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1

Electronic Resource

Dimethyl sulfide emissions from a sedimental microbial ecosystem subject to diel variations of oxic and anoxic conditions: a simple mathematical model (1998)

Berg, Hugo A. ; Jonkers, Henk M. ; Bergeijk, Stef A. ; [et al.]

Oxford, UK : Blackwell Publishing Ltd

FEMS microbiology ecology 26 (1998), S. 0

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ISSN: 1574-6941

Source: Blackwell Publishing Journal Backfiles 1879-2005

Topics: Biology

Notes: This modelling study relates dimethylsulfide emission from a microbial mat to the flux of dimethylsulfoniopropionate that is exuded into the interstitial space of the mat by phototrophs. Dimethylsulfoniopropionate may be either cleaved or demethylated. Only cleavage results in the production of dimethylsulfide, which itself is further oxidized or escapes from the mat. The fate of dimethylsulfoniopropionate depends on the functional group composition of the mat, the physiological characteristics of these groups, and the eco-physiological conditions oxic/anoxic and light/dark, which both vary in a diel cycle. These three factors are accounted for in a mathematical model of a microbial mat typical of the Wadden Islands of The Netherlands and Germany. Model simulations quantify increased dimethylsulfide production under alkaline stress as well as additional dimethylsulfoniopropionate loads.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1111/j.1574-6941.1998.tb01556.x

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2

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Microbial production and consumption of dimethyl sulfide (DMS) in a sea grass (Zostera noltii)-dominated marine intertidal sediment ecosystem (Bassin d'Arcachon, France) (2000)

Jonkers, Henk M. ; Bergeijk, Stef A. ; Gemerden, Hans

Oxford, UK : Blackwell Publishing Ltd

FEMS microbiology ecology 31 (2000), S. 0

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ISSN: 1574-6941

Source: Blackwell Publishing Journal Backfiles 1879-2005

Topics: Biology

Notes: The relation between net dimethyl sulfide (DMS) production and changes in near surface (0–5 mm) oxygen concentrations in a sea grass (Zostera noltii Hornem)-covered intertidal sediment ecosystem was examined during a diel cycle. Sediment covered with Zostera was found to be more oxygenated than uncovered sediment during the period of photosynthesis. This phenomenon was probably caused by radial oxygen loss of the Zostera root-rhizome system. The population sizes of the three functional groups of microbes mainly responsible for the concentration of DMS, the dimethylsulfoniopropionate (DMSP)-demethylating, DMSP-cleaving and DMS-oxidizing bacteria, were quantified by most probable number (MPN) methodologies. Sediments with Zostera supported substantially higher populations of both aerobic (149×106 cm−3 DMSP-utilizing and 0.4×106 cm−3 DMS-oxidizing) and anaerobic (43×106 cm−3 DMSP-utilizing and 0.4×106 cm−3 DMS-oxidizing) microorganisms than sediments without Zostera (DMSP-utilizing aerobes and anaerobes both 2×106 cm−3 and DMS-oxidizing aerobes and anaerobes both 0.2×106 cm−3). Experiments conducted with sediment cores and sediment slurries suggested that the net production of DMS in these sediments was significantly lower during oxic periods than during anoxic periods. Intact sediment cores with and without Zostera produced DMS when incubated under anoxic/dark conditions (97.0 and 53.6 nmol DMS m−2 h−1, respectively), while oxic/light-incubated cores did not produce detectable amounts of DMS. In addition, kinetic parameter values (Vmax and Km) for DMSP degradation in cell suspensions of isolated DMSP-demethylating and DMSP-cleaving bacteria were measured and compared to documented values for other strains. Both Vmax and Km values for DMSP-demethylating organisms were found to be relatively low (14.4–20.1 nmol DMSP mg protein−1 min−1 and 4.1–15.5 μM, respectively) while these parameter values varied widely in the group of the DMSP-cleaving organisms (6.7–1000 nmol DMSP mg protein−1 min−1 and 2–2000 μM, respectively). It was hypothesized that a diel rhythm in DMS emission occurred, with a relatively low net production during the day and a high net production during the night. Environmental changes which result in increased anoxic conditions in coastal sediments, such as an increase in eutrophication, may therefore result in increased atmospheric DMS emission rates.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1111/j.1574-6941.2000.tb00681.x

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3

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Turnover of dimethylsulfoniopropionate (DMSP) by the purple sulfur bacterium Thiocapsa roseopersicina M11: ecological implications (1998)

Jonkers, Henk M ; Bruin, Saskia ; Gemerden, Hans

Oxford, UK : Blackwell Publishing Ltd

FEMS microbiology ecology 27 (1998), S. 0

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ISSN: 1574-6941

Source: Blackwell Publishing Journal Backfiles 1879-2005

Topics: Biology

Notes: The use of dimethylsulfoniopropionate (DMSP) by the anoxygenic phototrophic purple sulfur bacterium Thiocapsa roseopersicina M11 under different environmental conditions was studied. Under anoxic/light conditions DMSP cleavage occurred both at low and intermediate salinities but at different growth phases: at low salinity (5‰ S) DMSP cleavage was observed in the exponential growth phase, whereas at intermediate salinity (35‰ S) cleavage was not observed until the stationary phase was reached. At higher salinities DMSP accumulated intracellularly, prior to cleavage, suggesting usage as compatible solute. Circumstantial evidence suggests that under anoxic/light conditions acrylate, one of the DMSP cleavage products, was reduced to propionate at the expense of intracellular sulfur oxidation, and subsequently used as carbon source. The addition of acrylate had an inhibitory effect on growth, the reduction of acrylate to propionate can thus play an additional role as a detoxification mechanism. Dimethyl sulfide (DMS), also a DMSP cleavage product, was not used under anoxic conditions. However, under oxic conditions both DMS and acrylate metabolization resulted in protein production. DMSP lyase in cell suspensions was induced by acrylate and activity was enhanced in the light. The latter suggests that DMSP cleavage is an energy dependent process. The potential anaerobic DMS production and aerobic consumption in T. roseopersicina M11 is in agreement with previously observed diurnal DMS dynamics in coastal marine sediments, the natural habitat of this anoxygenic phototrophic bacterium. This is the first report in which a bacterium is described that is able to cleave DMSP with subsequent metabolization of DMS.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1111/j.1574-6941.1998.tb00544.x

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4

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Diversity and vertical distribution of magnetotactic bacteria along chemical gradients in freshwater microcosms (2005)

Flies, Christine B. ; Jonkers, Henk M. ; Beer, Dirk ; [et al.]

Oxford, UK : Blackwell Publishing Ltd

FEMS microbiology ecology 52 (2005), S. 0

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ISSN: 1574-6941

Source: Blackwell Publishing Journal Backfiles 1879-2005

Topics: Biology

Notes: The vertical distribution of magnetotactic bacteria along various physico-chemical gradients in freshwater microcosms was analyzed by a combined approach of viable cell counts, 16S rRNA gene analysis, microsensor profiling and biogeochemical methods. The occurrence of magnetotactic bacteria was restricted to a narrow sediment layer overlapping or closely below the maximum oxygen and nitrate penetration depth. Different species showed different preferences within vertical gradients, but the largest proportion (63–98%) of magnetotactic bacteria was detected within the suboxic zone. In one microcosm the community of magnetotactic bacteria was dominated by one species of a coccoid “Alphaproteobacterium”, as detected by denaturing gradient gel electrophoresis in sediment horizons from 1 to 10 mm depth. Maximum numbers of magnetotactic bacteria were up to 1.5 × 107 cells/cm3, which corresponded to 1% of the total cell number in the upper sediment layer. The occurrence of magnetotactic bacteria coincided with the availability of significant amounts (6–60 μM) of soluble Fe(II), and in one sample with hydrogen sulfide (up to 40 μM). Although various trends were clearly observed, a strict correlation between the distribution of magnetotactic bacteria and individual geochemical parameters was absent. This is discussed in terms of metabolic adaptation of various strains of magnetotactic bacteria to stratified sediments and diversity of the magnetotactic bacterial communities.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1016/j.femsec.2004.11.006

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5

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Structural and functional analysis of a microbial mat ecosystem from a unique permanent hypersaline inland lake: ‘La Salada de Chiprana’ (NE Spain) (2003)

Jonkers, Henk M ; Ludwig, Rebecca ; Wit, Rutger ; [et al.]

Oxford, UK : Blackwell Publishing Ltd

FEMS microbiology ecology 44 (2003), S. 0

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ISSN: 1574-6941

Source: Blackwell Publishing Journal Backfiles 1879-2005

Topics: Biology

Notes: The benthic microbial mat community of the only permanent hypersaline natural inland lake of Western Europe, ‘La Salada de Chiprana’, northeastern Spain, was structurally and functionally analyzed. The ionic composition of the lake water is characterized by high concentrations of magnesium and sulfate, which were respectively 0.35 and 0.5 M at the time of sampling while the total salinity was 78 g l−1. Community composition was analyzed by microscopy, high-performance liquid chromatography (HPLC) pigment analyses and by studying culturable bacteria from different functional groups. Therefore, denaturing gradient gel electrophoresis (DGGE) was applied on most probable number (MPN) dilution cultures. Microscopy revealed that a thin layer of Chloroflexus-like bacteria overlaid various cyanobacteria-dominated layers each characterized by different morphotypes. DGGE analysis of MPN dilution cultures from distinct mat layers showed that various phylotypes of anoxygenic phototrophic, aerobic heterotrophic, colorless sulfur-, and sulfate-reducing bacteria were present. The mats were furthermore functionally studied and attention was focussed on the relationship between oxygenic primary production and the flow of carbon through the microbial community. Microsensor techniques, porewater and sediment photopigment analysis were applied in order to estimate oxygenic photosynthetic rates, daily dynamics of (in)organic carbon porewater concentration and migration behavior of phototrophs. Chiprana microbial mats produced dissolved organic carbon (DOC) both during the day and night. It was estimated that 14% of the mats gross photosynthetic production and 49% of the mats net photosynthetic production diffused out of the mat in the form of low molecular mass fatty acids, although these compounds made up only 2% of the total DOC pool. The high flux of dissolved fatty acids from the microbial mat to the water column may explain why in this system Chloroflexus-like bacteria proliferate on top of the cyanobacterial layers since these photoheterotrophic bacteria grow preferably on organic phototrophic exudates. Furthermore it may also explain why high numbers of viable sulfate-reducing bacteria were found in the fully oxygenated sediment surface layers. These organisms apparently do not have to compete with aerobic heterotrophic community members due to the ample availability of organic substrates. Moreover, the high production of DOC strongly indicates that the mat community was nutrient limited in its growth. Photopigment analysis revealed furthermore that chlorophyll a (Chla) and three of its allomeres had a complementary depth distribution what suggests that the Chla allomeres are functional adaptations to differences in light quality and/or quantity and may be species specific.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1016/S0168-6496(02)00464-6

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6

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Dimethylsulfoxide reduction by marine sulfate-reducing bacteria (1996)

Jonkers, Henk M. ; Der Maarel, Marc J.E.C. ; Gemerden, Hans ; [et al.]

Oxford, UK : Blackwell Publishing Ltd

FEMS microbiology letters 136 (1996), S. 0

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ISSN: 1574-6968

Source: Blackwell Publishing Journal Backfiles 1879-2005

Topics: Biology

Notes: Abstract Dimethylsulfoxide (DMSO) reduction occurred in five out of nine strains of sulfate-reducing bacteria from marine or saline environments, but not in three freshwater isolates. DMSO reduction supported growth in all positive strains. In Desulfovibrio desulfuricans strain PA2805, DMSO reduction occurred simultaneously with sulfate reduction and was not effectively inhibited by molybdate, a specific inhibitor of sulfate reduction. The growth yield per mol lactate was 26% higher with DMSO than with sulfate as electron acceptor. In extracts of cells of strain PA2805 grown on sulfate, a low level of DMSO-reducing activity was present (0.013 μmol (mg protein)− min−); higher levels were found in cells grown on DMSO (0.56 μmol (mg protein)− min−). In anoxic marine environments DMSO reduction by sulfate-reducing bacteria may lead to enhanced dimethylsulfide emission rates.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1111/j.1574-6968.1996.tb08062.x

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7

Electronic Resource

Aerobic turnover of dimethyl sulfide by the anoxygenic phototrophic bacterium Thiocapsa roseopersicina (1999)

Jonkers, Henk M. ; Jansen, Michael ; Van der Maarel, Marc J. E. C. ; [et al.]

Springer

Archives of microbiology 172 (1999), S. 150-156

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ISSN: 1432-072X

Keywords: Key words Purple sulfur bacterium ; Thiocapsa ; roseopersicina ; Dimethyl sulfide ; Dimethylsulfoniopropionate

Source: Springer Online Journal Archives 1860-2000

Topics: Biology

Notes: Abstract This is the first report describing the complete oxidation of dimethyl sulfide (DMS) to sulfate by an anoxygenic, phototrophic purple sulfur bacterium. Complete DMS oxidation was observed in cultures of Thiocapsa roseopersicina M11 incubated under oxic/light conditions, resulting in a yield of 30.1 mg protein mmol–1. No oxidation of DMS occurred under anoxic/light conditions. Chloroform, methyl butyl ether, and 3-amino-1,2,4-triazole, which are specific inhibitors of aerobic DMS oxidation in thiobacilli and hyphomicrobia, did not affect DMS oxidation in strain M11. This could be due to limited transport of the inhibitors through the cell membrane. The growth yield on sulfide as sole electron donor was 22.2 mg protein mmol–1 under anoxic/light conditions. Since aerobic respiration of sulfide would have resulted in yields lower than 22 mg protein mmol–1, the higher yield on DMS under oxic/light conditions suggests that the methyl groups of DMS have served as an additional carbon source or as an electron donor in addition to the sulfide moiety. The kinetic parameters V max and K m for DMS oxidation under oxic/light conditions were 12.4 ± 1.3 nmol (mg protein)–1 min–1 and 2 μM, respectively. T. roseopersicina M11 also produced DMS by cleavage of dimethylsulfoniopropionate (DMSP). Specific DMSP cleavage rates increased with increasing initial substrate concentrations, suggesting that DMSP lyase was only partly induced at lower initial DMSP concentrations. A comparison of T. roseopersicina strains revealed that only strain M11 was able to oxidize DMS and cleave DMSP. Both strain M11 and strain 5811 accumulated DMSP intracellularly during growth, while strain 1711 showed neither of these characteristics. Phylogenetic comparison based on 16S rRNA gene sequence revealed a similarity of 99.0% between strain M11 and strain 5811, and 97.6% between strain M11 and strain 1711. DMS and DMSP utilization thus appear to be strain-specific.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/s002030050754

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