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1.
Estimation of Sediment Denitrification Rates at In Situ Nitrate Concentrations 总被引:1,自引:9,他引:1
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The denitrification rates in a marine sediment, estimated by using 15N-nitrate, Vmax, Km, and sediment nitrate concentrations, were 12.5 and 2.0 nmol of N2-N cm−3 day−1 at 0 to 1 and 1 to 3 cm, respectively, at 12°C. The total rate was 165 nmol of N2-N m−2 day−1. 相似文献
2.
Comparison of In Situ and In Vitro Rates of Methane Release in Freshwater Sediments 总被引:6,自引:4,他引:2
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Anaerobic lake sediment incubated in vitro was investigated for its ability to mimic natural in situ sediment activities, using rate of methane production for the comparison. Two lakes with different rates and seasonal patterns of methanogenic activity were compared. There was good agreement (at the 97.5% confidence level) between rates of in situ methane release and initial (lasting an average of 120 h) rates of production measured in vitro in surface (0- to 3-cm) sediment. Evidence from this study, and others, indicated that it is the in situ surface sediment methane production which is primarily responsible for maintaining in situ methane release, and thus the above agreement was what was expected if surface in situ activity was maintained in vitro. When deeper sediment was investigated, however, the sum of in vitro rates from 0 to 20 cm (measured in 1.5- to 3-cm intervals) was much higher than in situ release rates and would have resulted in an impossibly high volume of gas. The extra gas could not have been stored within the sediments. We conclude that the in situ methanogenic activity of the 0- to 3-cm anaerobic surface sediments could be preserved during removal and laboratory incubation. However, similar treatment of deeper sediment appeared to stimulate methanogenic activity. 相似文献
3.
Determination of In Situ Bacterial Growth Rates in Aquifers and Aquifer Sediments 总被引:3,自引:1,他引:2
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Laboratory and field-scale studies with stained cells were performed to monitor cell growth in groundwater systems. During cell division, the fluorescence intensity of the protein stain 5-(and 6-)-carboxyfluorescein diacetate succinimidyl ester (CFDA/SE) for each cell is halved, and the intensity can be tracked with a flow cytometer. Two strains of bacteria, Comamonas sp. strain DA001 and Acidovorax sp. strain OY-107, both isolated from a shallow aquifer, were utilized in this study. The change in the average generation or the average fluorescence intensity of the CFDA/SE-stained cells could be used to obtain estimates of doubling times. In microcosm experiments, the CFDA/SE-based doubling times were similar to the values calculated by total cell counting and were independent of cell concentration. Intact and repacked sediment core experiments with the same bacteria indicated that changes in groundwater chemistry were just as important as growth rates in determining planktonic cell concentrations. The growth rates within the sediment cores were similar to those calculated in microcosm experiments, and preferential transport of the daughter cells was not observed. The experiments indicated that the growth rates could be determined in systems with cell losses due to other phenomena, such as attachment to sediment or predation. Application of this growth rate estimation method to data from a field-scale bacterial transport experiment indicated that the doubling time was approximately 15 days, which is the first known direct determination of an in situ growth rate for bacteria in an aquifer. 相似文献
4.
Measurement of Denitrification in Two Freshwater Sediments by an In Situ Acetylene Inhibition Method 总被引:7,自引:13,他引:7
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An acetylene inhibition method was satisfactorily used for the in situ measurement of denitrification in two sediment-water systems incubated for not more than 22 h. In the presence of added nitrate, denitrification acted as a source of nitrous oxide in a drainage pond, but acted as a sink in its absence. The averaged rates of nitrous oxide accumulation with nitrate enrichment in the absence and presence of acetylene were 0.15 and 0.30 mg of N m−2h−1, respectively. Acetylene reduction at an average rate of 0.07 mmol of C2H4 formed m−2h−1 was simultaneously measured in the absence of added nitrate. In a small eutrophic lake where nitrogen was nonlimiting, the in situ rates of sediment denitrification were 0.09 and 0.11 mg of N m−2h−1 in the presence and absence of macrophytes, respectively, and no acetylene reduction activity was found. 相似文献
5.
Kinetic Studies of Bacterial Sulfate Reduction in Freshwater Sediments by High-Pressure Liquid Chromatography and Microdistillation 总被引:7,自引:1,他引:6
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Kees A. Hordijk Charles P. M. M. Hagenaars Thomas E. Cappenberg 《Applied microbiology》1985,49(2):434-440
Indirect photometric chromatography and microdistillation enabled a simultaneous measurement of sulfate depletion and sulfide production in the top 3 cm of freshwater sediments to be made. The simultaneous measurement of sulfate depletion and sulfide production rates provided added insight into microbial sulfur metabolism. The lower sulfate reduction rates, as derived from the production of acid-volatile 35S2− only, were explained by a conversion of this pool to an undistillable fraction under acidic conditions during incubation. A mathematical model was applied to calculate sulfate reduction from sulfate gradients at the sediment-water interface. To avoid disturbance of these gradients, the sample volume was reduced to 0.2 g (wet weight) of sediment. Sulfate diffusion coefficients in the model were determined (Ds = 0.3 × 10−5 cm2 s−1 at 6°C). The results of the model were compared with those of radioactive sulfate turnover experiments by assessing the actual turnover rate constants (2 to 5 day−1) and pool sizes of sulfate at different sediment depths. 相似文献
6.
One arm of Lake Anna, Va., receives acid mine drainage (AMD) from Contrary Creek (SO42− concentration = 2 to 20 mM, pH = 2.5 to 3.5). Acid-volatile sulfide concentrations, SO42− reduction rates, and interstitial SO42− concentrations were measured at various depths in the sediment at four stations in four seasons to assess the effects of the AMD-added SO42− on bacterial SO42− reduction. Acid-volatile sulfide concentrations were always an order of magnitude higher at the stations receiving AMD than at a control station in another arm of the lake that received no AMD. Summer SO42− reduction rates were also an order of magnitude higher at stations that received AMD than at the control station (226 versus 13.5 mmol m−2 day−1), but winter values were inconclusive, probably due to low sediment temperature (6°C). Profiles of interstitial SO42− concentrations at the AMD stations showed a rapid decrease with depth (from 1,270 to 6 μM in the top 6 cm) due to rapid SO42− reduction. Bottom-water SO42− concentrations in the AMD-receiving arm were highest in winter and lowest in summer. These data support the conclusion that there is a significant enhancement of SO42− reduction in sediments receiving high SO42− inputs from AMD. 相似文献
7.
Sokratis Papaspyrou Cindy J. Smith Liang F. Dong Corinne Whitby Alex J. Dumbrell David B. Nedwell 《PloS one》2014,9(4)
Denitrification and dissimilatory nitrate reduction to ammonium (DNRA) are processes occurring simultaneously under oxygen-limited or anaerobic conditions, where both compete for nitrate and organic carbon. Despite their ecological importance, there has been little investigation of how denitrification and DNRA potentials and related functional genes vary vertically with sediment depth. Nitrate reduction potentials measured in sediment depth profiles along the Colne estuary were in the upper range of nitrate reduction rates reported from other sediments and showed the existence of strong decreasing trends both with increasing depth and along the estuary. Denitrification potential decreased along the estuary, decreasing more rapidly with depth towards the estuary mouth. In contrast, DNRA potential increased along the estuary. Significant decreases in copy numbers of 16S rRNA and nitrate reducing genes were observed along the estuary and from surface to deeper sediments. Both metabolic potentials and functional genes persisted at sediment depths where porewater nitrate was absent. Transport of nitrate by bioturbation, based on macrofauna distributions, could only account for the upper 10 cm depth of sediment. A several fold higher combined freeze-lysable KCl-extractable nitrate pool compared to porewater nitrate was detected. We hypothesised that his could be attributed to intracellular nitrate pools from nitrate accumulating microorganisms like Thioploca or Beggiatoa. However, pyrosequencing analysis did not detect any such organisms, leaving other bacteria, microbenthic algae, or foraminiferans which have also been shown to accumulate nitrate, as possible candidates. The importance and bioavailability of a KCl-extractable nitrate sediment pool remains to be tested. The significant variation in the vertical pattern and abundance of the various nitrate reducing genes phylotypes reasonably suggests differences in their activity throughout the sediment column. This raises interesting questions as to what the alternative metabolic roles for the various nitrate reductases could be, analogous to the alternative metabolic roles found for nitrite reductases. 相似文献
8.
Estimation of the State of the Bacterial Cell Wall by Fluorescent In Situ Hybridization 总被引:6,自引:3,他引:3
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Elena Bidnenko Carine Mercier Josselyne Tremblay Patrick Tailliez Saulius Kulakauskas 《Applied microbiology》1998,64(8):3059-3062
Fluorescent in situ hybridization (FISH) is now a widely used method for identification of bacteria at the single-cell level. With gram-positive bacteria, the thick peptidoglycan layer of a cell wall presents a barrier for entry of horseradish peroxidase (HRP)-labeled probes. Therefore, such probes do not give any signal in FISH unless cells are first treated with enzymes which hydrolyze the peptidoglycan. We explored this feature of FISH to detect cells which have undergone permeabilization due to expression of autolytic enzymes. Our results indicate that FISH performed with HRP-labeled probes provides a sensitive method to estimate the states of cell walls of individual gram-positive bacteria. 相似文献
9.
Electron microscope grids were submerged in Lake Washington, Seattle, Wash., in June 1996 as bait to which Caulobacter sp. swarmers would attach and on which they would then reproduce in situ. Enumeration of bands in the stalks of attached cells implied that the caulobacters were completing approximately three reproductive cycles per day. A succession of morphological types of caulobacters occurred, as well as an episode of bacteriovore grazing that slowed the accumulation of caulobacters and prevented the aging of the population. 相似文献
10.
11.
In Situ Detection of Freshwater Fungi in an Alpine Stream by New Taxon-Specific Fluorescence In Situ Hybridization Probes
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Christiane Baschien Werner Manz Thomas R. Neu Ludmila Marvanov Ulrich Szewzyk 《Applied microbiology》2008,74(20):6427-6436
New rRNA-targeting oligonucleotide probes permitted the fluorescence in situ hybridization (FISH) identification of freshwater fungi in an Austrian second-order alpine stream. Based on computer-assisted comparative sequence analysis, nine taxon-specific probes were designed and evaluated by whole-fungus hybridizations. Oligonucleotide probe MY1574, specific for a wide range of Eumycota, and the genus (Tetracladium)-specific probe TCLAD1395, as well as the species-specific probes ALacumi1698 (Alatospora acuminata), TRIang322 (Tricladium angulatum), and Alongi340 (Anguillospora longissima), are targeted against 18S rRNA, whereas probes TmarchB10, TmarchC1_1, TmarchC1_2, and AlongiB16 are targeted against the 28S rRNA of Tetracladium marchalianum and Anguillospora longissima, respectively. After 2 weeks and 3 months of exposure of polyethylene slides in the stream, attached germinating conidia and growing hyphae of freshwater fungi were accessible for FISH. Growing hyphae and germinating conidia on leaves and in membrane cages were also visualized by the new FISH probes. 相似文献
12.
Dissimilatory Nitrate Reduction in Anaerobic Sediments Leading to River Nitrite Accumulation 总被引:6,自引:3,他引:3
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Recent studies on Northern Ireland rivers have shown that summer nitrite (NO(inf2)(sup-)) concentrations greatly exceed the European Union guideline of 3 (mu)g of N liter(sup-1) for rivers supporting salmonid fisheries. In fast-flowing aerobic small streams, NO(inf2)(sup-) is thought to originate from nitrification, due to the retardation of Nitrobacter strains by the presence of free ammonia. Multiple regression analyses of NO(inf2)(sup-) concentrations against water quality variables of the six major rivers of the Lough Neagh catchment in Northern Ireland, however, suggested that the high NO(inf2)(sup-) concentrations found in the summer under warm, slow-flow conditions may result from the reduction of NO(inf3)(sup-). This hypothesis was supported by field observations of weekly changes in N species. Here, reduction of NO(inf3)(sup-) was observed to occur simultaneously with elevation of NO(inf2)(sup-) levels and subsequently NH(inf4)(sup+) levels, indicating that dissimilatory NO(inf3)(sup-) reduction to NH(inf4)(sup+) (DNRA) performed by fermentative bacteria (e.g., Aeromonas and Vibrio spp.) is responsible for NO(inf2)(sup-) accumulation in these large rivers. Mechanistic studies in which (sup15)N-labelled NO(inf3)(sup-) in sediment extracts was used provided further support for this hypothesis. Maximal concentrations of NO(inf2)(sup-) accumulation (up to 1.4 mg of N liter(sup-1)) were found in sediments deeper than 6 cm associated with a high concentration of metabolizable carbon and anaerobic conditions. The (sup15)N enrichment of the NO(inf2)(sup-) was comparable to that of the NO(inf3)(sup-) pool, indicating that the NO(inf2)(sup-) was predominantly NO(inf3)(sup-) derived. There is evidence which suggests that the high NO(inf2)(sup-) concentrations observed arose from the inhibition of the DNRA NO(inf2)(sup-) reductase system by NO(inf3)(sup-). 相似文献
13.
14.
García-Cantizano J Casamayor EO Gasol JM Guerrero R Pedrós-Alió C 《Microbial ecology》2005,50(2):230-241
Partitioning of CO2 incorporation into oxygenic phototrophic, anoxygenic phototrophic, and chemolithoautotrophic guilds was determined in a freshwater
lake (Lake Cisó, Banyoles, Spain). CO2 incorporation into the different types of microorganisms was studied at different depths, during diel cycles, and throughout
the year. During winter holomixis, the whole lake became anoxic and both the anoxygenic and chemolithoautotrophic guilds were
more active at the surface of the lake, whereas the activity of the oxygenic guild was negligible. During stratification,
the latter guild was more active in the upper metalimnion, whereas the anoxygenic guild was more active in the lower metalimnion.
Specific growth rates and doubling times were estimated for the most conspicuous phototrophic microorganisms. Doubling times
for Cryptomonas phaseolus ranged between 0.5 and 192 days, whereas purple sulfur bacteria (Chromatiaceae-like) ranged between 1.5 and 238 days. These growth rates were similar to those calculated with a different approach in previous
papers and indicate slow-growing populations with very large biomass. Overall, the annual total CO2 incorporation in Lake Cisó was 220 g C m−2. Most of the CO2 incorporation, however, was due to the chemolithoautotrophic guild (61% during holomixis and 56% during stratification),
followed by the anoxygenic phototrophic guild (35 and 19%, respectively) and the oxygenic phototrophs (4 and 25%, respectively),
making dark carbon fixation the key process in the autotrophic metabolism of the lake. 相似文献
15.
Henricus T. S. Boschker Diana Vasquez-Cardenas Henk Bolhuis Tanja W. C. Moerdijk-Poortvliet Leon Moodley 《PloS one》2014,9(7)
Chemoautotrophy has been little studied in typical coastal marine sediments, but may be an important component of carbon recycling as intense anaerobic mineralization processes in these sediments lead to accumulation of high amounts of reduced compounds, such as sulfides and ammonium. We studied chemoautotrophy by measuring dark-fixation of 13C-bicarbonate into phospholipid derived fatty acid (PLFA) biomarkers at two coastal sediment sites with contrasting sulfur chemistry in the Eastern Scheldt estuary, the Netherlands. At one site where free sulfide accumulated in the pore water right to the top of the sediment, PLFA labeling was restricted to compounds typically found in sulfur and ammonium oxidizing bacteria. At the other site, with no detectable free sulfide in the pore water, a very different PLFA labeling pattern was found with high amounts of label in branched i- and a-PLFA besides the typical compounds for sulfur and ammonium oxidizing bacteria. This suggests that other types of chemoautotrophic bacteria were also active, most likely Deltaproteobacteria related to sulfate reducers. Maximum rates of chemoautotrophy were detected in first 1 to 2 centimeters of both sediments and chemosynthetic biomass production was high ranging from 3 to 36 mmol C m−2 d−1. Average dark carbon fixation to sediment oxygen uptake ratios were 0.22±0.07 mol C (mol O2)−1, which is in the range of the maximum growth yields reported for sulfur oxidizing bacteria indicating highly efficient growth. Chemoautotrophic biomass production was similar to carbon mineralization rates in the top of the free sulfide site, suggesting that chemoautotrophic bacteria could play a crucial role in the microbial food web and labeling in eukaryotic poly-unsaturated PLFA was indeed detectable. Our study shows that dark carbon fixation by chemoautotrophic bacteria is a major process in the carbon cycle of coastal sediments, and should therefore receive more attention in future studies on sediment biogeochemistry and microbial ecology. 相似文献
16.
Nils Risgaard-Petersen Michael Kristiansen Rasmus B. Frederiksen Anders Lindequist Dittmer Jesper Tataru Bjerg Daniela Trojan Lars Schreiber Lars Riis Damgaard Andreas Schramm Lars Peter Nielsen 《Applied and environmental microbiology》2015,81(17):6003-6011
In marine sediments cathodic oxygen reduction at the sediment surface can be coupled to anodic sulfide oxidation in deeper anoxic layers through electrical currents mediated by filamentous, multicellular bacteria of the Desulfobulbaceae family, the so-called cable bacteria. Until now, cable bacteria have only been reported from marine environments. In this study, we demonstrate that cable bacteria also occur in freshwater sediments. In a first step, homogenized sediment collected from the freshwater stream Giber Å, Denmark, was incubated in the laboratory. After 2 weeks, pH signatures and electric fields indicated electron transfer between vertically separated anodic and cathodic half-reactions. Fluorescence in situ hybridization revealed the presence of Desulfobulbaceae filaments. In addition, in situ measurements of oxygen, pH, and electric potential distributions in the waterlogged banks of Giber Å demonstrated the presence of distant electric redox coupling in naturally occurring freshwater sediment. At the same site, filamentous Desulfobulbaceae with cable bacterium morphology were found to be present. Their 16S rRNA gene sequence placed them as a distinct sister group to the known marine cable bacteria, with the genus Desulfobulbus as the closest cultured lineage. The results of the present study indicate that electric currents mediated by cable bacteria could be important for the biogeochemistry in many more environments than anticipated thus far and suggest a common evolutionary origin of the cable phenotype within Desulfobulbaceae with subsequent diversification into a freshwater and a marine lineage. 相似文献
17.
Sulfate Reducers Can Outcompete Methanogens at Freshwater Sulfate Concentrations 总被引:7,自引:20,他引:7
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Acetate and hydrogen metabolism by sulfate reducers and methanogens in the profundal sediments of an oligotrophic lake were examined. Inhibition of sulfate reduction with molybdate stimulated methane production from both hydrogen and acetate. Molybdate did not stimulate methane production in sediments that were preincubated to deplete the sulfate pool. Sulfate reduction accounted for 30 to 81% of the total of terminal metabolism proceeding through sulfate reduction and methane production in Eckman grab samples of surface sediments. The ability of sulfate reducers to effectively compete with methanogens for acetate was related to the sulfate reducers' lower half-saturation constant for acetate metabolism at in situ sulfate concentrations. Processes other than sulfate reduction and methanogenesis consumed hydrogen at elevated hydrogen partial pressures and prevented a kinetic analysis of hydrogen uptake by sulfate reducers and methanogens. The demonstration that sulfate reducers can successfully compete with methanogens for hydrogen and acetate in sediments at in situ sulfate concentrations of 60 to 105 μM extends the known range of sediment habitats in which sulfate reduction can be a dominant terminal process. 相似文献
18.
Denitrification, Nitrate Reduction, and Oxygen Consumption in Coastal and Estuarine Sediments 总被引:6,自引:4,他引:6
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Denitrification and consumption of oxygen and nitrate in sediments from Tama Estuary, Odawa Bay, and Tokyo Bay were measured in an experimental sediment-water system. Filtered seawater containing [15N]nitrate flowed continuously over undisturbed sediments, and the concentrations of O2, nitrate, and nitrite in the influent and effluent and of 15N2 in the effluent were monitored. Under steady-state conditions, the rate of nitrate consumption was the same order of magnitude as the rate of oxygen consumption in Tama Estuary sediments, whereas the former rate was one order of magnitude lower than the latter rate in Odawa Bay and Tokyo Bay sediments. Denitrification accounted for 27 to 57% of the nitrate consumption. 相似文献
19.
Previous studies have demonstrated the wide occurrence of anaerobic ammonium oxidizing (anammox) bacteria; however, there is very limited information on the distribution of these bacteria in freshwater habitats. In this study, the anammox bacterial communities were detected by molecular analysis targeting the 16S rRNA genes in the sediments of Lake Taihu, a large and shallow eutrophic freshwater lake in China. The recovery of specific 16S rRNA sequences with two stable monophyletic clusters indicated that anammox bacteria were present in Lake Taihu. A phylogenetic analysis indicated that these two groups represent two novel lineages within the first subgroup of anammox bacteria, independent of the treeing methods. High intra-lake variability in anammox bacterial diversity and community composition was observed, in particular, based on a 1% cut-off of 16S rRNA sequence variation. The spatial variability was largely related to the substrate availability, which was denoted by the correlations between the relative abundance of the two Taihu anammox bacterial groups and the concentrations of ammonium and nitrite. This indicates that the niche differentiation of anammox bacteria is linked to the environmental heterogeneity. These findings suggest that the freshwater lakes may accommodate different anammox bacterial communities and, thus, expand our knowledge on the diversity and distribution of anammox bacteria. Supplemental materials are available for this article. Go to the publisher's online edition of Geomicrobiology Journal to view the free supplemental files. 相似文献
20.
In Situ Population Dynamics of Bacterial Viruses in a Terrestrial Environment 总被引:4,自引:3,他引:1
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Kevin E. Ashelford Martin J. Day Mark J. Bailey Andrew K. Lilley John C. Fry 《Applied microbiology》1999,65(1):169-174
Predation by bacteriophages is thought to control bacterial numbers and facilitate gene transfer among bacteria in the biosphere. A thorough understanding of phage population dynamics is therefore necessary if their significance in natural environments is to be fully appreciated. Here we describe the in situ population dynamics of three separate phage populations predating on separate bacterial species, living on the surface of field-grown sugar beet (Beta vulgaris var. Amethyst), as recorded over a 9-month period. The distributions of the three phage populations were different and fluctuated temporally in 1996 (peak density, ~103 PFU g−1). One of these populations, predating on the indigenous phytosphere bacterium Serratia liquefaciens CP6, consisted of six genetically distinct DNA phages that varied in relative abundance to the extent that an apparent temporal succession was observed between the two most abundant phages, ΦCP6-1 and ΦCP6-4. 相似文献