitation or nonpreferred sulfur sources, such as DMSP, DMS, and DMSO, etc. Importantly, SfnR2 (and not SfnR1) is essential for this induction. Expression of sfnR2 is induced under sulfur limitation but independently of SfnR1 or SfnR2. Finally, the results of this study suggest that the main function of SfnR2 is to direct the initial activation of the msuEDC-sfnR1 operon in response to sulfur limitation or nonpreferred sulfur sources. Once expressed, SfnR1 contributes to the expression of msuEDC-sfnR1, sfnG, and other target genes involved in DMS-related metabolism in P. aeruginosa PAO1.IMPORTANCE Dimethyl sulfide (DMS) is an important environmental source of sulfur, carbon, and/or energy for microorganisms. For various bacteria, including Pseudomonas, Xanthomonas, and Azotobacter, DMS utilization is thought to be controlled by the transcriptional regulator SfnR. Adding more complexity, some bacteria, such as Acinetobacter baumannii, Enterobacter cloacae, and Pseudomonas aeruginosa, possess two, nonidentical SfnR proteins. In this study, we demonstrate that SfnR2 and not SfnR1 is the principal regulator of DMS metabolism in P. aeruginosa PAO1. Results suggest that SfnR1 has a supportive but nonessential role in the positive regulation of genes required for DMS utilization. This study not only enhances our understanding of SfnR regulation but, importantly, also provides a framework for addressing gene regulation through dual SfnR proteins in other bacteria.

Not as easy as π: An insertional residue does not explain the π-helix gain-of-function in two-component FMN reductases

The π-helix located at the tetramer interface of two-component FMN-dependent reductases contributes to the structural divergence from canonical FMN-bound reductases within the NADPH:FMN reductase family. The π-helix in the SsuE FMN-dependent reductase of the alkanesulfonate monooxygenase system has been proposed to be generated by the insertion of a Tyr residue in the conserved α4-helix. Variants of Tyr118 were generated, and their X-ray crystal structures determined, to evaluate how these alterations affect the structural integrity of the π-helix. The structure of the Y118A SsuE π-helix was converted to an α-helix, similar to the FMN-bound members of the NADPH:FMN reductase family. Although the π-helix was altered, the FMN binding region remained unchanged. Conversely, deletion of Tyr118 disrupted the secondary structural properties of the π-helix, generating a random coil region in the middle of helix 4. Both the Y118A and Δ118 SsuE SsuE variants crystallize as a dimer. The MsuE FMN reductase involved in the desulfonation of methanesulfonates is structurally similar to SsuE, but the π-helix contains a His insertional residue. Exchanging the π-helix insertional residue of each enzyme did not result in equivalent kinetic properties. Structure-based sequence analysis further demonstrated the presence of a similar Tyr residue in an FMN-bound reductase in the NADPH:FMN reductase family that is not sufficient to generate a π-helix. Results from the structural and functional studies of the FMN-dependent reductases suggest that the insertional residue alone is not solely responsible for generating the π-helix, and additional structural adaptions occur to provide the altered gain of function.

Stoichiometry, polarity, and organometallics in solid-phase extracted dissolved organic matter of the Elbe-Weser estuary

Dissolved organic matter (DOM) is ubiquitous in natural waters and plays a central role in the biogeochemistry in riverine, estuarine and marine environments. This study quantifies and characterizes solid-phase extractable DOM and trace element complexation at different salinities in the Weser and Elbe River, northern Germany, and the North Sea. Dissolved organic carbon (DOC), total dissolved nitrogen (TDN), Co and Cu concentrations were analyzed in original water samples. Solid-phase extracted (SPE) water samples were analyzed for DOC (DOC_SPE), dissolved organic nitrogen (DON_SPE), sulfur (DOS_SPE) and trace metal (⁵¹V, ⁵²Cr, ⁵⁹Co, ⁶⁰Ni, ⁶³Cu, ⁷⁵As) concentrations. Additionally, different pre-treatment conditions (acidification vs. non-acidification prior to SPE) were tested. In agreement with previous studies, acidification led to generally higher recoveries for DOM and trace metals. Overall, higher DOM and trace metal concentrations and subsequently higher complexation of trace metals with carbon and sulfur-containing organic complexes were found in riverine compared to marine samples. With increasing salinity, the concentrations of DOM decreased due to estuarine mixing. However, the slightly lower relative decrease of both, DOC_SPE and DON_SPE (~77%) compared to DOS_SPE (~86%) suggests slightly faster removal processes for DOS_SPE. A similar distribution of trace metal and carbon and sulfur containing DOM concentrations with salinity indicates complexation of trace metals with organic ligands. This is further supported by an increase in Co and Cu concentration after oxidation of organic complexes by UV treatment. Additionally, the complexation of metals with organic ligands (analyzed by comparing metal/DOC_SPE and metal/DOS_SPE ratios) decreased in the order Cu > As > Ni > Cr > Co and thus followed the Irving-Williams order. Differences in riverine and marine trace metal containing DOM_SPE are summarized by their average molar ratios of (C₁₀₇N₄P_0.013S₁)₁₀₀₀V_0.05Cr_0.33Co_0.19Ni_0.39Cu_3.41As_0.47 in the riverine endmember and (C₁₆₃N₇P_0.055S₁)₁₀₀₀V_0.05Cr_0.47Co_0.16Ni_0.07Cu_4.05As_0.58 in the marine endmember.

Seasonal changes in the abundance of bacterial genes related to dimethylsulfoniopropionate catabolism in seawater from Ofunato Bay revealed by metagenomic analysis

Ofunato Bay is located in the northeastern Pacific Ocean area of Japan, and it has the highest biodiversity of marine organisms in the world, primarily due to tidal influences from the cold Oyashio and warm Kuroshio Currents. Our previous results from performing shotgun metagenomics indicated that Candidatus Pelagibacter ubique and Planktomarina temperata were the dominant bacteria (Reza et al., 2018a, 2018b). These bacteria are reportedly able to catabolize dimethylsulfoniopropionate (DMSP) produced from phytoplankton into dimethyl sulfide (DMS) or methanethiol (MeSH). This study was focused on seasonal changes in the abundances of bacterial genes (dddP, dmdA) related to DMSP catabolism in the seawater of Ofunato Bay by BLAST+ analysis using shotgun metagenomic datasets. We found seasonal changes among the Candidatus Pelagibacter ubique strains, including those of the HTCC1062 type and the Red Sea type. A good correlation was observed between the chlorophyll a concentrations and the abundances of the catabolic genes, suggesting that the bacteria directly interact with phytoplankton in the marine material cycle system and play important roles in producing DMS and MeSH from DMSP as signaling molecules for the possible formation of the scent of the tidewater or as fish attractants.

Distributions of four taste and odor compounds in the sediment and overlying water at different ecology environment in Taihu Lake

Organic matter-induced black blooms, such as cyanobacterial and vegetation blooms, are a serious ecosystem disasters that have occurred in Taihu Lake. After large-scale outbreaks of blooms in eutrophic water, a large number of cyanobacterial and vegetation residue accumulate in the coastal areas, and rapidly fermented into odorous compounds. In this study, four taste and odor compounds have been analyzed in sediments and overlying water of different ecology environment in Taihu Lake. High concentrations of DMDS (up to 7165.25 ngg^-1 dw^-1), DMTS (up to 50.93 ngg^-1 dw^-1), β-cyclocitral (up to 5441.69 ngg^-1 dw^-1), β-ionone (up to 1669.37 ngg^-1 dw^-1) were detected in sediments. Also, the spatial distributions of DMDS, DMTS, β-cyclocitral and β-ionone in the sediments were investigated. As the depth of sediment increases, nutrients and odorous compounds are greatly reduced. The results showed that during the degradation of cyanobacterial and vegetation residues, DMDS, DMTS, β-cyclocitral, β-ionone and nutrients are gradually released. In addition, when assessing the source of odorous compounds in overlying water, it should also be considered that it may be released from the sediment. This study shows that odorous compounds are ubiquitous in near-shore zones Taihu Lake, and may take potential hazard to aquatic ecosystems.

Two Distinct Aerobic Methionine Salvage Pathways Generate Volatile Methanethiol in Rhodopseudomonas palustris

5'-Methyl-thioadenosine (MTA) is a dead-end, sulfur-containing metabolite and cellular inhibitor that arises from S-adenosyl-l-methionine-dependent reactions. Recent studies have indicated that there are diverse bacterial methionine salvage pathways (MSPs) for MTA detoxification and sulfur salvage. Here, via a combination of gene deletions and directed metabolite detection studies, we report that under aerobic conditions the facultatively anaerobic bacterium Rhodopseudomonas palustris employs both an MTA-isoprenoid shunt identical to that previously described in Rhodospirillum rubrum and a second novel MSP, both of which generate a methanethiol intermediate. The additional R. palustris aerobic MSP, a dihydroxyacetone phosphate (DHAP)-methanethiol shunt, initially converts MTA to 2-(methylthio)ethanol and DHAP. This is identical to the initial steps of the recently reported anaerobic ethylene-forming MSP, the DHAP-ethylene shunt. The aerobic DHAP-methanethiol shunt then further metabolizes 2-(methylthio)ethanol to methanethiol, which can be directly utilized by O-acetyl-l-homoserine sulfhydrylase to regenerate methionine. This is in contrast to the anaerobic DHAP-ethylene shunt, which metabolizes 2-(methylthio)ethanol to ethylene and an unknown organo-sulfur intermediate, revealing functional diversity in MSPs utilizing a 2-(methylthio)ethanol intermediate. When MTA was fed to aerobically growing cells, the rate of volatile methanethiol release was constant irrespective of the presence of sulfate, suggesting a general housekeeping function for these MSPs up through the methanethiol production step. Methanethiol and dimethyl sulfide (DMS), two of the most important compounds of the global sulfur cycle, appear to arise not only from marine ecosystems but from terrestrial ones as well. These results reveal a possible route by which methanethiol might be biologically produced in soil and freshwater environments.IMPORTANCE Biologically available sulfur is often limiting in the environment. Therefore, many organisms have developed methionine salvage pathways (MSPs) to recycle sulfur-containing by-products back into the amino acid methionine. The metabolically versatile bacterium Rhodopseudomonas palustris is unusual in that it possesses two RuBisCOs and two RuBisCO-like proteins. While RuBisCO primarily serves as the carbon fixation enzyme of the Calvin cycle, RuBisCOs and certain RuBisCO-like proteins have also been shown to function in methionine salvage. This work establishes that only one of the R. palustris RuBisCO-like proteins functions as part of an MSP. Moreover, in the presence of oxygen, to salvage sulfur, R. palustris employs two pathways, both of which result in production of volatile methanethiol, a key compound of the global sulfur cycle. When total available sulfur was plentiful, methanethiol was readily released into the environment. However, when sulfur became limiting, methanethiol release decreased, presumably due to methanethiol utilization to regenerate needed methionine.

Photochemical oxidation of dimethylsulphide to dimethylsulphoxide in estuarine and coastal waters

Dimethylsulphide (DMS) photo-oxidation and dimethylsulphoxide (DMSO) photoproduction were estimated in 26 laboratory irradiations of coastal samples from NE England (Tyne estuary) and W Scotland (Loch Linnhe and River Nant at Taynuilt). Pseudo-first order rate constants of DMS photo-oxidation (0.038 h^-1 to 0.345 h^-1) and DMSO photo-production (0.017 h^-1 to 0.283 h^-1) varied by one order of magnitude and were lowest in the coastal North Sea. Estuarine samples (salinity S < 30) had a mean DMSO yield of 96 ± 16% (n = 14), consistent with 1:1 M conversion via photosensitised oxidation by singlet oxygen. Photochemical rate constants were strongly correlated with coloured dissolved organic matter (CDOM) absorption coefficients at 350 nm, a₃₅₀. Variations in a₃₅₀ explained 61% (R² = 0.61, n = 26) and 73% (R² = 0.73, n = 17) of the variability in DMS photo-oxidation and DMSO production, respectively. However, CDOM normalised photochemical rate constants increased strongly towards coastal waters exhibiting lowest CDOM absorbance, indicating water samples of marine character (S > 30) to be most reactive with respect to DMS photo-oxidation. Estimates of water column averaged DMS photo-oxidation rate constants, obtained by scaling to mean daily irradiance (July, NE England) and mid-UV underwater irradiance, were 0.012 d^-1, 0.019 d^-1, and 0.017 d^-1 for upper estuary (S < 20), lower estuary (20 < S < 30) and coastal waters (S > 30), at the lower end of previous observations. Comparing our water column averaged DMS photo-oxidation rate constants with estimated DMS losses via air-sea gas exchange and previously reported biological consumption implies that DMS photochemical removal is of only minor importance in our study area.

Bacterial SBP56 identified as a Cu-dependent methanethiol oxidase widely distributed in the biosphere

Oxidation of methanethiol (MT) is a significant step in the sulfur cycle. MT is an intermediate of metabolism of globally significant organosulfur compounds including dimethylsulfoniopropionate (DMSP) and dimethylsulfide (DMS), which have key roles in marine carbon and sulfur cycling. In aerobic bacteria, MT is degraded by a MT oxidase (MTO). The enzymatic and genetic basis of MT oxidation have remained poorly characterized. Here, we identify for the first time the MTO enzyme and its encoding gene (mtoX) in the DMS-degrading bacterium Hyphomicrobium sp. VS. We show that MTO is a homotetrameric metalloenzyme that requires Cu for enzyme activity. MTO is predicted to be a soluble periplasmic enzyme and a member of a distinct clade of the Selenium-binding protein (SBP56) family for which no function has been reported. Genes orthologous to mtoX exist in many bacteria able to degrade DMS, other one-carbon compounds or DMSP, notably in the marine model organism Ruegeria pomeroyi DSS-3, a member of the Rhodobacteraceae family that is abundant in marine environments. Marker exchange mutagenesis of mtoX disrupted the ability of R. pomeroyi to metabolize MT confirming its function in this DMSP-degrading bacterium. In R. pomeroyi, transcription of mtoX was enhanced by DMSP, methylmercaptopropionate and MT. Rates of MT degradation increased after pre-incubation of the wild-type strain with MT. The detection of mtoX orthologs in diverse bacteria, environmental samples and its abundance in a range of metagenomic data sets point to this enzyme being widely distributed in the environment and having a key role in global sulfur cycling.

The network of plants volatile organic compounds

Plants emission of Volatile Organic Compounds (VOCs) is involved in a wide class of ecological functions, as VOCs play a crucial role in plants interactions with biotic and abiotic factors. Accordingly, they vary widely across species and underpin differences in ecological strategy. In this paper, VOCs spontaneously emitted by 109 plant species (belonging to 56 different families) have been qualitatively and quantitatively analysed in order to provide an alternative classification of plants species. In particular, by using bipartite networks methodology from Complex Network Theory, and through the application of community detection algorithms, we show that is possible to classify species according to chemical classes such as terpenes and sulfur compounds. Such complex network analysis allows to uncover hidden plants relationships related to their evolutionary and adaptation to the environment story.

Methanethiol-dependent dimethylsulfide production in soil environments

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.

Volatile Metabolites Emission by In Vivo Microalgae-An Overlooked Opportunity?

Fragrances and malodors are ubiquitous in the environment, arising from natural and artificial processes, by the generation of volatile organic compounds (VOCs). Although VOCs constitute only a fraction of the metabolites produced by an organism, the detection of VOCs has a broad range of civilian, industrial, military, medical, and national security applications. The VOC metabolic profile of an organism has been referred to as its 'volatilome' (or 'volatome') and the study of volatilome/volatome is characterized as 'volatilomics', a relatively new category in the 'omics' arena. There is considerable literature on VOCs extracted destructively from microalgae for applications such as food, natural products chemistry, and biofuels. VOC emissions from living (in vivo) microalgae too are being increasingly appreciated as potential real-time indicators of the organism's state of health (SoH) along with their contributions to the environment and ecology. This review summarizes VOC emissions from in vivo microalgae; tools and techniques for the collection, storage, transport, detection, and pattern analysis of VOC emissions; linking certain VOCs to biosynthetic/metabolic pathways; and the role of VOCs in microalgae growth, infochemical activities, predator-prey interactions, and general SoH.

Methylsulfonylmethane: Applications and Safety of a Novel Dietary Supplement

Methylsulfonylmethane (MSM) has become a popular dietary supplement used for a variety of purposes, including its most common use as an anti-inflammatory agent. It has been well-investigated in animal models, as well as in human clinical trials and experiments. A variety of health-specific outcome measures are improved with MSM supplementation, including inflammation, joint/muscle pain, oxidative stress, and antioxidant capacity. Initial evidence is available regarding the dose of MSM needed to provide benefit, although additional work is underway to determine the precise dose and time course of treatment needed to provide optimal benefits. As a Generally Recognized As Safe (GRAS) approved substance, MSM is well-tolerated by most individuals at dosages of up to four grams daily, with few known and mild side effects. This review provides an overview of MSM, with details regarding its common uses and applications as a dietary supplement, as well as its safety for consumption.

Moderate Drought Stress Induces Increased Foliar Dimethylsulphoniopropionate (DMSP) Concentration and Isoprene Emission in Two Contrasting Ecotypes of Arundo donax

The function of dimethylsulphoniopropionate (DMSP) in plants is unclear. It has been proposed as an antioxidant, osmolyte and overflow for excess energy under stress conditions. The formation of DMSP is part of the methionine (MET) pathway that is involved in plant stress responses. We used a new analytical approach to accurately quantify the changes in DMSP concentration that occurred in two ecotypes of the biomass crop Arundo donax subject to moderate drought stress under field conditions. The ecotypes of A. donax were from a hot semi-arid habitat in Morocco and a warm-humid environment in Central Italy. The Moroccan ecotype showed more pronounced reductions in photosynthesis, stomatal conductance and photochemical electron transport than the Italian ecotype. An increase in isoprene emission occurred in both ecotypes alongside enhanced foliar concentrations of DMSP, indicative of a protective function of these two metabolites in the amelioration of the deleterious effects of excess energy and oxidative stress. This is consistent with the modification of carbon within the methyl-erythritol and MET pathways responsible for increased synthesis of isoprene and DMSP under moderate drought. The results of this study indicate that DMSP is an important adaptive component of the stress response regulated via the MET pathway in A. donax. DMSP is likely a multifunctional molecule playing a number of roles in the response of A. donax to reduced water availability.

Aromatic and proteomic analyses corroborate the distinction between Mediterranean landraces and modern varieties of durum wheat

In this paper volatile organic compounds (VOCs) from durum wheat cultivars and landraces were analyzed using PTR-TOF-MS. The aim was to characterize the VOC’s profile of the wholemeal flour and of the kernel to find out if any VOCs were specific to varieties and sample matrices. The VOC data is accompanied by SDS-PAGE analyses of the storage proteins (gliadins and glutenins). Statistical analyses was carried out both on the signals obtained by MS and on the protein profiles. The difference between the VOC profile of two cultivars or two preparations of the same sample - matrices, in this case kernel vs wholemeal flour - can be very subtle; the high resolution of PTR-TOF-MS - down to levels as low as pptv - made it possible to recognize these differences. The effects of grinding on the VOC profiles were analyzed using SIMPER and Tanglegram statistical methods. Our results show that it is possible describe samples using VOC profiles and protein data.

The reduced flavin-dependent monooxygenase SfnG converts dimethylsulfone to methanesulfinate

The biochemical pathway through which sulfur may be assimilated from dimethylsulfide (DMS) is proposed to proceed via oxidation of DMS to dimethylsulfoxide (DMSO) and subsequent conversion of DMSO to dimethylsulfone (DMSO2). Analogous chemical oxidation processes involving biogenic DMS in the atmosphere result in the deposition of DMSO2 into the terrestrial environment. Elucidating the enzymatic pathways that involve DMSO2 contribute to our understanding of the global sulfur cycle. Dimethylsulfone monooxygenase SfnG and flavin mononucleotide (FMN) reductase MsuE from the genome of the aerobic soil bacterium Pseudomonas fluorescens Pf0-1 were produced in Escherichia coli, purified, and biochemically characterized. The enzyme MsuE functions as a reduced nicotinamide adenine dinucleotide (NADH)-dependent FMN reductase with apparent steady state kinetic parameters of Km = 69 μM and kcat/Km = 9 min(-1) μM (-1) using NADH as the variable substrate, and Km = 8 μM and kcat/Km = 105 min(-1) μM (-1) using FMN as the variable substrate. The enzyme SfnG functions as a flavoprotein monooxygenase and converts DMSO2 to methanesulfinate in the presence of FMN, NADH, and MsuE, as evidenced by (1)H and (13)C nuclear magnetic resonance (NMR) spectroscopy. The results suggest that methanesulfinate is a biochemical intermediate in sulfur assimilation.

Optimum dredging time for inhibition and prevention of algae-induced black blooms in Lake Taihu, China

Dredging, which is the removal of polluted surface sediments from a water body, is an effective means of preventing the formation of algae-induced black blooms. However, an inappropriate dredging time may contribute to rather than inhibit the formation of black blooms. To determine the optimum dredging time, four treatments were simulated with sediment samples collected from Lake Taihu: dredging in January 2014 (DW), April 2014 (DA), July 2014 (DS), and no dredging (UD). Results showed that typical characteristics associated with black blooms, such as high levels of nutrients (NH4 (+)-N and PO4 (3-)-P), Fe(2+), ∑S(2-) ([HS(-)] + [S(2-)]), and volatile organic sulfur compounds (VOSCs), including dimethyl sulfide (DMS), dimethyl disulfide (DMDS), and dimethyl trisulfide (DMTS), were more effectively suppressed in the water column by DW treatment than by UD treatment and the other two dredging treatments. The highest concentrations of NH4 (+)-N and PO4 (3-)-P in the UD water column were 4.09 and 4.03 times, respectively, those in the DW water column. DMS levels in the UD and DS water columns were significantly higher (p < 0.05) than those in the DW water column, but DMDS and DMTS levels were not significantly different between the treatments. After several months of dredging, surface sediments of the DW and DA treatments were well oxidized, and concentrations of Fe(2+) and ∑S(2-) were lower than those in UD and DS treatments because of material circulation between sediments and the water column. Water content, which is important for the transport of matter to the overlying water, was lower in the dredged sediments than in the undredged sediments. These factors can suppress the release of Fe(2+) and ∑S(2-) into the water column, thereby inhibiting the formation of black blooms. Black coloration occurred in the UD water column on the seventh day, 2 days later, and earlier, respectively, than the DW and DS water columns and almost on the same day as in the DA water column. This phenomenon is mainly attributed to the oxidation of the new sediment surface in the DW and DA water columns, suppressing the release of sulfur into the water column, because of a long incubation period. Thus, dredging in the winter can prevent the formation of black blooms, while dredging in summer may contribute to them.

PAMP Activity of Cerato-Platanin during Plant Interaction: An -Omic Approach

Cerato-platanin (CP) is the founder of a fungal protein family consisting in non-catalytic secreted proteins, which work as virulence factors and/or as elicitors of defense responses and systemic resistance, thus acting as PAMPs (pathogen-associated molecular patterns). Moreover, CP has been defined an expansin-like protein showing the ability to weaken cellulose aggregates, like the canonical plant expansins do. Here, we deepen the knowledge on CP PAMP activity by the use of a multi-disciplinary approach: proteomic analysis, VOC (volatile organic compound) measurements, and gas exchange determination. The treatment of Arabidopsis with CP induces a differential profile either in protein expression or in VOC emission, as well changes in photosynthetic activity. In agreement with its role of defense activator, CP treatment induces down-expression of enzymes related to primary metabolism, such as RuBisCO, triosephosphate isomerase, and ATP-synthase, and reduces the photosynthesis rate. Conversely, CP increases expression of defense-related proteins and emission of some VOCs. Interestingly, CP exposure triggered the increase in enzymes involved in GSH metabolism and redox homeostasis (glutathione S-transferase, thioredoxin, Cys-peroxiredoxin, catalase) and in enzymes related to the “glucosinolate-myrosinase” system, which are the premise for synthesis of defence compounds, such as camalexin and some VOCs, respectively. The presented results are in agreement with the accepted role of CP as a PAMP and greatly increase the knowledge of plant primary defences induced by a purified fungal elicitor.

Increasing sulfate concentrations result in higher sulfide production and phosphorous mobilization in a shallow eutrophic freshwater lake

Increasing sulfate input has been seen as an issue in management of aquatic ecosystems, but its influences on eutrophic freshwater lakes is not clear. In this study, it was observed that increasing sulfate concentration without additional cyanobacterial bloom biomass (CBB) addition did not have an obvious effect on element cycling during 1-year continuous flow mesocosm experiments in which water and sediments were taken from a shallow eutrophic lake with sulfate levels near 1 mM. However, following addition of CBB to mesocosms, sulfate-reducing bacteria (SRB) were observed in the water column, and increasing numbers of SRB in the water column were associated with higher sulfate input. Sulfate amendment (0-70 mg L(-1)) also resulted in a larger amount of total dissolved sulfide (peak values of 5.90 ± 0.36 to 7.60 ± 0.12 mg L(-1)) in the water column and acid volatile sulfide (1081.71 ± 69.91 to 1557.98 ± 41.72 mg kg(-1)) in 0-1 cm surface sediments due to sulfate reduction. During the period of CBB decomposition, increasing sulfate levels in the water column were positively correlated with increasing diffusive phosphate fluxes of 1.23 ± 0.32 to 2.17 ± 0.01 mg m(-2) d(-1) at the water-sediment interface. As increases in sulfide and phosphate release rates deteriorated the water quality/ecosystem and even spurred the occurrence of a black water problem in lakes, the control of sulfate input level should be considered for shallow eutrophic lake management, especially during cyanobacterial bloom periods.

Biochemistry and genetics of taste- and odor-producing cyanobacteria

Cyanobacteria are one of the principal sources of volatile organic compounds (VOCs) which cause offensive taste and odor (T&O) in drinking and recreational water, fish, shellfish and other seafood. Although non-toxic to humans, these T&O compounds severely undermine public trust in these commodities, resulting in substantial costs in treatment, and lost revenue to drinking water, aquaculture, food and beverage and tourist/hospitality industries. Mitigation and control have been hindered by the complexity of the communities and processes which produce and modify T&O events, making it difficult to source-track the major producer(s) and the factors governing VOC production and fate. Over the past decade, however, advances in bioinformatics, enzymology, and applied detection technologies have greatly enhanced our understanding of the pathways, the enzymes and the genetic coding for some of the most problematic VOCs produced by cyanobacteria. This has led to the development of tools for rapid and sensitive detection and monitoring for the VOC production at source, and provided the basis for further diagnostics of endogenous and exogenous controls. This review provides an overview of current knowledge of the major cyanobacterial VOCs, the producers, the biochemistry and the genetics and highlight the current applications and further research needs in this area.

Characterization of the novel dimethyl sulfide-degrading bacterium Alcaligenes sp. SY1 and its biochemical degradation pathway

Recently, the biodegradation of volatile organic sulfur compounds (VOSCs) has become a burgeoning field, with a growing focus on the reduction of VOSCs. The reduction of VOSCs encompasses both organic emission control and odor control. Herein, Alcaligenes sp. SY1 was isolated from active sludge and found to utilize dimethyl sulfide (DMS) as a growth substrate in a mineral salt medium. Response surface methodology (RSM) analysis was applied to optimize the incubation conditions. The following conditions for optimal degradation were identified: temperature 27.03°C; pH 7.80; inoculum salinity 0.84%; and initial DMS concentration 1585.39 μM. Under these conditions, approximately 99% of the DMS was degraded within 30 h of incubation. Two metabolic compounds were detected and identified by gas chromatography-mass spectrometry (GC-MS): dimethyl disulfide (DMDS) and dimethyl trisulfide (DMTS). The DMS degradation kinetics for different concentrations were evaluated using the Haldane-Andrews model and the pseudo first-order model. The maximum specific growth rate and degradation rate of Alcaligenes sp. SY1 were 0.17 h(-1) and 0.63 gs gx(-1)h(-1). A possible degradation pathway is proposed, and the results suggest that Alcaligenes sp. SY1 has the potential to control odor emissions under aerobic conditions.

Under fungal attack on a metalliferous soil: ROS or not ROS? Insights from Silene paradoxa L. growing under copper stress

We investigated how the adaptation to metalliferous environments can influence the plant response to biotic stress. In a metallicolous and a non-metallicolous population of Silene paradoxa the induction of oxidative stress and the production of callose and volatiles were evaluated in the presence of copper and of the PAMP fungal protein cerato-platanin, separately and in combination. Our results showed incompatibility between the ordinary ROS-mediated response to fungal attack and the acquired mechanisms of preventing oxidative stress in the tolerant population. A similar situation was also demonstrated by the sensitive population growing in the presence of copper but, in this case, with a lack of certain responses, such as callose production. In addition, in terms of the joint behaviour of emitted volatiles, multivariate statistics showed that not only did the populations respond differently to the presence of copper or biotic stress, but also that the biotic and abiotic stresses interacted in different ways in the two populations. Our results demonstrated that the same incompatibility of hyperaccumulators in ROS-mediated biotic stress signals also seemed to be exhibited by the excluder metallophyte, but without the advantage of being able to rely on the elemental defence for plant protection from natural enemies.

Natural wetland emissions of methylated trace elements

Natural wetlands are well known for their significant methane emissions. However, trace element emissions via biomethylation and subsequent volatilization from pristine wetlands are virtually unstudied, even though wetlands constitute large reservoirs for trace elements. Here we show that the average volatile fluxes of selenium (<0.12 μg m(-2) day(-1)), sulphur (<37 μg m(-2) day(-1)) and arsenic (<0.54 μg m(-2) day(-1)) from a pristine peatland are considerable and consistent over two summers. We compare these fluxes with the total concentrations in the peat and show that selenium is up to 40 times more efficiently volatilized than arsenic, and over 100 times more efficiently volatilized than sulphur. We further show that the volatilization of selenium and arsenic increases with temperature, implying that emissions of these health-relevant trace elements will increase with global warming. We suggest that biomethylation and volatilization in wetlands play a crucial role in the mobilization and global biogeochemical cycling of trace elements.

Quantification of volatile-alkylated selenium and sulfur in complex aqueous media using solid-phase microextraction

Biologically produced volatile-alkylated Se and S compounds play an important role in the global biogeochemical Se and S cycles, are important constituents of odorous industrial emissions, and contribute to (off-)flavors in food and beverages. This study presents a fully automated direct-immersion solid-phase microextraction (DI-SPME) method coupled with capillary gas chromatography-mass spectrometry (GC/MS) for the simultaneous quantification of 10 volatile-alkylated Se and S compounds in complex aqueous media. Instrumental parameters of the SPME procedure were optimized to yield extraction efficiencies of up to 96% from complex aqueous matrices. The effects of sample matrix composition and analyte transformation during sample storage were critically assessed. With the use of internal standards and procedural calibrations, the DI-SPME-GC/MS method allows for trace-level quantification of volatile Se and S compounds in the ng/L range (e.g. down to 30 ng/L dimethyl sulfide and 75 ng/L dimethyl selenide). The applicability and robustness of the presented method demonstrate that the method may be used to quantify volatile Se and S compounds in complex aqueous samples, such as industrial effluents or food and beverage samples.

SIP metagenomics identifies uncultivated Methylophilaceae as dimethylsulphide degrading bacteria in soil and lake sediment

Dimethylsulphide (DMS) has an important role in the global sulphur cycle and atmospheric chemistry. Microorganisms using DMS as sole carbon, sulphur or energy source, contribute to the cycling of DMS in a wide variety of ecosystems. The diversity of microbial populations degrading DMS in terrestrial environments is poorly understood. Based on cultivation studies, a wide range of bacteria isolated from terrestrial ecosystems were shown to be able to degrade DMS, yet it remains unknown whether any of these have important roles in situ. In this study, we identified bacteria using DMS as a carbon and energy source in terrestrial environments, an agricultural soil and a lake sediment, by DNA stable isotope probing (SIP). Microbial communities involved in DMS degradation were analysed by denaturing gradient gel electrophoresis, high-throughput sequencing of SIP gradient fractions and metagenomic sequencing of phi29-amplified community DNA. Labelling patterns of time course SIP experiments identified members of the Methylophilaceae family, not previously implicated in DMS degradation, as dominant DMS-degrading populations in soil and lake sediment. Thiobacillus spp. were also detected in ¹³C-DNA from SIP incubations. Metagenomic sequencing also suggested involvement of Methylophilaceae in DMS degradation and further indicated shifts in the functional profile of the DMS-assimilating communities in line with methylotrophy and oxidation of inorganic sulphur compounds. Overall, these data suggest that unlike in the marine environment where gammaproteobacterial populations were identified by SIP as DMS degraders, betaproteobacterial Methylophilaceae may have a key role in DMS cycling in terrestrial environments.

Metabolic fingerprint of dimethyl sulfone (DMSO2) in microbial-mammalian co-metabolism

There is growing awareness that intestinal microbiota alters the energy harvesting capacity of the host and regulates metabolism. It has been postulated that intestinal microbiota are able to degrade unabsorbed dietary components and transform xenobiotic compounds. The resulting microbial metabolites derived from the gastrointestinal tract can potentially enter the circulation system, which, in turn, affects host metabolism. Yet, the metabolic capacity of intestinal microbiota and its interaction with mammalian metabolism remains largely unexplored. Here, we review a metabolic pathway that integrates the microbial catabolism of methionine with mammalian metabolism of methanethiol (MT), dimethyl sulfide (DMS), and dimethyl sulfoxide (DMSO), which together provide evidence that supports the microbial origin of dimethyl sulfone (DMSO2) in the human metabolome. Understanding the pathway of DMSO2 co-metabolism expends our knowledge of microbial-derived metabolites and motivates future metabolomics-based studies on ascertaining the metabolic consequences of intestinal microbiota on human health, including detoxification processes and sulfur xenobiotic metabolism.

Dimethyl sulfide as a source of the seaweed-like aroma in cooked soybeans and correlation with its precursor, S-methylmethionine (vitamin U)

Among the soybean germplasm in Japan, two varieties, Nishiyamahitashi 98-5 (NH) and Shinanokurakake (SKK), have an intense seaweed-like flavor after cooking. Gas-liquid chromatography with mass spectrometry (GC-MS) indicated that a significant amount (11.5 ± 3.46 μg g(-1) for NH and 6.66 ± 0.91 μg g(-1) for SKK) of dimethyl sulfide (DMS) was formed after heat treatment. DMS is formed from S-methylmethionine (SMM, vitamin U). SMM was detected in all soybean varieties examined here, but its concentration in NH and SKK seeds was >100-fold higher than in the other varieties and ranged from 75 to 290 μg g(-1). The SMM content and the ability to form DMS upon heat treatment correlated among them. The plumes and radicles contained SMM exclusively. This is the first report of soybean varieties containing SMM at a level equivalent to or higher than that in vegetables known to contain high levels of SMM, for example, turnip, cabbage, and celery.

Quantification of methylated selenium, sulfur, and arsenic in the environment

Biomethylation and volatilization of trace elements may contribute to their redistribution in the environment. However, quantification of volatile, methylated species in the environment is complicated by a lack of straightforward and field-deployable air sampling methods that preserve element speciation. This paper presents a robust and versatile gas trapping method for the simultaneous preconcentration of volatile selenium (Se), sulfur (S), and arsenic (As) species. Using HPLC-HR-ICP-MS and ESI-MS/MS analyses, we demonstrate that volatile Se and S species efficiently transform into specific non-volatile compounds during trapping, which enables the deduction of the original gaseous speciation. With minor adaptations, the presented HPLC-HR-ICP-MS method also allows for the quantification of 13 non-volatile methylated species and oxyanions of Se, S, and As in natural waters. Application of these methods in a peatland indicated that, at the selected sites, fluxes varied between 190–210 ng Se·m⁻²·d⁻¹, 90–270 ng As·m⁻²·d⁻¹, and 4–14 µg S·m⁻²·d⁻¹, and contained at least 70% methylated Se and S species. In the surface water, methylated species were particularly abundant for As (>50% of total As). Our results indicate that methylation plays a significant role in the biogeochemical cycles of these elements.

Odorous gaseous emissions as influence by process condition for the forced aeration composting of pig slaughterhouse sludge

Compost sustainability requires a better control of its gaseous emissions responsible for several impacts including odours. Indeed, composting odours have stopped the operation of many platforms and prevented the installation of others. Accordingly, present technologies collecting and treating gases emitted from composting are not satisfactory and alternative solutions must be found. Thus, the aim of this paper was to study the influence of composting process conditions on gaseous emissions. Pig slaughterhouse sludge mixed with wood chips was composted under forced aerationin 300 L laboratory reactors. The process conditions studied were: aeration rate of 1.68, 4.03, 6.22, 9.80 and 13.44 L/h/kg of wet sludge; incorporation ratio of 0.55, 0.83 and 1.1 (kg of wet wood chips/kg of wet sludge), and; bulking agent particles size of <10, 10<20 and 20<30 mm. Out-going gases were sampled every 2 days and their composition was analysed using gas chromatography coupled with mass spectrometry (GC-MS). Fifty-nine compounds were identified and quantified. Dividing the cumulated mass production over 30 days of composting, by odour threshold, 9 compounds were identified as main potential odour contributors: hydrogen sulphide, trimethylamine, ammonia, 2-pentanone, 1-propanol-2-methyl, dimethyl sulphide, dimethyl disulphide, dimethyl trisulphide and acetophenone. Five gaseous compounds were correlated with both aeration rate and bulking agent to waste ratio: hydrogen sulphide, trimethylamine, ammonia, 2-pentanone and 1-propanol-2-methyl. However, dropping the aeration rate and increasing the bulking agent to waste ratio reduced gaseous odour emissions by a factor of 5-10, when the required threshold dilution factor ranged from 10(5) to 10(6), to avoid nuisance at peak emission rates. Process influence on emissions of dimethyl sulphide, dimethyl disulphide, dimethyl trisulphide were poorly correlated with both aeration rate and bulking agent to waste ratio as a reaction with hydrogen sulphide was suspected. Acetophenone emissions originated from the wood chips. Olfactory measurements need to be correlated to gaseous emissions for a more accurate odour emission evaluation.

Microorganisms and typical organic matter responsible for lacustrine "black bloom"

Identifying the causation of the black substance in lacustrine "black bloom" is of great significance for forecasting and preventing black bloom in many waters of the world. In this research, an array of black bloom was simulated in a laboratory to investigate how microorganisms and organic matter affect black bloom. Sulphate-reducing bacteria (SRB) are the main biological factor, and protein is the key organic factor contributing to lacustrine black bloom. The black colour of black bloom is strongly associated with a relatively high SRB population density. Hydrogen sulphide concentration can serve as a predictor of black bloom.

Beyond hypoxia: occurrence and characteristics of black blooms due to the decomposition of the submerged plant Potamogeton crispus in a shallow lake

Organic matter-induced black blooms (hypoxia and an offensive odor) are a serious ecosystem disasters that have occurred in some large eutrophic shallow lakes in China. In this study, we investigated two separate black blooms that were induced by Potamogeton crispus in Lake Taihu, China. The main physical and chemical characteristics, including color- and odor-related substances, of the black blooms were analyzed. The black blooms were characterized by low dissolved oxygen concentration (close to 0 mg/L), low oxidation-reduction potential, and relatively low pH of overlying water. Notably higher Fe2+ and sigmaS(2-) were found in the black-bloom waters than in waters not affected by black blooms. The black color of the water may be attributable to the high concentration of these elements, as black FeS was considered to be the main substance causing the black color of blooms in freshwater lakes. Volatile organic sulfur compounds, including dimethyl sulfide, dimethyl disulfide, and dimethyl trisulfide, were very abundant in the black-bloom waters. The massive anoxic degradation of dead Potamogeton crispus plants released dimethyl sulfide, dimethyl disulfide, and dimethyl trisulfide, which were the main odor-causing compounds in the black blooms. The black blooms also induced an increase in ammonium nitrogen and soluble reactive phosphorus levels in the overlying waters. This extreme phenomenon not only heavily influenced the original lake ecosystem but also greatly changed the cycling of Fe, S, and nutrients in the water column.

Combining chemoinformatics with bioinformatics: in silico prediction of bacterial flavor-forming pathways by a chemical systems biology approach "reverse pathway engineering"

The incompleteness of genome-scale metabolic models is a major bottleneck for systems biology approaches, which are based on large numbers of metabolites as identified and quantified by metabolomics. Many of the revealed secondary metabolites and/or their derivatives, such as flavor compounds, are non-essential in metabolism, and many of their synthesis pathways are unknown. In this study, we describe a novel approach, Reverse Pathway Engineering (RPE), which combines chemoinformatics and bioinformatics analyses, to predict the “missing links” between compounds of interest and their possible metabolic precursors by providing plausible chemical and/or enzymatic reactions. We demonstrate the added-value of the approach by using flavor-forming pathways in lactic acid bacteria (LAB) as an example. Established metabolic routes leading to the formation of flavor compounds from leucine were successfully replicated. Novel reactions involved in flavor formation, i.e. the conversion of alpha-hydroxy-isocaproate to 3-methylbutanoic acid and the synthesis of dimethyl sulfide, as well as the involved enzymes were successfully predicted. These new insights into the flavor-formation mechanisms in LAB can have a significant impact on improving the control of aroma formation in fermented food products. Since the input reaction databases and compounds are highly flexible, the RPE approach can be easily extended to a broad spectrum of applications, amongst others health/disease biomarker discovery as well as synthetic biology.

Infrared studies of the reaction of methanesulfonic acid with trimethylamine on surfaces

Organosulfur compounds generated from a variety of biological as well as anthropogenic sources are oxidized in air to form sulfuric acid and methanesulfonic acid (MSA). Both of these acids formed initially in the gas phase react with ammonia and amines in air to form and grow new particles, which is important for visibility, human health and climate. A competing sink is deposition on surfaces in the boundary layer. However, relatively little is known about reactions after they deposit on surfaces. We report here diffuse reflectance infrared Fourier transform spectrometry (DRIFTS) studies of the reaction of MSA with trimethylamine (TMA) on a silicon powder at atmospheric pressure in synthetic air and at room temperature, either in the absence or in the presence of water vapor. In both cases, DRIFTS spectra of the product surface species are essentially the same as the transmission spectrum obtained for trimethylaminium methanesulfonate, indicating the formation of the salt on the surface with a lower limit to the reaction probability of γ > 10(-6). To the best of our knowledge, this is the first infrared study to demonstrate this chemistry from the heterogeneous reaction of MSA with an amine on a surface. This heterogeneous chemistry appears to be sufficiently fast that it could impact measurements of gas-phase amines through reactions with surface-adsorbed acids on sampling lines and inlets. It could also represent an additional sink for amines in the boundary layer, especially at night when the gas-phase reactions of amines with OH radical and ozone are minimized.