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Marine Sediments (marine + sediment)
Selected AbstractsVoltammetry as an Alternative Tool for Trace Metal Detection in Peloid Marine SedimentsELECTROANALYSIS, Issue 13 2007Irena Ciglene Abstract Here was demonstrated for the first time a possible application of abrasive stripping voltammetry in the direct measurement of trace metals in anoxic, sulfidic marine sediments (peloid mud) from a small and shallow (0.2,1,m) marine lagoon in Central Dalmatia, Croatia. Trace amounts of sample compounds are transferred to the graphite electrode surface and electrochemical reduction or oxidation processes are followed by the cyclic voltammetry in seawater or 0.55,M NaCl as electrolyte. After a preelectrolysis at potentials ranging from ,1.0 to ,1.5,V (vs. SCE) a well-defined anodic stripping peak corresponding to the oxidation of metal deposits generated at deposition potentials is obtained around ,0.74,V (vs. SCE). The same samples were studied by anodic stripping voltammetry at the Hg electrode and inductively coupled plasma-mass spectrometer (ICP-MS). ICP-MS showed higher concentrations of trace metals such as Al, Fe, Mo, Mn. A relatively high concentration of reduced sulfur species (RSS) (10,3 M) is determined electrochemically in porewater of the peloid mud, indicating that the magnitude of metal enrichment in the sediments is probably controlled by precipitation with sulfide. [source] Ecology of Marine Sediments: From Science to Management, 2nd ednMARINE ECOLOGY, Issue 3 2010Bettina Riedel No abstract is available for this article. [source] Thermophilic anaerobes in Arctic marine sediments induced to mineralize complex organic matter at high temperatureENVIRONMENTAL MICROBIOLOGY, Issue 4 2010Casey Hubert Summary Marine sediments harbour diverse populations of dormant thermophilic bacterial spores that become active in sediment incubation experiments at much higher than in situ temperature. This response was investigated in the presence of natural complex organic matter in sediments of two Arctic fjords, as well as with the addition of freeze-dried Spirulina or individual high-molecular-weight polysaccharides. During 50°C incubation experiments, Arctic thermophiles catalysed extensive mineralization of the organic matter via extracellular enzymatic hydrolysis, fermentation and sulfate reduction. This high temperature-induced food chain mirrors sediment microbial processes occurring at cold in situ temperatures (near 0°C), yet it is catalysed by a completely different set of microorganisms. Using sulfate reduction rates (SRR) as a proxy for organic matter mineralization showed that differences in organic matter reactivity determined the extent of the thermophilic response. Fjord sediments with higher in situ SRR also supported higher SRR at 50°C. Amendment with Spirulina significantly increased volatile fatty acids production and SRR relative to unamended sediment in 50°C incubations. Spirulina amendment also revealed temporally distinct sulfate reduction phases, consistent with 16S rRNA clone library detection of multiple thermophilic Desulfotomaculum spp. enriched at 50°C. Incubations with four different fluorescently labelled polysaccharides at 4°C and 50°C showed that the thermophilic population in Arctic sediments produce a different suite of polymer-hydrolysing enzymes than those used in situ by the cold-adapted microbial community. Over time, dormant marine microorganisms like these are buried in marine sediments and might eventually encounter warmer conditions that favour their activation. Distinct enzymatic capacities for organic polymer degradation could allow specific heterotrophic populations like these to play a role in sustaining microbial metabolism in the deep, warm, marine biosphere. [source] Digestive bioavailability to a deposit feeder (Arenicola marina) of polycyclic aromatic hydrocarbons associated with anthropogenic particles,ENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 11 2004Ian M. Voparil Abstract Marine sediments around urban areas serve as catch basins for anthropogenic particles containing polycyclic aromatic hydrocarbons (PAHs). Using incubations with gut fluids extracted from a deposit-feeding polychaete (Arenicola marina), we determined the digestive bioavailability of PAHs from fly ashes, coal dusts, diesel soots, tire tread materials, and urban particulates. We found that gut fluids solubilize significant concentrations of PAHs from two tire treads, two diesel soots, and the urban particulates. However, PAHs in fly ashes and coal dusts were not available to the digestive agents in gut fluid. Potential digestive exposure to PAHs is much greater than that predicted to be available from these materials using equilibrium partitioning theory (EqP). Amending an already-contaminated sediment with fly ash decreased phenanthrene solubilization by gut fluid. In contrast, addition of tire tread to the sediment resulted in increased solubilization of four PAHs by gut fluid. Therefore, addition of certain types of anthropogenic particles to sediments may result in an increase in bioavailable PAHs rather than a net decrease, as predicted by EqP. Difficulty in predicting the amount of change due to amendment may be due to interactions occurring among the mixture of compounds solubilized by gut fluid. [source] Sulfate-reducing bacteria in marine sediment (Aarhus Bay, Denmark): abundance and diversity related to geochemical zonationENVIRONMENTAL MICROBIOLOGY, Issue 5 2009Julie Leloup Summary In order to better understand the main factors that influence the distribution of sulfate-reducing bacteria (SRB), their population size and their metabolic activity in high- and low-sulfate zones, we studied the SRB diversity in 3- to 5-m-deep sediment cores, which comprised the entire sulfate reduction zone and the upper methanogenic zone. By combining EMA (ethidium monoazide that can only enter damaged/dead cells and may also bind to free DNA) treatment with real-time PCR, we determined the distributions of total intact bacteria (16S rDNA genes) and intact SRB (dsrAB gene), their relative population sizes, and the proportion of dead cells or free DNA with depth. The abundance of SRB corresponded in average to 13% of the total bacterial community in the sulfate zone, 22% in the sulfate,methane transition zone and 8% in the methane zone. Compared with the total bacterial community, there were relatively less dead/damaged cells and free DNA present than among the SRB and this fraction did not change systematically with depth. By DGGE analysis, based on the amplification of the dsrA gene (400 bp), we found that the richness of SRB did not change with depth through the geochemical zones; but the clustering was related to the chemical zonation. A full-length clone library of the dsrAB gene (1900 bp) was constructed from four different depths (20, 110, 280 and 500 cm), and showed that the dsrAB genes in the near-surface sediment (20 cm) was mainly composed of sequences close to the Desulfobacteraceae, including marine complete and incomplete oxidizers such as Desulfosarcina, Desulfobacterium and Desulfococcus. The three other libraries were predominantly composed of Gram-positive SRB. [source] Anaerobic degradation of benzene by a marine sulfate-reducing enrichment culture, and cell hybridization of the dominant phylotypeENVIRONMENTAL MICROBIOLOGY, Issue 1 2008Florin Musat Summary The anaerobic biodegradation of benzene, a common constituent of petroleum and one of the least reactive aromatic hydrocarbons, is insufficiently understood with respect to the involved microorganisms and their metabolism. To study these aspects, sulfate-reducing bacteria were enriched with benzene as sole organic substrate using marine sediment as inoculum. Repeated subcultivation yielded a sediment-free enrichment culture constituted of mostly oval-shaped cells and showing benzene-dependent sulfate reduction and growth under strictly anoxic conditions. Amplification and sequencing of 16S rRNA genes from progressively diluted culture samples revealed an abundant phylotype; this was closely related to a clade of Deltaproteobacteria that includes sulfate-reducing bacteria able to degrade naphthalene or other aromatic hydrocarbons. Cell hybridization with two specifically designed 16S rRNA-targeted fluorescent oligonucleotide probes showed that the retrieved phylotype accounted for more than 85% of the cells detectable via DAPI staining (general cell staining) in the enrichment culture. The result suggests that the detected dominant phylotype is the ,candidate species' responsible for the anaerobic degradation of benzene. Quantitative growth experiments revealed complete oxidation of benzene with stoichiometric coupling to the reduction of sulfate to sulfide. Suspensions of benzene-grown cells did not show metabolic activity towards phenol or toluene. This observation suggests that benzene degradation by the enriched sulfate-reducing bacteria does not proceed via anaerobic hydroxylation (mediated through dehydrogenation) to free phenol or methylation to toluene, respectively, which are formerly proposed alternative mechanisms for benzene activation. [source] Studies on bioremediation of polycyclic aromatic hydrocarbon-contaminated sediments: Bioavailability, biodegradability, and toxicity issuesENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 3 2003Henry H. Tabak Abstract The widespread contamination by polycyclic aromatic hydrocarbons (PAHs) has created a need for cost-effective bioremediation processes. This research studied a chronically PAH-contaminated estuarine sediment from the East River (ER; NY, USA) characterized by high concentrations of PAHs (,4,190 ppm), sulfide, and metals and a marine sediment from New York/New Jersey Harbor (NY/NJH; USA) with only trace quantities of PAHs (0.1,0.6 ppm). The focus was to examine the relationship between bioavailability of PAHs and their biological removal in a slurry system. Freshwater and marine sediment toxicity tests were conducted to measure baseline toxicity of both sediments to amphipods, aquatic worms, fathead and sheepshead minnow larvae, and a vascular plant; to determine the cause of toxicity; and to evaluate the effectiveness of the biotreatment strategies in reducing toxicity. Results showed the ER sediment was acutely toxic to all freshwater and marine organisms tested and that the toxicity was mainly caused by sulfide, PAHs, and metals present in the sediment. In spite of the high toxicity, most of the PAH compounds showed significant degradation in the aerobic sediment/water slurry system if the initial high oxygen demand due to the high sulfide content of the sediment was overcome. The removal of PAHs by biodegradation was closely related to their desorbed amount in 90% isopropanol solution during 24 h of contact, while the desorption of model PAH compounds from freshly spiked NY/NJH sediment did not describe the bioavailability of PAHs in the East River sediment well. The research improves our understanding of bioavailability as a controlling factor in bioremediation of PAHs and the potential of aerobic biodegradation for PAH removal and ecotoxicity reduction. [source] Phylogeny of cyclic nitramine-degrading psychrophilic bacteria in marine sediment and their potential role in the natural attenuation of explosivesFEMS MICROBIOLOGY ECOLOGY, Issue 3 2004Jian-Shen Zhao Abstract Previously we reported on in situ mineralization of cyclic nitramine explosives including hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) in marine sediment from Halifax Harbour. In the present study, we isolated several novel psychrophilic bacteria from the sediment with optimal growth temperature at 10 or 15 °C. Phylogenetic analysis of their 16S rRNA genes identified the isolates as members of the gamma and delta subdivisions of Proteobacteria, Fusobacteria and Clostridiales. The isolates mineralized 3.7,45.2% of RDX (92 ,M) in 82 days of incubation at 10 °C under oxygen-limited or anaerobic conditions with the gamma subdivision isolates demonstrating the highest mineralization (45.2% of total C). Removal of RDX by all isolates was accompanied by the formation of all three nitroso derivatives, with the mono nitroso derivative (MNX) being the major one. Isolates of the delta proteobacteria and Fusobacteria removed HMX with concurrent formation of the mononitroso derivative (NO-HMX). Using resting cells of isolates of the gamma subdivision, methylenedinitramine (MEDINA) and 4-nitro-2,4-diazabutanal (NDAB) were detected, suggesting ring-cleavage following denitration of either RDX and/or its initially reduced product, MNX. These results clearly demonstrate that psychrophilic bacteria capable of degrading cyclic nitramines are present in the marine sediment, and might contribute to the in situ biodegradation and natural attenuation of the chemicals. [source] Wave-induced progressive liquefaction in a poro-elastoplastic seabed: A two-layered modelINTERNATIONAL JOURNAL FOR NUMERICAL AND ANALYTICAL METHODS IN GEOMECHANICS, Issue 5 2009Z. Liu Abstract In this study, the prediction model proposed by Sassa et al. (Geotechnique 2001; 51(10):847,857) for the wave-induced progressive liquefaction in marine sediment, based on two-layered inviscid fluid system, is re-examined. An alternative approach with a similar framework of Sassa et al. (Geotechnique 2001; 51(10):847,857) is developed to correct the inappropriate mechanism of wave components used. Then, a two-layered wave model which includes viscous effects is established and applied to describe the progressive nature of wave-induced liquefaction. A comprehensive comparison shows that Sassa's model overestimates the maximum liquefaction depth. It is found that the viscosity of liquefied soil cannot be ignored and the solution for an infinite seabed is not suitable for liquefaction analysis of shallow seabed. A parametric study demonstrates the significant influence of numerous wave and soil characteristics on the liquefaction depth. Copyright © 2008 John Wiley & Sons, Ltd. [source] Wave-induced seepage flux into anisotropic seabedsINTERNATIONAL JOURNAL FOR NUMERICAL AND ANALYTICAL METHODS IN GEOMECHANICS, Issue 8 2001D. S. Jeng Abstract Considerable effort has been devoted to quantifying the wave-induced soil response in a porous seabed in the last few decades. Most previous investigations have focused on the analysis of pore pressure and effective stresses within isotropic sediments, despite strong evidence of anisotropic soil behaviour reported in the literature. Furthermore, the seepage flux, which is important in the context of contaminant transport, has not been examined. In this paper, we focus on water wave-driven seepage in anisotropic marine sediments of finite thickness. The numerical results predict that the effects of hydraulic anisotropy and anisotropic soil behaviour on the wave-driven seepage in marine sediment are significant. Copyright © 2001 John Wiley & Sons, Ltd. [source] Pigment and amylase production in Penicillium sp NIOM-02 and its radical scavenging activityINTERNATIONAL JOURNAL OF FOOD SCIENCE & TECHNOLOGY, Issue 12 2009Mohan Appasaheb Dhale Abstract Penicillium sp NIOM-02 was isolated from the marine sediment, produced red pigment. The pigment extracted from this fungus scavenged 2, 2-diphenyl-1-pycrylhydrazyl (DPPH) radical. Penicillium sp NIOM-02 grown in media containing corn steep liquor scavenged 72,88% of DPPH radical. During solid-state fermentation on wheat (S1), the fungus produced more pigment (9.232 OD Units). Penicillium sp NIOM-02 grown on sugarcane bagasse scavenged 91% of DPPH radicals. It secreted more amylase (246 U mg,1) in culture medium No. 5 and the zymogram analysis revealed its molecular mass (53 kDa). The taka-amylase like character of amylase was determined by acarbose incorporated studies in the culture media. Production of pigment and radical scavenging activity of Penicillium sp NIOM-02, suggested its applications in food, pharmaceuticals and nutraceutical industries. [source] Effect of salinity on denitrification under limited single carbon source by Marinobacter sp. isolated from marine sedimentJOURNAL OF BASIC MICROBIOLOGY, Issue 3 2010Miyo Nakano Abstract Marinobacter comprises Gram-negative, aerobic, motile, and rod-shaped bacteria within the ,-subclass of the Proteobacteria and is known to be halophilic or halotolerant, heterotrophic neutrophile. Two strains classified as belonging to Marinobacter, named PAD-2 and SeT-1, were isolated from marine sediment. The most closely related species of PAD-2 and SeT-1 are M. alkaliphilus and M. guinea, respectively. The strain PAD-2 exhibited remarkably higher denitrification at concentrations of 0.5 to 1 M NaCl (3,6% w/w) than at other salinities (2 and 3 M NaCl, 12,18% w/w), and optimal denitrification was observed in media with 0.5 M NaCl. The effect of pH on denitrification by strain PAD-2 was also examined, and the optimum denitrification occurred at neutral pH rather than under alkaline conditions. Overall, strain PAD-2 appears to be a novel halotolerant species belonging to the genus Marinobacter that shares many characteristics, such as substrate utilization profile and optimum NaCl concentration for growth with M. alkaliphilus. (© 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Optimisation of the headspace-solid phase microextraction for organomercury and organotin compound determination in sediment and biotaJOURNAL OF SEPARATION SCIENCE, JSS, Issue 4 2008Alejandra Delgado Abstract Headspace solid-phase microextraction was optimised for the simultaneous preconcentration of methylmercury (MeHg+), monobutyltin, dibutyltin, tributyltin, monophenyltin (MPhT), diphenyltin (DPhT), and triphenyltin (TPhT) from sediments and biota. Extraction time (3,24 min), extraction temperature (20,90°C), desorption time (1,10.4 min), desorption temperature (152,260°C), and sample volume (5,22 mL) were simultaneously optimised, while variables such as fibre type (30 ,m polydimethylsiloxane, PDMS), pH (acetic acid/sodium acetate, HOAc/NaOAc, 2 mol/L, pH , 4.8), the concentration of the derivatisation agent (sodium tetraethylborate, NaBEt4, 0.1% m/v), and the ionic strength (fixed by the buffer solution) were kept constant. The variables were optimised according to the experiments proposed by the MultiSimplex program and the responses were considered in order to establish the optimum conditions. The repeatability (relative standard deviation, RSD, 5,20.6%) and limits of detection (LODs, 0.05,0.97 ng/g) of the overall method were also estimated. The lowest precisions were obtained for DPhT and TPhT. The optimised preconcentration method was applied to the determination of MeHg+, butyl- and phenyltins in certified reference materials (IAEA-405 MeHg+ in estuarine sediment, BCR-646 butyl- and phenyltins in marine sediment, BCR-463 MeHg+ in tuna fish, DOLT-2 MeHg+ in dogfish liver, and BCR-477 butyltins in mussel tissue) by GC with microwave-induced plasma/atomic-emission detection. [source] A versatile method for stable carbon isotope analysis of carbohydrates by high-performance liquid chromatography/isotope ratio mass spectrometryRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 23 2008H. T. S. Boschker We have developed a method to analyze stable carbon isotope (13C/12C) ratios in a variety of carbohydrates using high-performance liquid chromatography/isotope ratio mass spectrometry (HPLC/IRMS). The chromatography is based on strong anion-exchange columns with low strength NaOH eluents. An eluent concentration of 1,mM resulted in low background signals and good separation of most of the typical plant neutral carbohydrates. We also show that more strongly bound carbohydrates such as acidic carbohydrates can be separated by inclusion of NO as an inorganic pusher ion in the eluent. Analyses of neutral carbohydrate concentrations and their stable carbon isotope ratios are shown for plant materials and marine sediment samples both at natural abundance and for 13C-enriched samples. The main advantage of HPLC/IRMS analysis over traditional gas chromatography based methods is that no derivatization is needed resulting in simple sample treatment and improved accuracy and reproducibility. Copyright © 2008 John Wiley & Sons, Ltd. [source] Distribution and fate of biologically formed organoarsenicals in coastal marine sedimentAPPLIED ORGANOMETALLIC CHEMISTRY, Issue 8 2005Mio Takeuchi Abstract Marine organisms, including phyto- and zoo-plankton, macroalgae, and animals, concentrate arsenic in various organic forms. However, the distribution and fate of these organoarsenicals in marine environments remains unclear. In this study, the distribution of organoarsenicals in coastal marine sediment in Otsuchi Bay, Japan, has been determined. Methylarsonic acid, dimethylarsinic acid, trimethylarsine oxide, arsenobetaine, arsenocholine and other unidentified arsenic species were detected in marine sediment by high-performance liquid chromatography,inductively coupled plasma mass spectrometry analysis of methanol,water extracts. Arsenobetaine was the dominant organoarsenical at four of the seven stations where tests were carried out, and unidentified species or dimethylarsinic acid dominated at the other stations. Total organoarsenicals (as arsenic) in the surface sediment amounted to 10.6,47.5 µg kg,1 dry sediment. Core analysis revealed that concentrations of organoarsenicals decreased with depth, and they are considered to be degraded within 60 years of deposition. These results show that organoarsenicals formed by marine organisms are delivered to the sediment and can be degraded within several decades. Copyright © 2005 John Wiley & Sons, Ltd. [source] Preliminary evidence for in vitro methylation of tributyltin in a marine sedimentAPPLIED ORGANOMETALLIC CHEMISTRY, Issue 11 2001Alfred J. Vella Abstract Recent reports from our laboratory on the occurrence of methylbutyltins in marine sediments and seawater suggest that these compounds are formed in the environment by the methylation of both tributyltin (TBT) and thatof its degradation products, i.e. dibutyltin and monobutyltin, to give MenBu(4,n)Sn for which n,=,1, 2 and 3 respectively. We investigated the possibility of inducing methylation of TBT in seawater,sediment mixtures in experiments carried out in vitro using environmental materials collected from a yacht marina in Msida, Malta. Three water,sediment mixtures, which were shown to contain TBT, dibutyltin and monobutyltin but no other organotins, were spiked with tributyltin chloride (90,mg in 100,ml sea-water/100,ml sediment); to one mixture was added sodium acetate and to another methanol, to act as possible additional carbon sources, and all mixtures were allowed to stand at 25,°C in stoppered clear-glass bottles in diffused light for a maximum of 315 days. Speciation and quantification of organotins was performed using aqueous phase boroethylation with simultaneous solvent extraction followed by gas chromatography with flame photometric detection. The atmosphere inside the bottles quickly became reducing with abundant presence of H2S, and after an induction period of about 112 days, and only in the reaction mixture containing methanol, methyltributyltin (MeBu3Sn) was observed in both sediment (maximum concentration 0.87 µgSn g,1) and overlying water (maximum concentration 6.0 µgSn l,1). The minimum conversion yield of TBT into MeBu3Sn was estimated to be 0.3%. MeBu3Sn has a significantly lower affinity for sediment than TBT and, therefore, is more mobile in the marine environment, possibly also migrating into the atmosphere to generate a hitherto unsuspected flux of organotin into that phase. Copyright © 2001 John Wiley & Sons, Ltd. [source] Voltammetry as an Alternative Tool for Trace Metal Detection in Peloid Marine SedimentsELECTROANALYSIS, Issue 13 2007Irena Ciglene Abstract Here was demonstrated for the first time a possible application of abrasive stripping voltammetry in the direct measurement of trace metals in anoxic, sulfidic marine sediments (peloid mud) from a small and shallow (0.2,1,m) marine lagoon in Central Dalmatia, Croatia. Trace amounts of sample compounds are transferred to the graphite electrode surface and electrochemical reduction or oxidation processes are followed by the cyclic voltammetry in seawater or 0.55,M NaCl as electrolyte. After a preelectrolysis at potentials ranging from ,1.0 to ,1.5,V (vs. SCE) a well-defined anodic stripping peak corresponding to the oxidation of metal deposits generated at deposition potentials is obtained around ,0.74,V (vs. SCE). The same samples were studied by anodic stripping voltammetry at the Hg electrode and inductively coupled plasma-mass spectrometer (ICP-MS). ICP-MS showed higher concentrations of trace metals such as Al, Fe, Mo, Mn. A relatively high concentration of reduced sulfur species (RSS) (10,3 M) is determined electrochemically in porewater of the peloid mud, indicating that the magnitude of metal enrichment in the sediments is probably controlled by precipitation with sulfide. [source] Phylogenetic diversity and metagenomics of candidate division OP3ENVIRONMENTAL MICROBIOLOGY, Issue 5 2010Jana Glöckner Summary Except for environmental 16S rRNA gene sequences, no information is available for members of the candidate division OP3. These bacteria appear to thrive in anoxic environments, such as marine sediments, hypersaline deep sea, freshwater lakes, aquifers, flooded paddy soils and methanogenic bioreactors. The 16S rRNA phylogeny suggests that OP3 belongs to the Planctomycetes/Verrucomicrobia/Chlamydiae (PVC) superphylum. Metagenomic fosmid libraries were constructed from flooded paddy soil and screened for 16S rRNA gene-containing fragments affiliated with the PVC superphylum. The screening of 63 000 clones resulted in 23 assay-positive fosmids, of which three clones were affiliated with OP3. The 16S rRNA gene sequence divergence between the fragments OP3/1, OP3/2 and OP3/3 ranges from 18% to 25%, indicating that they belong to different OP3 subdivisions. The 23S rRNA phylogeny confirmed the membership of OP3 in the PVC superphylum. Sequencing the OP3 fragments resulted in a total of 105 kb of genomic information and 90 ORFs, of which 47 could be assigned a putative function and 11 were conserved hypothetical. Using BLASTP searches, a high proportion of ORFs had best matches to homologues from Deltaproteobacteria, rather than to those of members of the PVC superphylum. On the fragment OP3/3, a cluster of nine ORFs was predicted to encode the bacterial NADH dehydrogenase I. Given the high proportion of homologues present in deltaproteobacteria and anoxic conditions in the natural environment of OP3 bacteria, the detection of NADH dehydrogenase I may suggest an anaerobic respiration mode. Oligonucleotide frequencies calculated for OP3/1, OP3/2 and OP/3 show high intraphylum correlations. This novel sequence information could therefore be used to identify OP3-related fragments in large metagenomic data sets using marker gene-independent procedures in the future. In addition to the OP3 fragments, a single metagenomic fragment affiliated with the candidate division BRC1 was obtained and analysed. [source] Thermophilic anaerobes in Arctic marine sediments induced to mineralize complex organic matter at high temperatureENVIRONMENTAL MICROBIOLOGY, Issue 4 2010Casey Hubert Summary Marine sediments harbour diverse populations of dormant thermophilic bacterial spores that become active in sediment incubation experiments at much higher than in situ temperature. This response was investigated in the presence of natural complex organic matter in sediments of two Arctic fjords, as well as with the addition of freeze-dried Spirulina or individual high-molecular-weight polysaccharides. During 50°C incubation experiments, Arctic thermophiles catalysed extensive mineralization of the organic matter via extracellular enzymatic hydrolysis, fermentation and sulfate reduction. This high temperature-induced food chain mirrors sediment microbial processes occurring at cold in situ temperatures (near 0°C), yet it is catalysed by a completely different set of microorganisms. Using sulfate reduction rates (SRR) as a proxy for organic matter mineralization showed that differences in organic matter reactivity determined the extent of the thermophilic response. Fjord sediments with higher in situ SRR also supported higher SRR at 50°C. Amendment with Spirulina significantly increased volatile fatty acids production and SRR relative to unamended sediment in 50°C incubations. Spirulina amendment also revealed temporally distinct sulfate reduction phases, consistent with 16S rRNA clone library detection of multiple thermophilic Desulfotomaculum spp. enriched at 50°C. Incubations with four different fluorescently labelled polysaccharides at 4°C and 50°C showed that the thermophilic population in Arctic sediments produce a different suite of polymer-hydrolysing enzymes than those used in situ by the cold-adapted microbial community. Over time, dormant marine microorganisms like these are buried in marine sediments and might eventually encounter warmer conditions that favour their activation. Distinct enzymatic capacities for organic polymer degradation could allow specific heterotrophic populations like these to play a role in sustaining microbial metabolism in the deep, warm, marine biosphere. [source] Genome sequence of Desulfobacterium autotrophicum HRM2, a marine sulfate reducer oxidizing organic carbon completely to carbon dioxideENVIRONMENTAL MICROBIOLOGY, Issue 5 2009Axel W. Strittmatter Summary Sulfate-reducing bacteria (SRB) belonging to the metabolically versatile Desulfobacteriaceae are abundant in marine sediments and contribute to the global carbon cycle by complete oxidation of organic compounds. Desulfobacterium autotrophicum HRM2 is the first member of this ecophysiologically important group with a now available genome sequence. With 5.6 megabasepairs (Mbp) the genome of Db. autotrophicum HRM2 is about 2 Mbp larger than the sequenced genomes of other sulfate reducers (SRB). A high number of genome plasticity elements (> 100 transposon-related genes), several regions of GC discontinuity and a high number of repetitive elements (132 paralogous genes Mbp,1) point to a different genome evolution when comparing with Desulfovibrio spp. The metabolic versatility of Db. autotrophicum HRM2 is reflected in the presence of genes for the degradation of a variety of organic compounds including long-chain fatty acids and for the Wood,Ljungdahl pathway, which enables the organism to completely oxidize acetyl-CoA to CO2 but also to grow chemolithoautotrophically. The presence of more than 250 proteins of the sensory/regulatory protein families should enable Db. autotrophicum HRM2 to efficiently adapt to changing environmental conditions. Genes encoding periplasmic or cytoplasmic hydrogenases and formate dehydrogenases have been detected as well as genes for the transmembrane TpII- c3, Hme and Rnf complexes. Genes for subunits A, B, C and D as well as for the proposed novel subunits L and F of the heterodisulfide reductases are present. This enzyme is involved in energy conservation in methanoarchaea and it is speculated that it exhibits a similar function in the process of dissimilatory sulfate reduction in Db. autotrophicum HRM2. [source] New alk genes detected in Antarctic marine sedimentsENVIRONMENTAL MICROBIOLOGY, Issue 3 2009Emanuele Kuhn Summary Alkane monooxygenases (Alk) are the key enzymes for alkane degradation. In order to understand the dispersion and diversity of alk genes in Antarctic marine environments, this study analysed by clone libraries the presence and diversity of alk genes (alkB and alkM) in sediments from Admiralty Bay, King George Island, Peninsula Antarctica. The results show a differential distribution of alk genes between the sites, and the predominant presence of new alk genes, mainly in the pristine site. Sequences presented 53.10,69.60% nucleotide identity and 50.90,73.40% amino acid identity to alkB genes described in Silicibacter pomeroyi, Gordonia sp., Prauserella rugosa, Nocardioides sp., Rhodococcus sp., Nocardia farcinica, Pseudomonas putida, Acidisphaera sp., Alcanivorax borkumensis, and alkM described in Acinetobacter sp. This is the first time that the gene alkM was detected and described in Antarctic marine environments. The presence of a range of previously undescribed alk genes indicates the need for further studies in this environment. [source] Multiple bacterial symbionts in two species of co-occurring gutless oligochaete worms from Mediterranean sea grass sedimentsENVIRONMENTAL MICROBIOLOGY, Issue 12 2008Caroline Ruehland Summary Gutless oligochaete worms are found worldwide in the pore waters of marine sediments and live in symbiosis with chemoautotrophic sulfur-oxidizing bacteria. In the Mediterranean, two species of gutless oligochaete worms, Olavius algarvensis and O. ilvae, co-occur in sediments around sea grass beds. These sediments have extremely low sulfide concentrations (< 1 ,M), raising the question if O. ilvae, as shown previously for O. algarvensis, also harbours sulfate-reducing symbionts that provide its sulfur-oxidizing symbionts with reduced sulfur compounds. In this study, we used fluorescence in situ hybridization (FISH) and comparative sequence analysis of genes for 16S rRNA, sulfur metabolism (aprA and dsrAB), and autotrophic carbon fixation (cbbL) to examine the microbial community of O. ilvae and re-examine the O. algarvensis symbiosis. In addition to the four previously described symbionts of O. algarvensis, in this study a fifth symbiont belonging to the Spirochaetes was found in these hosts. The symbiotic community of O. ilvae was similar to that of O. algarvensis and also included two gammaproteobacterial sulfur oxidizers and two deltaproteobacterial sulfate reducers, but not a spirochete. The phylogenetic and metabolic similarity of the symbiotic communities in these two co-occurring host species that are not closely related to each other indicates that syntrophic sulfur cycling provides a strong selective advantage to these worms in their sulfide-poor environment. [source] On the relationship between methane production and oxidation by anaerobic methanotrophic communities from cold seeps of the Gulf of MexicoENVIRONMENTAL MICROBIOLOGY, Issue 5 2008Beth! Orcutt Summary The anaerobic oxidation of methane (AOM) in the marine subsurface is a significant sink for methane in the environment, yet our understanding of its regulation and dynamics is still incomplete. Relatively few groups of microorganisms consume methane in subsurface environments , namely the anaerobic methanotrophic archaea (ANME clades 1, 2 and 3), which are phylogenetically related to methanogenic archaea. Anaerobic oxidation of methane presumably proceeds via a ,reversed' methanogenic pathway. The ANME are generally associated with sulfate-reducing bacteria (SRB) and sulfate is the only documented final electron acceptor for AOM in marine sediments. Our comparative study explored the coupling of AOM with sulfate reduction (SR) and methane generation (MOG) in microbial communities from Gulf of Mexico cold seep sediments that were naturally enriched with methane and other hydrocarbons. These sediments harbour a variety of ANME clades and SRB. Following enrichment under an atmosphere of methane, AOM fuelled 50,100% of SR, even in sediment slurries containing petroleum-associated hydrocarbons and organic matter. In the presence of methane and sulfate, the investigated microbial communities produce methane at a small fraction (,10%) of the AOM rate. Anaerobic oxidation of methane, MOG and SR rates decreased significantly with decreasing concentration of methane, and in the presence of the SR inhibitor molybdate, but reacted differently to the MOG inhibitor 2-bromoethanesulfonate (BES). The addition of acetate, a possible breakdown product of petroleum in situ and a potential intermediate in AOM/SR syntrophy, did not suppress AOM activity; rather acetate stimulated microbial activity in oily sediment slurries. [source] Integron-associated gene cassettes in Halifax Harbour: assessment of a mobile gene pool in marine sedimentsENVIRONMENTAL MICROBIOLOGY, Issue 4 2008J. E. Koenig Summary The integron/gene cassette systems identified in bacteria comprise a class of genetic elements that allow adaptation by acquisition of gene cassettes. Integron gene cassettes have been shown to facilitate the spread of drug resistance in human pathogens but their role outside a clinical setting has not been explored extensively. We sequenced 2145 integron gene cassettes from four marine sediment samples taken from the vicinity of Halifax Nova Scotia, Canada, increasing the number of gene cassettes obtained from environmental microbial communities by 10-fold. Sequence analyses reveals that the majority of these cassettes encode novel proteins and that this study is consistent with previous claims of high cassette diversity as we estimate a Chao1 diversity index of ,3000 cassettes from these samples. The functional distribution of environmental cassettes recovered in this study, when compared with that of cassettes from the only other source with significant sampling (Vibrio genomes) suggests that alternate selection regimes might be acting on these two gene pools. The majority of cassettes recovered in this study encode novel, unknown proteins. In instances where we obtained multiple alleles of a novel protein we demonstrate that non-synonymous versus synonymous substitution rates ratios suggest relaxed selection. Cassette-encoded proteins with known homologues represent a variety of functions and prevalent among these are isochorismatases; proteins involved in iron scavenging. Phylogenetic analysis of these isochorismatases as well as of cassette-encoded acetyltransferases reveals a patchy distribution, suggesting multiple sources for the origin of these cassettes. Finally, the two most environmentally similar sample sites considered in this study display the greatest overlap of cassette types, consistent with the hypothesis that cassette genes encode adaptive proteins. [source] Hydrogen ,leakage' during methanogenesis from methanol and methylamine: implications for anaerobic carbon degradation pathways in aquatic sedimentsENVIRONMENTAL MICROBIOLOGY, Issue 4 2007Niko Finke Summary The effect of variations in H2 concentrations on methanogenesis from the non-competitive substrates methanol and methylamine (used by methanogens but not by sulfate reducers) was investigated in methanogenic marine sediments. Imposed variations in sulfate concentration and temperature were used to drive systematic variations in pore water H2 concentrations. Specifically, increasing sulfate concentrations and decreasing temperatures both resulted in decreasing H2 concentrations. The ratio of CO2 and CH4 produced from 14C-labelled methylamine and methanol showed a direct correlation with the H2 concentration, independent of the treatment, with lower H2 concentrations resulting in a shift towards CO2. We conclude that this correlation is driven by production of H2 by methylotrophic methanogens, followed by loss to the environment with a magnitude dependent on the extracellular H2 concentrations maintained by hydrogenotrophic methanogens (in the case of the temperature experiment) or sulfate reducers (in the case of the sulfate experiment). Under sulfate-free conditions, the loss of reducing power as H2 flux out of the cell represents a loss of energy for the methylotrophic methanogens while, in the presence of sulfate, it results in a favourable free energy yield. Thus, hydrogen leakage might conceivably be beneficial for methanogens in marine sediments dominated by sulfate reduction. In low-sulfate systems such as methanogenic marine or freshwater sediments it is clearly detrimental , an adverse consequence of possessing a hydrogenase that is subject to externally imposed control by pore water H2 concentrations. H2 leakage in methanogens may explain the apparent exclusion of acetoclastic methanogenesis in sediments dominated by sulfate reduction. [source] Biogeography of the marine actinomycete SalinisporaENVIRONMENTAL MICROBIOLOGY, Issue 11 2006Paul R. Jensen Summary Marine actinomycetes belonging to the genus Salinispora were cultured from marine sediments collected at six geographically distinct locations. Detailed phylogenetic analyses of both 16S rRNA and gyrB gene sequences reveal that this genus is comprised of three distinct but closely related clades corresponding to the species Salinispora tropica, Salinispora arenicola and a third species for which the name ,Salinispora pacifica' is proposed. Salinispora arenicola was cultured from all locations sampled and provides clear evidence for the cosmopolitan distribution of an individual bacterial species. The co-occurrence of S. arenicola with S. tropica and S. pacifica suggests that ecological differentiation as opposed to geographical isolation is driving speciation within the genus. All Salinispora strains cultured to date share greater than 99% 16S rRNA gene sequence identity and thus comprise what has been described as a microdiverse ribotype cluster. The description of this cluster as a new genus, containing multiple species, provides clear evidence that fine-scale 16S rDNA sequence analysis can be used to delineate among closely related species and that more conservative operational taxonomic unit values may significantly underestimate global species diversity. [source] Quantification of microbial communities in near-surface and deeply buried marine sediments on the Peru continental margin using real-time PCRENVIRONMENTAL MICROBIOLOGY, Issue 7 2006Axel Schippers Summary Deeply buried marine sediments harbour a large fraction of all prokaryotes on Earth but it is still unknown which phylogenetic and physiological microbial groups dominate the deep biosphere. In this study real-time PCR allowed a comparative quantitative microbial community analysis in near-surface and deeply buried marine sediments from the Peru continental margin. The 16S rRNA gene copy numbers of prokaryotes and Bacteria were almost identical with a maximum of 108,1010 copies cm,3 in the near-surface sediments. Archaea exhibited one to three orders of magnitude lower 16S rRNA gene copy numbers. The 18S rRNA gene of Eukarya was always at least three orders of magnitude less abundant than the 16S rRNA gene of prokaryotes. The 16S rRNA gene of the Fe(III)- and Mn(IV)-reducing bacterial family Geobacteraceae and the dissimilatory (bi)sulfite reductase gene (dsrA) of sulfate-reducing prokaryotes were abundant with 106,108 copies cm,3 in near-surface sediments but showed lower numbers and an irregular distribution in the deep sediments. The copy numbers of all genes decreased with sediment depth exponentially. The depth gradients were steeper for the gene copy numbers than for numbers of total prokaryotes (acridine orange direct counts), which reflects the ongoing degradation of the high-molecular-weight DNA with sediment age and depth. The occurrence of eukaryotic DNA also suggests DNA preservation in the deeply buried sediments. [source] DNA extraction procedure: a critical issue for bacterial diversity assessment in marine sedimentsENVIRONMENTAL MICROBIOLOGY, Issue 2 2006Gian Marco Luna Summary In order to evaluate whether different DNA extraction procedures can affect estimates of benthic bacterial diversity, based on 16S rRNA gene terminal restriction fragment length polymorphism (T-RFLP) fingerprinting technique, we compared two in situ lysis procedures (a SDS-based protocol and a commercial kit for DNA recovery) and one cell-extraction protocol on a variety of marine sediments. Despite the two in situ lysis procedures resulted in significantly different DNA yields (highest with the SDS in situ lysis), estimates of bacterial diversity provided a not significantly different ribotype richness, as well as similar values of the Shannon-Wiener (H,) and Margalef (d) indices of biodiversity and of evenness (Pielou index, J). Conversely, the cell-extraction procedure for DNA extraction resulted always in a significantly lower ribotype richness and diversity. The analysis of similarities (anosim) among the T-RFLP electropherograms allowed concluding that ribotypes composition did not change significantly using different protocols. However, the analysis of ,-diversity (turnover diversity) revealed that a large number of ribotypes was observed exclusively with one of the three protocols utilized. When unshared ribotypes from in situ lysis and cell extraction were pooled together, total ribotype richness resulted much higher (up to 80%). Our results indicate that estimates of ribotype diversity based on a single protocol of DNA extraction can significantly underestimate the total number of bacterial ribotypes present in the benthic domain. We recommend that future studies will not only integrate different DNA extraction procedures, but also will explore the possibility of integrating two or more different genetic markers in order to increase our ability to detect the actual bacterial diversity in environmental samples. [source] Contaminated suspended sediments toxic to an Antarctic filter feeder: Aqueous- and particulate-phase effectsENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 2 2009Nicole A. Hill Abstract Disturbances such as dredging, storms, and bioturbation result in the resuspension of sediments. This may affect sessile organisms that live on hard substrates directly above the sediment. Localized sediment contamination exists around many Antarctic research stations, often resulting in elevated contamination loads in marine sediments. To our knowledge, the potential impact of resuspended contaminated sediments on sessile fauna has not been considered, so in the present study, we assessed the sensitivity of Antarctic spirorbid polychaetes to aqueous metals and to metal-contaminated sediments that had been experimentally resuspended. Worms were first exposed to aqueous metals, both singly and in combination, over 10 d. Spirorbid mortality was tolerant to copper (median lethal concentration [LC50], 570 ,g/L), zinc (LC50, >4,910 ,g/L), and lead (LC50, >2,905 ,g/L); however, spirorbid behavior responded to copper concentrations as low as 20,g/L. When in combination, zinc significantly reduced mortality caused by copper. A novel technique was used to resuspend sediments spiked with four concentrations of three metals (up to 450 ,g/g dry wt of copper, 525 ,g/g dry wt of lead, and 2,035 ,g/g dry wt of zinc). The response of spirorbids to unfiltered suspended sediment solutions and filtered solutions (aqueous metal exposure) was measured. Suspended sediments were toxic to filter-feeding spirorbids at concentrations approximating those found in contaminated Antarctica areas. Toxicity resulted both from aqueous metals and from metals associated with the suspended sediments, although suspended clean sediments had no impact. To our knowledge, the present study is the first to show that resuspension of contaminated sediments can be an important pathway for toxicity to Antarctic hard substrate organisms. Based on the present results, current sediment-quality guidelines used in the evaluation of Australian sediments may be applicable to Antarctic ecosystems. [source] Effects of dose and particle size on activated carbon treatment to sequester polychlorinated biphenyls and polycyclic aromatic hydrocarbons in marine sedimentsENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 7 2005John R. Zimmerman Abstract Recent laboratory studies show that mixing activated carbon with contaminated sediment reduces the chemical and biological availability of hydrophobic organic contaminants. In this study, we test the effects of varying the activated carbon dose and particle size in reducing the aqueous availability of polychlorinated biphenyls (PCBs) and polycyclic aromatic hydrocarbons (PAHs) and the uptake of PCBs by two benthic organisms. We mixed PCB- and PAH-contaminated sediment from Hunters Point Naval Shipyard, San Francisco Bay (CA, USA), for one month with activated carbon, at doses of 0.34, 1.7, and 3.4% dry mass basis. We found that increasing the carbon dose increased the effectiveness in reducing PCB bioaccumulation. In 56-d uptake tests with the benthic organisms Neanthes arenaceodentata and Leptocheirus plumulosus, PCB bioaccumulation was reduced by 93 and 90%, respectively, with 3.4% carbon. Increasing the dose also increased the effectiveness in reducing PCB and PAH aqueous concentrations and uptake by semipermeable membrane devices and quiescent flux of PCBs to overlying water. Decreasing activated carbon particle size increased treatment effectiveness in reducing PCB aqueous concentration, and larger-sized activated carbon (400,1,700 ,m) was ineffective with a contact period of one month. We invoke a numerical model based on intraparticle diffusion in sediment and activated carbon particles to help interpret our experimental results. This model was useful in explaining the trends for the effect of activated carbon dose and particle size on PCB aqueous concentrations in well-mixed systems. [source] | |||||||||||||||||||||||||||||||