Microbial diversity in cold seep sediments from the northern South China Sea

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Yong Zhang

2012-05-01

Full Text Available South China Sea (SCS is the largest Western Pacific marginal sea. However, microbial studies have never been performed in the cold seep sediments in the SCS. In 2004, “SONNE” 177 cruise found two cold seep areas with different water depth in the northern SCS. Haiyang 4 area, where the water depth is around 3000 m, has already been confirmed for active seeping on the seafloor, such as microbial mats, authigenic carbonate crusts and bivalves. We investigated microbial abundance and diversity in a 5.55-m sediment core collected from this cold seep area. An integrated approach was employed including geochemistry and 16S rRNA gene phylogenetic analyses. Here, we show that microbial abundance and diversity along with geochemistry profiles of the sediment core revealed a coupled reaction between sulphate reduction and methane oxidation. Acridine orange direct count results showed that microbial abundance ranges from 105 to 106 cells/g sediment (wet weight. The depth-related variation of the abundance showed the same trend as the methane concentration profile. Phylogenetic analysis indicated the presence of sulphate-reducing bacteria and anaerobic methane-oxidizing archaea. The diversity was much higher at the surface, but decreased sharply with depth in response to changes in the geochemical conditions of the sediments, such as methane, sulphate concentration and total organic carbon. Marine Benthic Group B, Chloroflexi and JS1 were predominant phylotypes of the archaeal and bacterial libraries, respectively.

The Abundance and Activity of Nitrate-Reducing Microbial Populations in Estuarine Sediments

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Cardarelli, E.; Francis, C. A.

2014-12-01

Estuaries are productive ecosystems that ameliorate nutrient and metal contaminants from surficial water supplies. At the intersection of terrestrial and aquatic environments, estuarine sediments host major microbially-mediated geochemical transformations. These include denitrification (the conversion of nitrate to nitrous oxide and/or dinitrogen) and dissimilatory nitrate reduction to ammonium (DNRA). Denitrification has historically been seen as the predominant nitrate attenuation process and functions as an effective sink for nitrate. DNRA has previously been believed to be a minor nitrate reduction process and transforms nitrate within the ecosystem to ammonium, a more biologically available N species. Recent studies have compared the two processes in coastal environments and determined fluctuating environmental conditions may suppress denitrification, supporting an increased role for DNRA in the N cycle. Nitrate availability and salinity are factors thought to influence the membership of the microbial communities present, and the nitrate reduction process that predominates. The aim of this study is to investigate how nitrate concentration and salinity alter the transcript abundances of N cycling functional gene markers for denitrification (nirK, nirS) and DNRA (nrfA) in estuarine sediments at the mouth of the hypernutrified Old Salinas River, CA. Short-term whole core incubations amended with artificial freshwater/artificial seawater (2 psu, 35 psu) and with varying NO3- concentrations (200mM, 2000mM) were conducted to assess the activity as well as the abundance of the nitrate-reducing microbial populations present. Gene expression of nirK, nirS, and nrfA at the conclusion of the incubations was quantified using reverse transcription quantitative polymerase chain reaction (RT-qPCR). High abundances of nirK, nirS, and nrfA under particular conditions coupled with the resulting geochemical data ultimately provides insight onto how the aforementioned factors

Energy Gradients Structure Microbial Communities Across Sediment Horizons in Deep Marine Sediments of the South China Sea

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Michael F. Graw

2018-04-01

Full Text Available The deep marine subsurface is a heterogeneous environment in which the assembly of microbial communities is thought to be controlled by a combination of organic matter deposition, electron acceptor availability, and sedimentology. However, the relative importance of these factors in structuring microbial communities in marine sediments remains unclear. The South China Sea (SCS experiences significant variability in sedimentation across the basin and features discrete changes in sedimentology as a result of episodic deposition of turbidites and volcanic ashes within lithogenic clays and siliceous or calcareous ooze deposits throughout the basin's history. Deep subsurface microbial communities were recently sampled by the International Ocean Discovery Program (IODP at three locations in the SCS with sedimentation rates of 5, 12, and 20 cm per thousand years. Here, we used Illumina sequencing of the 16S ribosomal RNA gene to characterize deep subsurface microbial communities from distinct sediment types at these sites. Communities across all sites were dominated by several poorly characterized taxa implicated in organic matter degradation, including Atribacteria, Dehalococcoidia, and Aerophobetes. Sulfate-reducing bacteria comprised only 4% of the community across sulfate-bearing sediments from multiple cores and did not change in abundance in sediments from the methanogenic zone at the site with the lowest sedimentation rate. Microbial communities were significantly structured by sediment age and the availability of sulfate as an electron acceptor in pore waters. However, microbial communities demonstrated no partitioning based on the sediment type they inhabited. These results indicate that microbial communities in the SCS are structured by the availability of electron donors and acceptors rather than sedimentological characteristics.

Microbial processes in North Atlantic pelagic sediments, and potential risks of deep-sea waste disposal

International Nuclear Information System (INIS)

Bolliger, R.; Hanselmann, K.W.; Bachofen, R.

1989-01-01

From the results for waste disposal on deep sea sediments, it was concluded: As waste canisters are buried in the sediment to a depth of 15 to 20 cm, they are in contact with the zone that contains the highest potential bacterial activity through a relatively large surface. An input of oxidizable organic matter to the sediment surface zone will stimulate microbial activity and therefore increase the risk for solubilization and redistribution of elements in the ocean water. Waste canisters lying on the sediment surface cut off the oxygen supply from the ocean water and ease the shift to anaerobiosis. This initiates microbial activities through which metals are changed into their mobile species as a consequence of the altered environmental redox potential. The risk for steel corrosion by hydrogen sulfide, which could be produced by sulfate reducing bacteria, is minimal since this physiological group is not active in the North Atlantic sediments examined

Microcosm studies on iron and arsenic mobilization from aquifer sediments under different conditions of microbial activity and carbon source

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Duan, Mengyu; Xie, Zuoming; Wang, Yanxin; Xie, Xianjun

2009-05-01

Microcosm experiments were conducted to understand the mechanism of microbially mediated mobilization of Fe and As from high arsenic aquifer sediments. Arsenic-resistant strains isolated from aquifer sediments of a borehole specifically drilled for this study at Datong basin were used as inoculated strains, and glucose and sodium acetate as carbon sources for the experiments. In abiotic control experiments, the maximum concentrations of Fe and As were only 0.47 mg/L and 0.9 μg/L, respectively. By contrast, the maximum contents of Fe and As in anaerobic microcosm experiments were much higher (up to 1.82 mg/L and 12.91 μg/L, respectively), indicating the crucial roles of microbial activities in Fe and As mobilization. The observed difference in Fe and As release with different carbon sources may be related to the difference in growth pattern and composition of microbial communities that develop in response to the type of carbon sources.

Anoxia stimulates microbially catalyzed metal release from Animas River sediments.

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Saup, Casey M; Williams, Kenneth H; Rodríguez-Freire, Lucía; Cerrato, José M; Johnston, Michael D; Wilkins, Michael J

2017-04-19

The Gold King Mine spill in August 2015 released 11 million liters of metal-rich mine waste to the Animas River watershed, an area that has been previously exposed to historical mining activity spanning more than a century. Although adsorption onto fluvial sediments was responsible for rapid immobilization of a significant fraction of the spill-associated metals, patterns of longer-term mobility are poorly constrained. Metals associated with river sediments collected downstream of the Gold King Mine in August 2015 exhibited distinct presence and abundance patterns linked to location and mineralogy. Simulating riverbed burial and development of anoxic conditions, sediment microcosm experiments amended with Animas River dissolved organic carbon revealed the release of specific metal pools coupled to microbial Fe- and SO 4 2- -reduction. Results suggest that future sedimentation and burial of riverbed materials may drive longer-term changes in patterns of metal remobilization linked to anaerobic microbial metabolism, potentially driving decreases in downstream water quality. Such patterns emphasize the need for long-term water monitoring efforts in metal-impacted watersheds.

Anoxia stimulates microbially catalyzed metal release from Animas River sediments

International Nuclear Information System (INIS)

Saup, Casey M.; Williams, Kenneth H.; Rodríguez-Freire, Lucía; Cerrato, José M.; Johnston, Michael D.; Wilkins, Michael J.

2017-01-01

The Gold King Mine spill in August 2015 released 11 million liters of metal-rich mine waste to the Animas River watershed, an area that has been previously exposed to historical mining activity spanning more than a century. Although adsorption onto fluvial sediments was responsible for rapid immobilization of a significant fraction of the spill-associated metals, patterns of longer-term mobility are poorly constrained. Metals associated with river sediments collected downstream of the Gold King Mine in August 2015 exhibited distinct presence and abundance patterns linked to location and mineralogy. Simulating riverbed burial and development of anoxic conditions, sediment microcosm experiments amended with Animas River dissolved organic carbon revealed the release of specific metal pools coupled to microbial Fe- and SO 4 2- reduction. Results suggest that future sedimentation and burial of riverbed materials may drive longer-term changes in patterns of metal remobilization linked to anaerobic microbial metabolism, potentially driving decreases in downstream water quality. Such patterns emphasize the need for long-term water monitoring efforts in metal-impacted watersheds.

Opportunistic Pathogens and Microbial Communities and Their Associations with Sediment Physical Parameters in Drinking Water Storage Tank Sediments

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Qin, Ke; Struewing, Ian; Domingo, Jorge Santo; Lytle, Darren

2017-01-01

The occurrence and densities of opportunistic pathogens (OPs), the microbial community structure, and their associations with sediment elements from eight water storage tanks in Ohio, West Virginia, and Texas were investigated. The elemental composition of sediments was measured through X-ray fluorescence (XRF) spectra. The occurrence and densities of OPs and amoeba hosts (i.e., Legionella spp. and L. pneumophila, Mycobacterium spp., P. aeruginosa, V. vermiformis, Acanthamoeba spp.) were determined using genus- or species-specific qPCR assays. Microbial community analysis was performed using next generation sequencing on the Illumina Miseq platform. Mycobacterium spp. were most frequently detected in the sediments and water samples (88% and 88%), followed by Legionella spp. (50% and 50%), Acanthamoeba spp. (63% and 13%), V. vermiformis (50% and 25%), and P. aeruginosa (0 and 50%) by qPCR method. Comamonadaceae (22.8%), Sphingomonadaceae (10.3%), and Oxalobacteraceae (10.1%) were the most dominant families by sequencing method. Microbial communities in water samples were mostly separated with those in sediment samples, suggesting differences of communities between two matrices even in the same location. There were associations of OPs with microbial communities. Both OPs and microbial community structures were positively associated with some elements (Al and K) in sediments mainly from pipe material corrosions. Opportunistic pathogens presented in both water and sediments, and the latter could act as a reservoir of microbial contamination. There appears to be an association between potential opportunistic pathogens and microbial community structures. These microbial communities may be influenced by constituents within storage tank sediments. The results imply that compositions of microbial community and elements may influence and indicate microbial water quality and pipeline corrosion, and that these constituents may be important for optimal storage tank management

Interconnection of Key Microbial Functional Genes for Enhanced Benzo[a]pyrene Biodegradation in Sediments by Microbial Electrochemistry.

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Yan, Zaisheng; He, Yuhong; Cai, Haiyuan; Van Nostrand, Joy D; He, Zhili; Zhou, Jizhong; Krumholz, Lee R; Jiang, He-Long

2017-08-01

Sediment microbial fuel cells (SMFCs) can stimulate the degradation of polycyclic aromatic hydrocarbons in sediments, but the mechanism of this process is poorly understood at the microbial functional gene level. Here, the use of SMFC resulted in 92% benzo[a]pyrene (BaP) removal over 970 days relative to 54% in the controls. Sediment functions, microbial community structure, and network interactions were dramatically altered by the SMFC employment. Functional gene analysis showed that c-type cytochrome genes for electron transfer, aromatic degradation genes, and extracellular ligninolytic enzymes involved in lignin degradation were significantly enriched in bulk sediments during SMFC operation. Correspondingly, chemical analysis of the system showed that these genetic changes resulted in increases in the levels of easily oxidizable organic carbon and humic acids which may have resulted in increased BaP bioavailability and increased degradation rates. Tracking microbial functional genes and corresponding organic matter responses should aid mechanistic understanding of BaP enhanced biodegradation by microbial electrochemistry and development of sustainable bioremediation strategies.

Groundwater shapes sediment biogeochemistry and microbial diversity in a submerged Great Lake sinkhole.

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Kinsman-Costello, L E; Sheik, C S; Sheldon, N D; Allen Burton, G; Costello, D M; Marcus, D; Uyl, P A Den; Dick, G J

2017-03-01

For a large part of earth's history, cyanobacterial mats thrived in low-oxygen conditions, yet our understanding of their ecological functioning is limited. Extant cyanobacterial mats provide windows into the putative functioning of ancient ecosystems, and they continue to mediate biogeochemical transformations and nutrient transport across the sediment-water interface in modern ecosystems. The structure and function of benthic mats are shaped by biogeochemical processes in underlying sediments. A modern cyanobacterial mat system in a submerged sinkhole of Lake Huron (LH) provides a unique opportunity to explore such sediment-mat interactions. In the Middle Island Sinkhole (MIS), seeping groundwater establishes a low-oxygen, sulfidic environment in which a microbial mat dominated by Phormidium and Planktothrix that is capable of both anoxygenic and oxygenic photosynthesis, as well as chemosynthesis, thrives. We explored the coupled microbial community composition and biogeochemical functioning of organic-rich, sulfidic sediments underlying the surface mat. Microbial communities were diverse and vertically stratified to 12 cm sediment depth. In contrast to previous studies, which used low-throughput or shotgun metagenomic approaches, our high-throughput 16S rRNA gene sequencing approach revealed extensive diversity. This diversity was present within microbial groups, including putative sulfate-reducing taxa of Deltaproteobacteria, some of which exhibited differential abundance patterns in the mats and with depth in the underlying sediments. The biological and geochemical conditions in the MIS were distinctly different from those in typical LH sediments of comparable depth. We found evidence for active cycling of sulfur, methane, and nutrients leading to high concentrations of sulfide, ammonium, and phosphorus in sediments underlying cyanobacterial mats. Indicators of nutrient availability were significantly related to MIS microbial community composition, while LH

Elucidating Microbial Species-Specific Effects on Organic Matter Transformation in Marine Sediments

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Mahmoudi, N.; Enke, T. N.; Beaupre, S. R.; Teske, A.; Cordero, O. X.; Pearson, A.

2017-12-01

Microbial transformation and decomposition of organic matter in sediments constitutes one of the largest fluxes of carbon in marine environments. Mineralization of sedimentary organic matter by microorganisms results in selective degradation such that bioavailable or accessible compounds are rapidly metabolized while more recalcitrant, complex compounds are preserved and buried in sediment. Recent studies have found that the ability to use different carbon sources appears to vary among microorganisms, suggesting that the availability of certain pools of carbon can be specific to the taxa that utilize the pool. This implies that organic matter mineralization in marine environments may depend on the metabolic potential of the microbial populations that are present and active. The goal of our study was to investigate the extent to which organic matter availability and transformation may be species-specific using sediment from Guaymas Basin (Gulf of California). We carried out time-series incubations using bacterial isolates and sterilized sediment in the IsoCaRB system which allowed us to measure the production rates and natural isotopic signatures (δ13C and Δ14C) of microbially-respired CO2. Separate incubations using two different marine bacterial isolates (Vibrio sp. and Pseudoalteromonas sp.) and sterilized Guaymas Basin sediment under oxic conditions showed that the rate and total quantity of organic matter metabolized by these two species differs. Approximately twice as much CO2 was collected during the Vibrio sp. incubation compared to the Pseudoalteromonas sp. incubation. Moreover, the rate at which organic matter was metabolized by the Vibrio sp. was much higher than the Pseudoalteromonas sp. indicating the intrinsic availability of organic matter in sediments may depend on the species that is present and active. Isotopic analyses of microbially respired CO2 will be used to constrain the type and age of organic matter that is accessible to each species

Microbial diversity and stratification of South Pacific abyssal marine sediments.

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Durbin, Alan M; Teske, Andreas

2011-12-01

Abyssal marine sediments cover a large proportion of the ocean floor, but linkages between their microbial community structure and redox stratification have remained poorly constrained. This study compares the downcore gradients in microbial community composition to porewater oxygen and nitrate concentration profiles in an abyssal marine sediment column in the South Pacific Ocean. Archaeal 16S rRNA clone libraries showed a stratified archaeal community that changed from Marine Group I Archaea in the aerobic and nitrate-reducing upper sediment column towards deeply branching, uncultured crenarchaeotal and euryarchaeotal lineages in nitrate-depleted, anaerobic sediment horizons. Bacterial 16S rRNA clone libraries revealed a similar shift on the phylum and subphylum level within the bacteria, from a complex community of Alpha-, Gamma- and Deltaproteobacteria, Actinobacteria and Gemmatimonadetes in oxic surface sediments towards uncultured Chloroflexi and Planctomycetes in the anaerobic sediment column. The distinct stratification of largely uncultured bacterial and archaeal groups within the oxic and nitrate-reducing marine sediment column provides initial constraints for their microbial habitat preferences. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

Microbial communities in methane- and short chain alkane-rich hydrothermal sediments of Guaymas Basin

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Frederick eDowell

2016-01-01

Full Text Available The hydrothermal sediments of Guaymas Basin, an active spreading center in the Gulf of California (Mexico, are rich in porewater methane, short-chain alkanes, sulfate and sulfide, and provide a model system to explore habitat preferences of microorganisms, including sulfate-dependent, methane- and short chain alkane-oxidizing microbial communities. In this study, sediments (above 60˚C covered with sulfur-oxidizing microbial mats surrounding a hydrothermal mound (termed Mat Mound were characterized by porewater geochemistry of methane, C2-C6 short-chain alkanes, sulfate, sulfide, sulfate reduction rate measurements, in-situ temperature gradients, bacterial and archaeal 16S rRNA gene clone libraries and V6 tag pyrosequencing. The most abundantly detected groups in the Mat mound sediments include anaerobic methane-oxidizing archaea of the ANME-1 lineage and its sister clade ANME-1Guaymas, the uncultured bacterial groups SEEP-SRB2 within the Deltaproteobacteria and the separately branching HotSeep-1 Group; these uncultured bacteria are candidates for sulfate-reducing alkane oxidation and for sulfate-reducing syntrophy with ANME archaea. The archaeal dataset indicates distinct habitat preferences for ANME-1, ANME-1-Guaymas and ANME-2 archaea in Guaymas Basin hydrothermal sediments. The bacterial groups SEEP-SRB2 and HotSeep-1 co-occur with ANME-1 and ANME-1Guaymas in hydrothermally active sediments underneath microbial mats in Guaymas Basin. We propose the working hypothesis that this mixed bacterial and archaeal community catalyzes the oxidation of both methane and short-chain alkanes, and constitutes a microbial community signature that is characteristic for hydrothermal and/or cold seep sediments containing both substrates.

Alternation of Sediment Characteristics during Sediment Microbial Fuel Cells Amended Biochar

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Yang, Xunan; Chen, Shanshan

2018-01-01

Sediment microbial fuel cells (SMFCs) are considered as a new technology in sediment remediation, while biochars can promote interspecies electron transfer in bioelectrochemical systems. We conducted the SMFCs amended with biochars to investigate their effects on of sediment characteristics. Results showed that the anode of SMFCs could oxidize the chemical oxidizable matter in sediments (by 4%-16%) correlating with the maximum power density (r=0.982, palternations under SMFC operation, which gave information on the element pool related to pollutants and the risk of the application of SMFCs.

Using geochemical indicators to distinguish high biogeochemical activity in floodplain soils and sediments

Energy Technology Data Exchange (ETDEWEB)

Kenwell, Amy [Hydrologic Sciences and Engineering Program, Colorado School of Mines, 1500 Illinois St., Golden, CO 80401 (United States); Navarre-Sitchler, Alexis, E-mail: asitchle@mines.edu [Hydrologic Sciences and Engineering Program, Colorado School of Mines, 1500 Illinois St., Golden, CO 80401 (United States); Prugue, Rodrigo [Hydrologic Sciences and Engineering Program, Colorado School of Mines, 1500 Illinois St., Golden, CO 80401 (United States); Spear, John R. [Department of Civil and Environmental Engineering, Colorado School of Mines, 1500 Illinois St., Golden, CO 80401 (United States); Hering, Amanda S. [Department of Applied Mathematics and Statistics, Colorado School of Mines, 1500 Illinois St., Golden, CO 80401 (United States); Maxwell, Reed M. [Hydrologic Sciences and Engineering Program, Colorado School of Mines, 1500 Illinois St., Golden, CO 80401 (United States); Carroll, Rosemary W.H. [Desert Research Institute, Division of Hydrologic Sciences, 2215 Raggio Parkway, Reno, NV 89512 (United States); Williams, Kenneth H. [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States)

2016-09-01

A better understanding of how microbial communities interact with their surroundings in physically and chemically heterogeneous subsurface environments will lead to improved quantification of biogeochemical reactions and associated nutrient cycling. This study develops a methodology to predict potential elevated rates of biogeochemical activity (microbial “hotspots”) in subsurface environments by correlating microbial DNA and aspects of the community structure with the spatial distribution of geochemical indicators in subsurface sediments. Multiple linear regression models of simulated precipitation leachate, HCl and hydroxylamine extractable iron and manganese, total organic carbon (TOC), and microbial community structure were used to identify sample characteristics indicative of biogeochemical hotspots within fluvially-derived aquifer sediments and overlying soils. The method has been applied to (a) alluvial materials collected at a former uranium mill site near Rifle, Colorado and (b) relatively undisturbed floodplain deposits (soils and sediments) collected along the East River near Crested Butte, Colorado. At Rifle, 16 alluvial samples were taken from 8 sediment cores, and at the East River, 46 soil/sediment samples were collected across and perpendicular to 3 active meanders and an oxbow meander. Regression models using TOC and TOC combined with extractable iron and manganese results were determined to be the best fitting statistical models of microbial DNA (via 16S rRNA gene analysis). Fitting these models to observations in both contaminated and natural floodplain deposits, and their associated alluvial aquifers, demonstrates the broad applicability of the geochemical indicator based approach. - Highlights: • Biogeochemical characterization of alluvial floodplain soils and sediments was performed to investigate parameters that may indicate microbial hot spot formation. • A correlation between geochemical parameters (total organic carbon and

Using geochemical indicators to distinguish high biogeochemical activity in floodplain soils and sediments

International Nuclear Information System (INIS)

Kenwell, Amy; Navarre-Sitchler, Alexis; Prugue, Rodrigo; Spear, John R.; Hering, Amanda S.; Maxwell, Reed M.; Carroll, Rosemary W.H.; Williams, Kenneth H.

2016-01-01

A better understanding of how microbial communities interact with their surroundings in physically and chemically heterogeneous subsurface environments will lead to improved quantification of biogeochemical reactions and associated nutrient cycling. This study develops a methodology to predict potential elevated rates of biogeochemical activity (microbial “hotspots”) in subsurface environments by correlating microbial DNA and aspects of the community structure with the spatial distribution of geochemical indicators in subsurface sediments. Multiple linear regression models of simulated precipitation leachate, HCl and hydroxylamine extractable iron and manganese, total organic carbon (TOC), and microbial community structure were used to identify sample characteristics indicative of biogeochemical hotspots within fluvially-derived aquifer sediments and overlying soils. The method has been applied to (a) alluvial materials collected at a former uranium mill site near Rifle, Colorado and (b) relatively undisturbed floodplain deposits (soils and sediments) collected along the East River near Crested Butte, Colorado. At Rifle, 16 alluvial samples were taken from 8 sediment cores, and at the East River, 46 soil/sediment samples were collected across and perpendicular to 3 active meanders and an oxbow meander. Regression models using TOC and TOC combined with extractable iron and manganese results were determined to be the best fitting statistical models of microbial DNA (via 16S rRNA gene analysis). Fitting these models to observations in both contaminated and natural floodplain deposits, and their associated alluvial aquifers, demonstrates the broad applicability of the geochemical indicator based approach. - Highlights: • Biogeochemical characterization of alluvial floodplain soils and sediments was performed to investigate parameters that may indicate microbial hot spot formation. • A correlation between geochemical parameters (total organic carbon and

Effects of engineered nanomaterials on microbial catalyzed biogeochemical processes in sediments

Energy Technology Data Exchange (ETDEWEB)

Gao Jie, E-mail: jgao@perc.ufl.edu [Department of Environmental Engineering Sciences, University of Florida, Gainesville, FL 32611 (United States); Wang Yu; Hovsepyan, Anna [Department of Environmental Engineering Sciences, University of Florida, Gainesville, FL 32611 (United States); Bonzongo, Jean-Claude J., E-mail: bonzongo@ufl.edu [Department of Environmental Engineering Sciences, University of Florida, Gainesville, FL 32611 (United States)

2011-02-15

Engineered nanomaterials (ENMs) are anticipated to find use in many human activities and commercial products. Concerns are therefore being raised regarding their environmental fate and toxicological implications, which remain largely unknown. In this study, we investigate the effects of C{sub 60}, nano-Ag and CdSe quantum dots (QD) on microbial-catalyzed oxidation of organic matter in freshwater sediments. Sediment slurries spiked with sodium acetate at a final concentration of 150 mg/L were separately treated with pre-identified toxic levels of the tested ENMs. The study focused primarily on acetate oxidation by nitrate reducing bacteria. Sediment slurries were incubated under anaerobic conditions in parallel with control samples, and changes in concentrations of acetate, nitrate and nitrite tracked over time. The results showed that tested C{sub 60} concentration completely inhibited the microbial oxidation of acetate, whereas the addition of nano-Ag and CdSe QD to sediment slurries negatively affected the rates of acetate oxidation. Under conditions with nitrate as prevalent electron acceptor, reaction rates of acetate degradation decreased from 0.44 day{sup -1} in control slurries to 0.24 day{sup -1} and 0.20 day{sup -1} in slurries treated with nano-Ag and CdSe QD, respectively. These preliminary results call for further investigations on potential long-term effects of ENMs on microbial driven basic ecosystem services.

Relating groundwater and sediment chemistry to microbial characterization at a BTEX-contaminated site

International Nuclear Information System (INIS)

Pfiffner, S.M.; Palumbo, A.V.; McCarthy, J.F.; Gibson, T.

1996-01-01

The National Center for Manufacturing Science is investigating bioremediation of petroleum hydrocarbon at a site in Belleville, Michigan. As part of this study we examined the microbial communities to help elucidate biodegradative processes currently active at the site. We observed high densities of aerobic hydrocarbon degraders and denitrifiers in the less-contaminated sediments. Low densities of iron and sulfate reducers were measured in the same sediments. In contrast, the highly-contaminated sediments showed low densities of aerobic hydrocarbon degraders and denitrifiers and high densities of iron and sulfate reducers. Methanogens were also found in these highly-contaminated sediments. These contaminated sediments also showed a higher biomass, by phospholipid fatty acids, and greater ratios of phospholipid fatty acids which indicate stress within the microbial community. Aquifer chemistry analyses indicated that the more-contaminated area was more reduced and had lower sulfate than the less-contaminated area. These conditions suggest that the subsurface environment at the highly-contaminated area had progressed into sulfate reduction and methanogensis. The less-contaminated area, although less reduced, also appeared to be progressing into primarily iron- and sulfate-reducing microbial communities. The proposed treatment to stimulate bioremediation includes addition of oxygen and nitrate. Groundwater chemistry and microbial analyses revealed significant differences resulted from the injection of dissolved oxygen and nitrate in the subsurface. These differences included increases in pH and Eh and large decreases in BTEX, dissolved iron, and sulfate concentrations at the injection well

Degradation potential and microbial community structure of heavy oil-enriched microbial consortia from mangrove sediments in Okinawa, Japan.

Science.gov (United States)

Bacosa, Hernando P; Suto, Koichi; Inoue, Chihiro

2013-01-01

Mangroves constitute valuable coastal resources that are vulnerable to oil pollution. One of the major processes to remove oil from contaminated mangrove sediment is microbial degradation. A study on heavy oil- and hydrocarbon-degrading bacterial consortia from mangrove sediments in Okinawa, Japan was performed to evaluate their capacity to biodegrade and their microbial community composition. Surface sediment samples were obtained from mangrove sites in Okinawa (Teima, Oura, and Okukubi) and enriched with heavy oil as the sole carbon and energy source. The results revealed that all enriched microbial consortia degraded more than 20% of heavy oil in 21 days. The K1 consortium from Okukubi site showed the most extensive degradative capacity after 7 and 21 days. All consortia degraded more than 50% of hexadecane but had little ability to degrade polycyclic aromatic hydrocarbons (PAHs). The consortia were dominated by Pseudomonas or Burkholderia. When incubated in the presence of hydrocarbon compounds, the active bacterial community shifted to favor the dominance of Pseudomonas. The K1 consortium was a superior degrader, demonstrating the highest ability to degrade aliphatic and aromatic hydrocarbon compounds; it was even able to degrade heavy oil at a concentration of 15%(w/v). The dominance and turn-over of Pseudomonas and Burkholderia in the consortia suggest an important ecological role for and relationship between these two genera in the mangrove sediments of Okinawa.

The Rhizosphere Zone: A Hot Spot of Microbial Activity and Methylmercury Production in Saltmarsh Sediments of San Francisco Bay, California

Science.gov (United States)

Windham-Myers, L.; Marvin-Dipasquale, M.; Voytek, M.; Kirshtein, J.; Krabbenhoft, D. P.; Agee, J. L.; Cox, M.; Kakouros, E.; Collins, J. N.; Yee, D.

2008-12-01

Tidal marshes of varying hydrology and salinity have been shown to have high rates of microbial methylmercury (MeHg) production, especially the periodically flooded, higher elevations which are densely vegetated with shallowly rooted plants. The specific influence of emergent wetland plants and their active rhizosphere (root zone) on mercury (Hg) biogeochemistry, however, is poorly understood. Seasonal and spatial patterns of Hg biogeochemistry were examined in 2005 and 2006 at three marshes along a salinity gradient of the Petaluma River, in Northern San Francisco Bay, California. In addition, to directly examine the influence of rhizosphere activity on MeHg production, a suite of devegetation experiments was conducted in 2006 within each marsh using paired vegetated and devegetated plots in two marsh subhabitats: poorly- drained interior sites and well-drained "edge" sites near slough channels. Surface sediment (0-2cm) was sampled in both April and August from these plots, as well as from 1st and 3rd order slough channels that were naturally free of vegetation. Vegetated marsh sites produced 3- to19-fold more MeHg than did slough sites, and MeHg production rates were greater in marsh interior sites compared to more oxic marsh "edge" sites. Microbial biomass (ng DNA gdrysed) was greater in vegetated marsh settings, compared to slough channels, and increased significantly between April and August at all marsh sites. Despite this seasonal increase in microbial biomass, MeHg concentrations and production rates decreased from April to August in vegetated surface sediments. Microbial indicators of methylation also decreased from April to August, including rates of microbial sulfate reduction and the abundance of iron- and sulfate- reducing bacterial DNA. Results from the devegetated plots suggest that root exudation of fermentative labile carbon to surface soils is responsible for the higher microbial biomass, and the higher relative abundance of iron- and sulfate

Distribution of the dominant microbial communities in marine sediments containing high concentrations of gas hydrates

Energy Technology Data Exchange (ETDEWEB)

Briggs, B.; Colwell, F.; Carini, P.; Torres, M. [Oregon State Univ., Corvallis, OR (United States); Hangsterfer, A.; Kastner, M. [California Univ., San Diego, CA (United States). Scripps Inst. of Oceanography; Brodie, E. [Lawrence Berkeley National Laboratory, Berkeley, CA (United States). Center for Environmental Biotechnology; Daly, R. [California Univ., Berkeley, CA (United States); Holland, M. [GeoTek, Daventry, Northants (United Kingdom); Long, P.; Schaef, H. [Pacific Northwest National Laboratory, Richland, WA (United States). Environmental Technology; Delwiche, M. [Idaho National Laboratory, Idaho Falls, ID (United States). Biotechnology; Winters, W. [United States Geological Survey, Woods Hole, MA (United States). Woods Hole Science Center; Riedel, M. [McGill Univ., Montreal, PQ (Canada). Dept. of Earth and Planetary Sciences

2008-07-01

Methane produced by microorganisms represents a large portion of the methane that occurs in marine sediments where gas hydrates are present. The diverse communities that populate these formations have been documented by cultures or through molecular traces. Previous studies have explored the biogeography of hydrate-bearing systems by comparing clone libraries developed from sediments where hydrates are abundant with those developed from sediments that lack hydrates. There is a distinct microbial community present in sediments that have methane hydrates. This paper presented an investigation into finer-scale biogeography, in order to determine how factors such as the presence or absence of hydrates, grain size, and the depositional environment in marine sediments may control the number, type and distribution of microbial communities in sediments. The purpose of the study was to understand the controls on the distribution and activity of all microbes that contribute to the conversion of organic matter to methane. To this aim, DNA was extracted from deep marine sediments cored from continental slope locations including offshore India and the Cascadia Margin. The data from the study was used to refine computational models that require biological rate terms that are consistent with sediment conditions in order to accurately describe the dynamics of this large methane reservoir. The paper discussed the materials and methods used for the study, including the sample site, sample collection and microbiological analysis. Results were presented in terms of DNA extractions; microbial diversity; and biofilm analyses. It was concluded that the findings from the study complemented previously reported studies which indicated the presence of diverse microbial communities in sediments containing methane hydrates. 9 refs., 5 figs.

Effect of biostimulation on the microbial community in PCB-contaminated sediments through periodic amendment of sediment with iron.

Science.gov (United States)

Srinivasa Varadhan, A; Khodadoust, Amid P; Brenner, Richard C

2011-10-01

Reductive dehalogenation of polychlorinated biphenyls (PCBs) by indigenous dehalorespiring microorganisms in contaminated sediments may be enhanced via biostimulation by supplying hydrogen generated through the anaerobic corrosion of elemental iron added to the sediment. In this study, the effect of periodic amendment of sediment with various dosages of iron on the microbial community present in sediment was investigated using phospholipid fatty acid analysis (PLFA) over a period of 18 months. Three PCB-contaminated sediments (two freshwater lake sediments and one marine sediment) were used. Signature biomarker analysis of the microbial community present in all three sediments revealed the enrichment of Dehalococcoides species, the population of which was sustained for a longer period of time when the sediment microcosms were amended with the lower dosage of iron (0.01 g iron per g dry sediment) every 6 months as compared to the blank system (without iron). Lower microbial stress levels were reported for the system periodically amended with 0.01 g of iron per g dry sediment every 6 months, thus reducing the competition from other hydrogen-utilizing microorganisms like methanogens, iron reducers, and sulfate reducers. The concentration of hydrogen in the system was found to be an important factor influencing the shift in microbial communities in all sediments with time. Periodic amendment of sediment with larger dosages of iron every 3 months resulted in the early prevalence of Geobacteraceae and sulfate-reducing bacteria followed by methanogens. An average pH of 8.4 (range of 8.2-8.6) and an average hydrogen concentration of 0.75% (range of 0.3-1.2%) observed between 6 and 15 months of the study were found to be conducive to sustaining the population of Dehalococcoides species in the three sediments amended with 0.01 g iron per g dry sediment. Biostimulation of indigenous PCB dechlorinators by the periodic amendment of contaminated sediments with low dosages of

Energy Harvesting From River Sediment Using a Microbial Fuel Cell: Preliminary Results

Directory of Open Access Journals (Sweden)

Philippe Namour

2014-05-01

Full Text Available We have built a sedimentary fuel cell or Sediment Microbial Fuel Cell (SMFC. The device works on the principle of microbial fuel cells by exploiting directly the energy contained in sedimentary organic matter. It converts in electricity the sediment potential, thanks to microorganisms able to waste electrons from their metabolism directly to a solid anode instead of their natural electron acceptors, such as oxygen or nitrate. The sediment microbial fuel cell was made of a non-corrodible anode (graphite buried in anoxic sediments layer and connected via an electrical circuit to a cathode installed in surface water. We present the first results of laboratory sedimentary fuel cell and a prototype installed in the river.

Enzyme activity and kinetics in substrate-amended river sediments

Energy Technology Data Exchange (ETDEWEB)

Duddridge, J E; Wainwright, M

1982-01-01

In determining the effects of heavy metals in microbial activity and litter degradation in river sediments, one approach is to determine the effects of these pollutants on sediment enzyme activity and synthesis. Methods to assay amylase, cellulase and urease activity in diverse river sediments are reported. Enzyme activity was low in non-amended sediments, but increased markedly when the appropriate substrate was added, paralleling both athropogenic and natural amendment. Linear relationships between enzyme activity, length of incubation, sample size and substrate concentration were established. Sediment enzyme activity generally obeyed Michaelis-Menton kinetics, but of the three enzymes, urease gave least significant correlation coefficients when the data for substrate concentration versus activity was applied to the Eadie-Hofstee transformation of the Michaelis-Menten equation. K/sub m/ and V/sub max/ for amylase, cellulase and urease in sediments are reported. (JMT)

Identification of active dehalorespiring microbial populations in anoxic river sediment by RNA-based stable isotope probing

Science.gov (United States)

Kittelmann, S.; Friedrich, M. W.

2005-12-01

Tetrachloroethene (perchloroethylene, PCE), a persistent contaminant in aquifers, soils and sediments, can be reductively dechlorinated by anaerobic microorganisms in a process referred to as dehalorespiration. However, the biodiversity of dehalorespiring microorganisms and their distribution especially in pristine environments is largely unexplored. Therefore, the aim of this study was to detect potentially novel PCE-dehalorespiring microorganisms by using stable isotope probing (SIP), a technique that allows to directly identify the function of uncultivated microbial populations. We simulated a PCE contamination by incubating pristine river sediment in the presence of PCE at a steady, low aqueous concentration (20 μM). Dehalogenation activity in microcosms (20 nmol cis-dichloroethene per ml slurry per day formed) was detected already after 4 weeks at 20°C with sediment indigenous electron donors. The microbial community in sediment incubations was probed with 13C-labelled acetate (0.5 mM) as electron donor and carbon source at 15°C for 3 days. After RNA extraction, "heavy" 13C-rRNA and light 12C-rRNA were separated by isopycnic centrifugation, and Bacteria-related populations in gradient fractions were characterised by terminal restriction fragment length polymorphism analysis and cloning. In heavy gradient fractions from the microcosm with PCE, we detected a prominent 506-bp terminal restriction fragment (T-RF) and a few minor T-RFs only. In contrast, in the control without PCE, Bacteria-specific rRNA was restricted to light gradient fractions, and the prominent T-RFs found in the PCE-dechlorinating microcosm were of minor importance. Apparently, 13C-acetate was incorporated into bacterial rRNA more effectively in PCE-respiring microcosms. Thus, rRNA-SIP provides strong evidence for the presence of PCE-dehalorespiring, 13C-acetate-utilising populations in river sediment microcosms. Cloning/sequencing analysis identified the prominent members of the heavy

Development of autochthonous microbial consortia for enhanced phytoremediation of salt-marsh sediments contaminated with cadmium.

Science.gov (United States)

Teixeira, Catarina; Almeida, C Marisa R; Nunes da Silva, Marta; Bordalo, Adriano A; Mucha, Ana P

2014-09-15

Microbial assisted phytoremediation is a promising, though yet poorly explored, new remediation technique. The aim of this study was to develop autochthonous microbial consortia resistant to cadmium that could enhance phytoremediation of salt-marsh sediments contaminated with this metal. The microbial consortia were selectively enriched from rhizosediments colonized by Juncus maritimus and Phragmites australis. The obtained consortia presented similar microbial abundance but a fairly different community structure, showing that the microbial community was a function of the sediment from which the consortia were enriched. The effect of the bioaugmentation with the developed consortia on cadmium uptake, and the microbial community structure associated to the different sediments were assessed using a microcosm experiment. Our results showed that the addition of the cadmium resistant microbial consortia increased J. maritimus metal phytostabilization capacity. On the other hand, in P. australis, microbial consortia amendment promoted metal phytoextraction. The addition of the consortia did not alter the bacterial structure present in the sediments at the end of the experiments. This study provides new evidences that the development of autochthonous microbial consortia for enhanced phytoremediation of salt-marsh sediments contaminated with cadmium might be a simple, efficient, and environmental friendly remediation procedure. Development of autochthonous microbial consortia resistant to cadmium that enhanced phytoremediation by salt-marsh plants, without a long term effect on sediment bacterial diversity. Copyright © 2014 Elsevier B.V. All rights reserved.

Development of autochthonous microbial consortia for enhanced phytoremediation of salt-marsh sediments contaminated with cadmium

International Nuclear Information System (INIS)

Teixeira, Catarina; Almeida, C. Marisa R.; Nunes da Silva, Marta; Bordalo, Adriano A.; Mucha, Ana P.

2014-01-01

Microbial assisted phytoremediation is a promising, though yet poorly explored, new remediation technique. The aim of this study was to develop autochthonous microbial consortia resistant to cadmium that could enhance phytoremediation of salt-marsh sediments contaminated with this metal. The microbial consortia were selectively enriched from rhizosediments colonized by Juncus maritimus and Phragmites australis. The obtained consortia presented similar microbial abundance but a fairly different community structure, showing that the microbial community was a function of the sediment from which the consortia were enriched. The effect of the bioaugmentation with the developed consortia on cadmium uptake, and the microbial community structure associated to the different sediments were assessed using a microcosm experiment. Our results showed that the addition of the cadmium resistant microbial consortia increased J. maritimus metal phytostabilization capacity. On the other hand, in P. australis, microbial consortia amendment promoted metal phytoextraction. The addition of the consortia did not alter the bacterial structure present in the sediments at the end of the experiments. This study provides new evidences that the development of autochthonous microbial consortia for enhanced phytoremediation of salt-marsh sediments contaminated with cadmium might be a simple, efficient, and environmental friendly remediation procedure. Capsule abstract: Development of autochthonous microbial consortia resistant to cadmium that enhanced phytoremediation by salt-marsh plants, without a long term effect on sediment bacterial diversity. - Highlights: • Cd resistant microbial consortia were developed and applied to salt-marsh sediments. • In Phragmites australis the consortia amendment promoted metal phytoextraction. • The consortia addition increased Juncus maritimus phytostabilization capacity. • No long term changes on the rhizosediment bacterial structure were observed

Development of autochthonous microbial consortia for enhanced phytoremediation of salt-marsh sediments contaminated with cadmium

Energy Technology Data Exchange (ETDEWEB)

Teixeira, Catarina [Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR/CIMAR), Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto (Portugal); Laboratório de Hidrobiologia e Ecologia, Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto (Portugal); Almeida, C. Marisa R.; Nunes da Silva, Marta [Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR/CIMAR), Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto (Portugal); Bordalo, Adriano A. [Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR/CIMAR), Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto (Portugal); Laboratório de Hidrobiologia e Ecologia, Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto (Portugal); Mucha, Ana P., E-mail: amucha@ciimar.up.pt [Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR/CIMAR), Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto (Portugal)

2014-09-15

Microbial assisted phytoremediation is a promising, though yet poorly explored, new remediation technique. The aim of this study was to develop autochthonous microbial consortia resistant to cadmium that could enhance phytoremediation of salt-marsh sediments contaminated with this metal. The microbial consortia were selectively enriched from rhizosediments colonized by Juncus maritimus and Phragmites australis. The obtained consortia presented similar microbial abundance but a fairly different community structure, showing that the microbial community was a function of the sediment from which the consortia were enriched. The effect of the bioaugmentation with the developed consortia on cadmium uptake, and the microbial community structure associated to the different sediments were assessed using a microcosm experiment. Our results showed that the addition of the cadmium resistant microbial consortia increased J. maritimus metal phytostabilization capacity. On the other hand, in P. australis, microbial consortia amendment promoted metal phytoextraction. The addition of the consortia did not alter the bacterial structure present in the sediments at the end of the experiments. This study provides new evidences that the development of autochthonous microbial consortia for enhanced phytoremediation of salt-marsh sediments contaminated with cadmium might be a simple, efficient, and environmental friendly remediation procedure. Capsule abstract: Development of autochthonous microbial consortia resistant to cadmium that enhanced phytoremediation by salt-marsh plants, without a long term effect on sediment bacterial diversity. - Highlights: • Cd resistant microbial consortia were developed and applied to salt-marsh sediments. • In Phragmites australis the consortia amendment promoted metal phytoextraction. • The consortia addition increased Juncus maritimus phytostabilization capacity. • No long term changes on the rhizosediment bacterial structure were observed.

High activity and low temperature optima of extracellular enzymes in Arctic sediments: implications for carbon cycling by heterotrophic microbial communities

DEFF Research Database (Denmark)

Arnosti, C.; Jørgensen, BB

2003-01-01

(chondroitin sulfate, fucoidan, xylan and pullulan) to determine the temperature-activity responses of hydrolysis of a related class of compounds. All 4 enzyme activities showed similarly low temperature optima in the range of 15 to 18degreesC. These temperature optima are considerably lower than most previous......The rate of the initial step in microbial remineralization of organic carbon, extracellular enzymatic hydrolysis, was investigated as a function of temperature in permanently cold sediments from 2 fjords on the west coast of Svalbard (Arctic Ocean). We used 4 structurally distinct polysaccharides...... reports of temperature optima for enzyme activities in marine sediments. At 0degreesC, close to the in situ temperature, these enzyme activities achieved 13 to 38% of their rates at optimum temperatures. In one experiment, sulfate reduction rates were measured in parallel with extracellular enzymatic...

Microbial biogeography of San Francisco Bay sediments

Science.gov (United States)

Lee, J. A.; Francis, C. A.

2014-12-01

The largest estuary on the west coast of North America, San Francisco Bay is an ecosystem of enormous biodiversity, and also enormous human impact. The benthos has experienced dredging, occupation by invasive species, and over a century of sediment input as a result of hydraulic mining. Although the Bay's great cultural and ecological importance has inspired numerous surveys of the benthic macrofauna, to date there has been almost no investigation of the microbial communities on the Bay floor. An understanding of those microbial communities would contribute significantly to our understanding of both the biogeochemical processes (which are driven by the microbiota) and the physical processes (which contribute to microbial distributions) in the Bay. Here, we present the first broad survey of bacterial and archaeal taxa in the sediments of the San Francisco Bay. We conducted 16S rRNA community sequencing of bacteria and archaea in sediment samples taken bimonthly for one year, from five sites spanning the salinity gradient between Suisun and Central Bay, in order to capture the effect of both spatial and temporal environmental variation on microbial diversity. From the same samples we also conducted deep sequencing of a nitrogen-cycling functional gene, nirS, allowing an assessment of evolutionary diversity at a much finer taxonomic scale within an important and widespread functional group of bacteria. We paired these sequencing projects with extensive geochemical metadata as well as information about macrofaunal distribution. Our data reveal a diversity of distinct biogeographical patterns among different taxa: clades ubiquitous across sites; clades that respond to measurable environmental drivers; and clades that show geographical site-specificity. These community datasets allow us to test the hypothesis that salinity is a major driver of both overall microbial community structure and community structure of the denitrifying bacteria specifically; and to assess

The life sulfuric: microbial ecology of sulfur cycling in marine sediments.

Science.gov (United States)

Wasmund, Kenneth; Mußmann, Marc; Loy, Alexander

2017-08-01

Almost the entire seafloor is covered with sediments that can be more than 10 000 m thick and represent a vast microbial ecosystem that is a major component of Earth's element and energy cycles. Notably, a significant proportion of microbial life in marine sediments can exploit energy conserved during transformations of sulfur compounds among different redox states. Sulfur cycling, which is primarily driven by sulfate reduction, is tightly interwoven with other important element cycles (carbon, nitrogen, iron, manganese) and therefore has profound implications for both cellular- and ecosystem-level processes. Sulfur-transforming microorganisms have evolved diverse genetic, metabolic, and in some cases, peculiar phenotypic features to fill an array of ecological niches in marine sediments. Here, we review recent and selected findings on the microbial guilds that are involved in the transformation of different sulfur compounds in marine sediments and emphasise how these are interlinked and have a major influence on ecology and biogeochemistry in the seafloor. Extraordinary discoveries have increased our knowledge on microbial sulfur cycling, mainly in sulfate-rich surface sediments, yet many questions remain regarding how sulfur redox processes may sustain the deep-subsurface biosphere and the impact of organic sulfur compounds on the marine sulfur cycle. © 2017 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Organic priority substances and microbial processes in river sediments subject to contrasting hydrological conditions.

Science.gov (United States)

Zoppini, Annamaria; Ademollo, Nicoletta; Amalfitano, Stefano; Casella, Patrizia; Patrolecco, Luisa; Polesello, Stefano

2014-06-15

Flood and drought events of higher intensity and frequency are expected to increase in arid and semi-arid regions, in which temporary rivers represent both a water resource and an aquatic ecosystem to be preserved. In this study, we explored the variation of two classes of hazardous substances (Polycyclic Aromatic Hydrocarbons and Nonylphenols) and the functioning of the microbial community in river sediments subject to hydrological fluctuations (Candelaro river basin, Italy). Overall, the concentration of pollutants (∑PAHs range 8-275ngg(-1); ∑NPs range 299-4858ngg(-1)) suggests a moderate degree of contamination. The conditions in which the sediments were tested, flow (high/low) and no flow (wet/dry/arid), were associated to significant differences in the chemical and microbial properties. The total organic carbon contribution decreased together with the stream flow reduction, while the contribution of C-PAHs and C-NPs tended to increase. NPs were relatively more concentrated in sediments under high flow, while the more hydrophobic PAHs accumulated under low and no flow conditions. Passing from high to no flow conditions, a gradual reduction of microbial processes was observed, to reach the lowest specific bacterial carbon production rates (0.06fmolCh(-1)cell(-1)), extracellular enzyme activities, and the highest doubling time (40h) in arid sediments. In conclusion, different scenarios for the mobilization of pollutants and microbial processes can be identified under contrasting hydrological conditions: (i) the mobilization of pollutants under high flow and a relatively higher probability for biodegradation; (ii) the accumulation of pollutants during low flow and lower probability for biodegradation; (iii) the drastic reduction of pollutant concentrations under dry and arid conditions, probably independently from the microbial activity (abiotic processes). Our findings let us infer that a multiple approach has to be considered for an appropriate water

Distributions of microbial activities in deep subseafloor sediments RID D-2690-2009 RID C-7675-2009 RID B-8817-2009 RID C-2958-2008 RID B-1731-2010

DEFF Research Database (Denmark)

D'Hondt, S.; Jørgensen, BB; Miller, DJ

2004-01-01

Diverse microbial communities and numerous energy-yielding activities occur in deeply buried sediments of the eastern Pacific Ocean. Distributions of metabolic activities often deviate from the standard model. Rates of activities, cell concentrations, and populations of cultured bacteria vary...

Microbially catalyzed nitrate-dependent metal/radionuclide oxidation in shallow subsurface sediments

Science.gov (United States)

Weber, K.; Healy, O.; Spanbauer, T. L.; Snow, D. D.

2011-12-01

Anaerobic, microbially catalyzed nitrate-dependent metal/radionuclide oxidation has been demonstrated in a variety of sediments, soils, and groundwater. To date, studies evaluating U bio-oxidation and mobilization have primarily focused on anthropogenically U contaminated sites. In the Platte River Basin U originating from weathering of uranium-rich igneous rocks in the Rocky Mountains was deposited in shallow alluvial sediments as insoluble reduced uranium minerals. These reduced U minerals are subject to reoxidation by available oxidants, such nitrate, in situ. Soluble uranium (U) from natural sources is a recognized contaminant in public water supplies throughout the state of Nebraska and Colorado. Here we evaluate the potential of anaerobic, nitrate-dependent microbially catalyzed metal/radionuclide oxidation in subsurface sediments near Alda, NE. Subsurface sediments and groundwater (20-64ft.) were collected from a shallow aquifer containing nitrate (from fertilizer) and natural iron and uranium. The reduction potential revealed a reduced environment and was confirmed by the presence of Fe(II) and U(IV) in sediments. Although sediments were reduced, nitrate persisted in the groundwater. Nitrate concentrations decreased, 38 mg/L to 30 mg/L, with increasing concentrations of Fe(II) and U(IV). Dissolved U, primarily as U(VI), increased with depth, 30.3 μg/L to 302 μg/L. Analysis of sequentially extracted U(VI) and U(IV) revealed that virtually all U in sediments existed as U(IV). The presence of U(IV) is consistent with reduced Fe (Fe(II)) and low reduction potential. The increase in aqueous U concentrations with depth suggests active U cycling may occur at this site. Tetravalent U (U(IV)) phases are stable in reduced environments, however the input of an oxidant such as oxygen or nitrate into these systems would result in oxidation. Thus co-occurrence of nitrate suggests that nitrate could be used by bacteria as a U(IV) oxidant. Most probable number

Diversity and survivability of microbial community in ancient permafrost sediment of northeast Siberia

Science.gov (United States)

Liang, R.; Lau, M.; Vishnivetskaya, T. A.; Lloyd, K. G.; Pfiffner, S. M.; Rivkina, E.; Onstott, T. C.

2017-12-01

The prevalence of microorganisms in frozen permafrost has been well documented in ancient sediment up to several million years old. However, the long term survivability and metabolic activity of microbes over geological timespans remain underexplored. Siberian permafrost sediment was collected at various depths (1.4m, 11.8 m and 24.8m) to represent a wide range of geological time from thousands to millions of years. Extracellular (eDNA) and intracellular DNA (iDNA) was simultaneously recovered for sequencing to characterize the potentially extinct and extant microbial community. Additionally, aspartic acid racemization assay (D/L Asp) was used to infer the metabolic activity of microbes in ancient permafrost. As compared with the young sample (1.4m), DNA yield and content of aspartic acid dramatically decreased in old samples (11.8m and 24.8m). However, D/L Asp and eDNA/iDNA significantly increased with the geological age. Such findings suggested that ancient microbiomes might be subjected to racemization or even DNA/proteins degradation at subzero temperature over the wide geological time scale. Preliminary characterization of microbial community indicated that the majority of sequences in old samples were identified as bacteria and only a small fraction was identified as archaea from the iDNA pool. While the eDNA and iDNA fractions shared similar dominant taxa at phylum level, the relative abundance of Proteobacteria in eDNA library was much higher than iDNA. By contrast, the phylum affiliated with Firmicutes was more numerically abundant in the iDNA fraction. More dramatic differences were observed between eDNA and iDNA library at lower taxonomic levels. Particularly, the microbial lineages affiliated with the genera Methanoregula, Desulfosporosinus and Syntrophomonas were only detected in the iDNA library. Such taxonomic difference between the relic eDNA and iDNA suggested that numerous species become locally "extinct" whereas many other taxa might survive in

Microbial responses to polycyclic aromatic hydrocarbon contamination in temporary river sediments: Experimental insights.

Science.gov (United States)

Zoppini, Annamaria; Ademollo, Nicoletta; Amalfitano, Stefano; Capri, Silvio; Casella, Patrizia; Fazi, Stefano; Marxsen, Juergen; Patrolecco, Luisa

2016-01-15

Temporary rivers are characterized by dry-wet phases and represent an important water resource in semi-arid regions worldwide. The fate and effect of contaminants have not been firmly established in temporary rivers such as in other aquatic environments. In this study, we assessed the effects of sediment amendment with Polycyclic Aromatic Hydrocarbons (PAHs) on benthic microbial communities. Experimental microcosms containing natural (Control) and amended sediments (2 and 20 mg PAHs kg(-1) were incubated for 28 days. The PAH concentrations in sediments were monitored weekly together with microbial community structural (biomass and phylogenetic composition by TGGE and CARD-FISH) and functional parameters (ATP concentration, community respiration rate, bacterial carbon production rate, extracellular enzyme activities). The concentration of the PAH isomers did not change significantly with the exception of phenanthrene. No changes were observed in the TGGE profiles, whereas the occurrence of Alpha- and Beta-Proteobacteria was significantly affected by the treatments. In the amended sediments, the rates of carbon production were stimulated together with aminopeptidase enzyme activity. The community respiration rates showed values significantly lower than the Control after 1 day from the amendment then recovering the Control values during the incubation. A negative trend between the respiration rates and ATP concentration was observed only in the amended sediments. This result indicates a potential toxic effect on the oxidative phosphorylation processes. The impoverishment of the energetic resources that follows the PAH impact may act as a domino on the flux of energy from prokaryotes to the upper level of the trophic chain, with the potential to alter the temporary river functioning.

Microbial Reduction of Fe(III) and SO42- and Associated Microbial Communities in the Alluvial Aquifer Groundwater and Sediments.

Science.gov (United States)

Lee, Ji-Hoon; Lee, Bong-Joo

2017-11-25

Agricultural demands continuously increased use of groundwater, causing drawdown of water table and need of artificial recharge using adjacent stream waters. River water intrusion into groundwater can alter the geochemical and microbiological characteristics in the aquifer and subsurface. In an effort to investigate the subsurface biogeochemical activities before operation of artificial recharge at the test site, established at the bank of Nakdong River, Changwon, South Korea, organic carbon transported from river water to groundwater was mimicked and the effect on the indigenous microbial communities was investigated with the microcosm incubations of the groundwater and subsurface sediments. Laboratory incubations indicated microbial reduction of Fe(III) and sulfate. Next-generation Illumina MiSeq sequences of V4 region of 16S rRNA gene provided that the shifts of microbial taxa to Fe(III)-reducing and/or sulfate-reducing microorganisms such as Geobacter, Albidiferax, Desulfocapsa, Desulfuromonas, and Desulfovibrio were in good correlation with the sequential flourishment of microbial reduction of Fe(III) and sulfate as the incubations progressed. This suggests the potential role of dissolved organic carbons migrated with the river water into groundwater in the managed aquifer recharge system on the indigenous microbial community composition and following alterations of subsurface biogeochemistry and microbial metabolic activities.

Microbial Community Response to Simulated Petroleum Seepage in Caspian Sea Sediments

Directory of Open Access Journals (Sweden)

Katrin Knittel

2017-04-01

Full Text Available Anaerobic microbial hydrocarbon degradation is a major biogeochemical process at marine seeps. Here we studied the response of the microbial community to petroleum seepage simulated for 190 days in a sediment core from the Caspian Sea using a sediment-oil-flow-through (SOFT system. Untreated (without simulated petroleum seepage and SOFT sediment microbial communities shared 43% bacterial genus-level 16S rRNA-based operational taxonomic units (OTU0.945 but shared only 23% archaeal OTU0.945. The community differed significantly between sediment layers. The detection of fourfold higher deltaproteobacterial cell numbers in SOFT than in untreated sediment at depths characterized by highest sulfate reduction rates and strongest decrease of gaseous and mid-chain alkane concentrations indicated a specific response of hydrocarbon-degrading Deltaproteobacteria. Based on an increase in specific CARD-FISH cell numbers, we suggest the following groups of sulfate-reducing bacteria to be likely responsible for the observed decrease in aliphatic and aromatic hydrocarbon concentration in SOFT sediments: clade SCA1 for propane and butane degradation, clade LCA2 for mid- to long-chain alkane degradation, clade Cyhx for cycloalkanes, pentane and hexane degradation, and relatives of Desulfobacula for toluene degradation. Highest numbers of archaea of the genus Methanosarcina were found in the methanogenic zone of the SOFT core where we detected preferential degradation of long-chain hydrocarbons. Sequencing of masD, a marker gene for alkane degradation encoding (1-methylalkylsuccinate synthase, revealed a low diversity in SOFT sediment with two abundant species-level MasD OTU0.96.

High rates of microbial carbon turnover in sediments in the deepest oceanic trench on Earth

DEFF Research Database (Denmark)

Glud, Ronnie N.; Wenzhoefer, Frank; Middelboe, Mathias

2013-01-01

Microbes control the decomposition of organic matter in marine sediments. Decomposition, in turn, contributes to oceanic nutrient regeneration and influences the preservation of organic carbon(1). Generally, rates of benthic decomposition decline with increasing water depth, although given the vast...... extent of the abyss, deep-sea sediments are quantitatively important for the global carbon cycle(2,3). However, the deepest regions of the ocean have remained virtually unexplored(4). Here, we present observations of microbial activity in sediments at Challenger Deep in the Mariana Trench in the central...

Structural and functional diversity of microbial communities from a lake sediment contaminated with trenbolone, an endocrine-disrupting chemical

International Nuclear Information System (INIS)

Radl, Viviane; Pritsch, Karin; Munch, Jean Charles; Schloter, Michael

2005-01-01

Effects of trenbolone (TBOH), a hormone used in cattle production, on the structure and function of microbial communities in a fresh water sediment from a lake in Southern Germany were studied in a microcosm experiment. The microbial community structure and the total gene pool of the sediment, assessed by 16S rRNA/rDNA and RAPD fingerprint analysis, respectively, were not significantly affected by TBOH. In contrast, the N-acetyl-glucosaminidase activity was almost 50% lower in TBOH treated samples (P<0.05). Also, the substrate utilization potential, measured using the BIOLOG[reg] system, was reduced after TBOH treatment. Interestingly, this potential did not recover at the end of the experiment, i.e. 19 days after the addition of the chemical. Repeated application of TBOH did not lead to an additional reduction in the substrate utilization potential. Overall results indicate that microbial community function was more sensitive to TBOH treatment than the community structure and the total gene pool. - The steroid hormone trenbolone affects microbial community function in a lake sediment

Structural and functional diversity of microbial communities from a lake sediment contaminated with trenbolone, an endocrine-disrupting chemical

Energy Technology Data Exchange (ETDEWEB)

Radl, Viviane [GSF National Research Center for Environment and Health, Institute of Soil Ecology, PO Box 1129, D-85764, Neuherberg (Germany)]. E-mail: barbosa@gsf.de; Pritsch, Karin [GSF National Research Center for Environment and Health, Institute of Soil Ecology, PO Box 1129, D-85764, Neuherberg (Germany); Munch, Jean Charles [GSF National Research Center for Environment and Health, Institute of Soil Ecology, PO Box 1129, D-85764, Neuherberg (Germany); Schloter, Michael [GSF National Research Center for Environment and Health, Institute of Soil Ecology, PO Box 1129, D-85764, Neuherberg (Germany)

2005-09-15

Effects of trenbolone (TBOH), a hormone used in cattle production, on the structure and function of microbial communities in a fresh water sediment from a lake in Southern Germany were studied in a microcosm experiment. The microbial community structure and the total gene pool of the sediment, assessed by 16S rRNA/rDNA and RAPD fingerprint analysis, respectively, were not significantly affected by TBOH. In contrast, the N-acetyl-glucosaminidase activity was almost 50% lower in TBOH treated samples (P<0.05). Also, the substrate utilization potential, measured using the BIOLOG[reg] system, was reduced after TBOH treatment. Interestingly, this potential did not recover at the end of the experiment, i.e. 19 days after the addition of the chemical. Repeated application of TBOH did not lead to an additional reduction in the substrate utilization potential. Overall results indicate that microbial community function was more sensitive to TBOH treatment than the community structure and the total gene pool. - The steroid hormone trenbolone affects microbial community function in a lake sediment.

Microbial community changes along the active seepage site of one cold seep in the Red Sea.

KAUST Repository

Cao, Huiluo

2015-07-21

The active seepage of the marine cold seeps could be a critical process for the exchange of energy between the submerged geosphere and the sea floor environment through organic-rich fluids, potentially even affecting surrounding microbial habitats. However, few studies have investigated the associated microbial community changes. In the present study, 16S rRNA genes were pyrosequenced to decipher changes in the microbial communities from the Thuwal seepage point in the Red Sea to nearby marine sediments in the brine pool, normal marine sediments and water, and benthic microbial mats. An unexpected number of reads from unclassified groups were detected in these habitats; however, the ecological functions of these groups remain unresolved. Furthermore, ammonia-oxidizing archaeal community structures were investigated using the ammonia monooxygenase subunit A (amoA) gene. Analysis of amoA showed that planktonic marine habitats, including seeps and marine water, hosted archaeal ammonia oxidizers that differed from those in microbial mats and marine sediments, suggesting modifications of the ammonia oxidizing archaeal (AOA) communities along the environmental gradient from active seepage sites to peripheral areas. Changes in the microbial community structure of AOA in different habitats (water vs. sediment) potentially correlated with changes in salinity and oxygen concentrations. Overall, the present results revealed for the first time unanticipated novel microbial groups and changes in the ammonia-oxidizing archaea in response to environmental gradients near the active seepages of a cold seep.

Microbial community changes along the active seepage site of one cold seep in the Red Sea.

KAUST Repository

Cao, Huiluo; Zhang, Weipeng; Wang, Yong; Qian, Pei-Yuan

2015-01-01

The active seepage of the marine cold seeps could be a critical process for the exchange of energy between the submerged geosphere and the sea floor environment through organic-rich fluids, potentially even affecting surrounding microbial habitats. However, few studies have investigated the associated microbial community changes. In the present study, 16S rRNA genes were pyrosequenced to decipher changes in the microbial communities from the Thuwal seepage point in the Red Sea to nearby marine sediments in the brine pool, normal marine sediments and water, and benthic microbial mats. An unexpected number of reads from unclassified groups were detected in these habitats; however, the ecological functions of these groups remain unresolved. Furthermore, ammonia-oxidizing archaeal community structures were investigated using the ammonia monooxygenase subunit A (amoA) gene. Analysis of amoA showed that planktonic marine habitats, including seeps and marine water, hosted archaeal ammonia oxidizers that differed from those in microbial mats and marine sediments, suggesting modifications of the ammonia oxidizing archaeal (AOA) communities along the environmental gradient from active seepage sites to peripheral areas. Changes in the microbial community structure of AOA in different habitats (water vs. sediment) potentially correlated with changes in salinity and oxygen concentrations. Overall, the present results revealed for the first time unanticipated novel microbial groups and changes in the ammonia-oxidizing archaea in response to environmental gradients near the active seepages of a cold seep.

MICROBIAL DIVERSITY IN SURFACE SEDIMENTS: A COMPARISON OF TWO ESTUARINE CONTINUUMS

Science.gov (United States)

The microbial diversity in estuarine sediments of the Altamaha and Savannah Rivers in Georgia were compared temporally and spatially using phospholipid fatty acid (PLFA) analysis. Surface sediment samples collected along a salinity gradient were also analyzed for ATP, TOC, and C ...

Microbial reduction of uranium(VI) in sediments of different lithologies collected from Sellafield

International Nuclear Information System (INIS)

Newsome, Laura; Morris, Katherine; Trivedi, Divyesh; Atherton, Nick; Lloyd, Jonathan R.

2014-01-01

Highlights: • U(VI) (aq) mobility can be controlled by stimulating biogeochemical interactions. • Indigenous microbes in varied sediments reduced U(VI) to insoluble U(IV). • Sediment cell numbers and amount of bioavailable Fe(III) could limit this process. - Abstract: The presence of uranium in groundwater at nuclear sites can be controlled by microbial processes. Here we describe the results from stimulating microbial reduction of U(VI) in sediment samples obtained from a nuclear-licensed site in the UK. A variety of different lithology sediments were selected to represent the heterogeneity of the subsurface at a site underlain by glacial outwash deposits and sandstone. The natural sediment microbial communities were stimulated via the addition of an acetate/lactate electron donor mix and were monitored for changes in geochemistry and molecular ecology. Most sediments facilitated the removal of 12 ppm U(VI) during the onset of Fe(III)-reducing conditions; this was reflected by an increase in the proportion of known Fe(III)- and U(VI)-reducing species. However U(VI) remained in solution in two sediments and Fe(III)-reducing conditions did not develop. Sequential extractions, addition of an Fe(III)-enrichment culture and most probable number enumerations revealed that a lack of bioavailable iron or low cell numbers of Fe(III)-reducing bacteria may be responsible. These results highlight the potential for stimulation of microbial U(VI)-reduction to be used as a bioremediation strategy at UK nuclear sites, and they emphasise the importance of both site-specific and borehole-specific investigations to be completed prior to implementation

Microbial Community Response to Carbon Substrate Amendment in Mercury Impacted Sediments: Implications on Microbial Methylation of Mercury.

Science.gov (United States)

Elias, D. A.; Somenahally, A. C.; Moberly, J. G.; Hurt, R. A., Jr.; Brown, S. D.; Podar, M.; Palumbo, A. V.; Gilmour, C. C.

2015-12-01

Methylmercury (MeHg) is a neurotoxic and bio-accumulative product of the microbial methylation of inorganic mercury (Hg(II)). Methylating organisms are now known to exist in almost all anaerobic niches including fermentation, Fe(III)- and sulfate- reduction as well as methanogenesis. The study objective was to determine the effect of different carbon sources on the microbial community and methylating populations in particular along a Hg contaminated creek. Sediment cores from upstream and downstream at the Hg contaminated East Fork Poplar Creek (EFPC), Oak Ridge TN, and a background site were sectioned by depth, and Hg-methylation potential (HgMP) assays were performed using stable isotope spikes. Sediments from the lowest depth possessed the highest in-situ activity. Replicate samples were amended with different carbon substrates (cellulose, acetate, propionate, lactate, ethanol and methanol), spiked with stable isotopes for HgMP assays and incubated for 24hrs. Sequencing of the 16S rRNA gene was performed to determine alterations in Bacterial and Archaeal population dynamics. Additionally, bioinformatics and our new qualitative and quantitative hgcAB primers were utilized to determine microbial community structure alterations and correlate organism and gene abundance with altered MeHg generation. HgMP was significantly reduced in cellulose amended sediments while acetate and propionate slightly decreased HgMP in both sites. Methanol, ethanol and lactate increased the HgMP in EFPC downstream while cellulose amendment significantly decreased the Proteobacteria, and the Firmicutes increased but none are currently known to produce MeHg. Geobacter bemidjiensis in particular significantly decreased in cellulose amended sediments in all three sites from being predominant in-situ. This suggests that in EFPC downstream and background sites, the prevalent Hg-methyaltors might be Deltaprotebacteria, since upstream, cellulose amendment did not reduce HgMP even though

Dredging effects on selected nutrient concentrations and ecoenzymatic activity in two drainage ditch sediments in the lower Mississippi River Valley

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Matt Moore

2017-09-01

Full Text Available Agricultural drainage ditches are conduits between production acreage and receiving aquatic systems. Often overlooked for their mitigation capabilities, agricultural drainage ditches provide an important role for nutrient transformation via microbial metabolism. Variations in ecoenzyme activities have been used to elucidate microbial metabolism and resource demand of microbial communities to better understand the relationship between altered nutrient ratios and microbial activity in aquatic ecosystems. Two agricultural drainage ditches, one in the northeast portion of the Arkansas Delta and the other in the lower Mississippi Delta, were monitored for a year. Sediment samples were collected prior to each ditch being dredged (cleaned, and subsequent post-dredging samples occurred as soon as access was available. Seasonal samples were then collected throughout a year to examine effects of dredging on selected nutrient concentrations and ecoenzymatic activity recovery in drainage ditch sediments. Phosphorus concentrations in sediments after dredging decreased 33–66%, depending on ditch and phosphorus extraction methodology. Additionally, ecoenzymatic activity was significantly decreased in most sediment samples after dredging. Fluorescein diacetate hydrolysis activity, an estimate of total microbial activity, decreased 56–67% after dredging in one of the two ditches. Many sample sites also had significant phosphorus and ecoenzymatic activity differences between the post-dredge samples and the year-long follow-up samples. Results indicate microbial metabolism in dredged drainage ditches may take up to a year or more to recover to pre-dredged levels. Likewise, while sediment nutrient concentrations may be decreased through dredging and removal, runoff and erosion events over time tend to quickly replenish nutrient concentrations in replaced sediments. Understanding nutrient dynamics and microbial metabolism within agricultural drainage ditches is

Microbial-meiofaunal interrelationships in coastal sediments of the Red Sea.

Science.gov (United States)

El-Serehy, Hamed A; Al-Rasheid, Khaled A; Al-Misned, Fahad A; Al-Talasat, Abdul Allah R; Gewik, Mohamed M

2016-05-01

Population density and biomass of bacteria and meiofauna were investigated seasonally in the sediments of the north-western bank of Red Sea. Samples of sediments were collected seasonally from three different stations to determine microphytobenthic biomass (chlorophyll a), protein, lipid, carbohydrate, and total organic matter concentrations. These investigations revealed that microbial components tended to increase their dominancy, whereas sensitive meiofauna were extremely reduced during the entire study period. Thus a very low density of the total meiofauna (with an annual average of 109 ± 26 ind./10 cm(2)) was recorded whilst the benthic microbial population densities exhibited higher values (ranging from 0.31 ± 0.02 × 10(8) to 43.67 ± 18.62 × 10(8)/g dry sediment). These changes in the relative importance analysis of benthic microbial components versus meiofaunal ones seem to be based on the impact of organic matter accumulation on the function and structure of these benthic communities. Proteins, lipids and carbohydrates showed very low concentration values, and the organic matter mostly consisted of carbohydrates, reflecting lower nutritional values for benthic fauna in general and meiofauna in particular. The distribution of microbial and meiofaunal communities seems to be dependent on the quality of the organic matter rather than on its quantity. Total organic matter concentrations varied between 5.8 and 7.6 mg/g, with organic carbon accounting for only 32% of the total organic matter. Chlorophyll a attained very low values, fluctuating between 0.11 and 0.56 μg/g, indicating the oligotrophy of the studied area. The very low concentration of chlorophyll a in the Red Sea sediment suggests that the sedimentary organic matter, heterotrophic bacteria and/or protozoa constitute an alternative resource that is consumed by meiofauna when algae are less abundant. Protozoa, therefore, represent the "missing link in bacteria-meiofauna interaction

Microbial community responses to organophosphate substrate additions in contaminated subsurface sediments.

Directory of Open Access Journals (Sweden)

Robert J Martinez

Full Text Available BACKGROUND: Radionuclide- and heavy metal-contaminated subsurface sediments remain a legacy of Cold War nuclear weapons research and recent nuclear power plant failures. Within such contaminated sediments, remediation activities are necessary to mitigate groundwater contamination. A promising approach makes use of extant microbial communities capable of hydrolyzing organophosphate substrates to promote mineralization of soluble contaminants within deep subsurface environments. METHODOLOGY/PRINCIPAL FINDINGS: Uranium-contaminated sediments from the U.S. Department of Energy Oak Ridge Field Research Center (ORFRC Area 2 site were used in slurry experiments to identify microbial communities involved in hydrolysis of 10 mM organophosphate amendments [i.e., glycerol-2-phosphate (G2P or glycerol-3-phosphate (G3P] in synthetic groundwater at pH 5.5 and pH 6.8. Following 36 day (G2P and 20 day (G3P amended treatments, maximum phosphate (PO4(3- concentrations of 4.8 mM and 8.9 mM were measured, respectively. Use of the PhyloChip 16S rRNA microarray identified 2,120 archaeal and bacterial taxa representing 46 phyla, 66 classes, 110 orders, and 186 families among all treatments. Measures of archaeal and bacterial richness were lowest under G2P (pH 5.5 treatments and greatest with G3P (pH 6.8 treatments. Members of the phyla Crenarchaeota, Euryarchaeota, Bacteroidetes, and Proteobacteria demonstrated the greatest enrichment in response to organophosphate amendments and the OTUs that increased in relative abundance by 2-fold or greater accounted for 9%-50% and 3%-17% of total detected Archaea and Bacteria, respectively. CONCLUSIONS/SIGNIFICANCE: This work provided a characterization of the distinct ORFRC subsurface microbial communities that contributed to increased concentrations of extracellular phosphate via hydrolysis of organophosphate substrate amendments. Within subsurface environments that are not ideal for reductive precipitation of uranium

Effects of gamma-sterilization on DOC, uranium and arsenic remobilization from organic and microbial rich stream sediments

International Nuclear Information System (INIS)

Schaller, Joerg; Weiske, Arndt; Dudel, E. Gert

2011-01-01

Organic-rich sediments are known to be effective accumulators for uranium and arsenic. Much is known about the capacity for metal or metalloid fixation by microbes and organic compounds as well as inorganic sediment particles. Experiments investigating the effect of microbes on the process of metal fixation in sediments require sterilized sediments as control treatment which is often realized by gamma-sterilization. Only few studies show that gamma-sterilization has an effect on the remobilization of metal and metalloids and on their physico-chemical properties. These studies deal with sediments with negligible organic content whereas almost nothing is known about organic-rich sediments including a probably high microbial activity. In view of this, we investigated the effect of gamma-sterilization of organic-rich sediments on uranium and arsenic fixation and release. After ten days within an exposure experiment we found a significant higher remobilization of uranium and arsenic in sterile compared to unsterile treatments. In line with these findings the content of dissolved organic carbon (DOC), manganese, and iron increased to even significantly higher concentration in the sterile compared to unsterile treatment. Gamma-sterilization seems to change the physico-chemical properties of organic-rich sediments. Microbial activity is effectively eliminated. From increased DOC concentrations in overlaying water it is concluded that microbes are eventually killed with leaching of cellular compounds in the overlaying water. This decreases the adsorption capacity of the sediment and leads to enhanced uranium and arsenic remobilization. - Research highlight s : →Remobilization of uranium and arsenic is higher in gamma-sterile treatments. →DOC mobilization is also higher in sterilized treatment. →Adsorption capacity in sediments is reduced by release of DOC.

Shifts in coastal sediment oxygenation cause pronounced changes in microbial community composition and associated metabolism.

Science.gov (United States)

Broman, Elias; Sjöstedt, Johanna; Pinhassi, Jarone; Dopson, Mark

2017-08-09

A key characteristic of eutrophication in coastal seas is the expansion of hypoxic bottom waters, often referred to as 'dead zones'. One proposed remediation strategy for coastal dead zones in the Baltic Sea is to mix the water column using pump stations, circulating oxygenated water to the sea bottom. Although microbial metabolism in the sediment surface is recognized as key in regulating bulk chemical fluxes, it remains unknown how the microbial community and its metabolic processes are influenced by shifts in oxygen availability. Here, coastal Baltic Sea sediments sampled from oxic and anoxic sites, plus an intermediate area subjected to episodic oxygenation, were experimentally exposed to oxygen shifts. Chemical, 16S rRNA gene, metagenomic, and metatranscriptomic analyses were conducted to investigate changes in chemistry fluxes, microbial community structure, and metabolic functions in the sediment surface. Compared to anoxic controls, oxygenation of anoxic sediment resulted in a proliferation of bacterial populations in the facultative anaerobic genus Sulfurovum that are capable of oxidizing toxic sulfide. Furthermore, the oxygenated sediment had higher amounts of RNA transcripts annotated as sqr, fccB, and dsrA involved in sulfide oxidation. In addition, the importance of cryptic sulfur cycling was highlighted by the oxidative genes listed above as well as dsvA, ttrB, dmsA, and ddhAB that encode reductive processes being identified in anoxic and intermediate sediments turned oxic. In particular, the intermediate site sediments responded differently upon oxygenation compared to the anoxic and oxic site sediments. This included a microbial community composition with more habitat generalists, lower amounts of RNA transcripts attributed to methane oxidation, and a reduced rate of organic matter degradation. These novel data emphasize that genetic expression analyses has the power to identify key molecular mechanisms that regulate microbial community responses

Prokaryotic diversity, composition structure, and phylogenetic analysis of microbial communities in leachate sediment ecosystems.

Science.gov (United States)

Liu, Jingjing; Wu, Weixiang; Chen, Chongjun; Sun, Faqian; Chen, Yingxu

2011-09-01

In order to obtain insight into the prokaryotic diversity and community in leachate sediment, a culture-independent DNA-based molecular phylogenetic approach was performed with archaeal and bacterial 16S rRNA gene clone libraries derived from leachate sediment of an aged landfill. A total of 59 archaeal and 283 bacterial rDNA phylotypes were identified in 425 archaeal and 375 bacterial analyzed clones. All archaeal clones distributed within two archaeal phyla of the Euryarchaeota and Crenarchaeota, and well-defined methanogen lineages, especially Methanosaeta spp., are the most numerically dominant species of the archaeal community. Phylogenetic analysis of the bacterial library revealed a variety of pollutant-degrading and biotransforming microorganisms, including 18 distinct phyla. A substantial fraction of bacterial clones showed low levels of similarity with any previously documented sequences and thus might be taxonomically new. Chemical characteristics and phylogenetic inferences indicated that (1) ammonium-utilizing bacteria might form consortia to alleviate or avoid the negative influence of high ammonium concentration on other microorganisms, and (2) members of the Crenarchaeota found in the sediment might be involved in ammonium oxidation. This study is the first to report the composition of the microbial assemblages and phylogenetic characteristics of prokaryotic populations extant in leachate sediment. Additional work on microbial activity and contaminant biodegradation remains to be explored.

Cambrian rivers and floodplains: the significance of microbial cementation, groundwater and aeolian sediment transport

Science.gov (United States)

Reesink, A. J. H.; Best, J.; Freiburg, J. T.; Nathan, W.

2016-12-01

Rivers that existed before land plants colonized the Earth are commonly considered to be unaffected by microbial activity on their floodplains, because the limited cementation produced by microbial activity is insufficient to stabilize the river banks. Although this assumption is likely correct, such emphasis on channel dynamics ignores the potential role of floodplain dynamics as an integral component of the river system. Detailed analysis of cores from the Cambrian Mount Simon Sandstone, Illinois, suggests that a significant proportion of the terrestrial sequence is composed of flat-bedded `crinkly' structures that provide evidence of cementation by soil crusts and microbial biofilms, and that promoted the adhesion of sediment to sticky surfaces. Wind ripples and local desert pavements were abundant. These findings highlight that sediment deposition on Cambrian floodplains was often dominated by wind in locations where the ground water table reached the surface, and was thus likely independent of sediment transport within the river channel. Erosion by wind would thus have been hindered by surface cementation and the formation of desert pavements. Such ground water control on deposition, and resistance to erosion by floodplain surface hardening, appear to have been the primary controls on Cambrian floodplain topography. Because floodplain topography poses a key control on channel and floodplain flow, these processes may have affected patterns of erosion and deposition, as well as reach-scale dynamics such as channel avulsions. The autonomous operation of wind-and-groundwater controlled floodplains makes pre-vegetated river systems more sensitive to climatic conditions such as precipitation and evaporation, and strikingly different from those that occurred after the development of land plants.

Microbial diversity in Brazilian mangrove sediments – a mini review

Science.gov (United States)

Ghizelini, Angela Michelato; Mendonça-Hagler, Leda Cristina Santana; Macrae, Andrew

2012-01-01

The importance and protection of mangrove ecosystems has been recognized in Brazilian Federal law since 1965. Being protected in law, however, has not always guaranteed their protection in practice. Mangroves are found in coastal and estuarine locations, which are prime real estate for the growth of cities, ports and other economic activities important for Brazilian development. In this mini-review we introduce what mangroves are and why they are so important. We give a brief overview of the microbial diversity found in mangrove sediments and then focus on diversity studies from Brazilian mangroves. We highlight the breadth and depth of knowledge about mangrove microbial communities gained from studying Brazilian mangroves. We report on the exciting findings of molecular microbial ecology methods that have been very successfully applied to study bacterial communities. We note that there have been fewer studies that focus on fungal communities and that fungal diversity studies deserve more attention. The review ends with a look at how a combination of new molecular biology methods and isolation studies are being developed to monitor and conserve mangrove ecosystems and their associated microbial communities. These recent studies are having a global impact and we hope they will help to protect and re-establish mangrove ecosystems. PMID:24031949

Metal impacts on microbial biomass in the anoxic sediments of a contaminated lake

Energy Technology Data Exchange (ETDEWEB)

Gough, Heidi L.; Dahl, Amy L.; Nolan, Melissa A.; Gaillard, Jean-Francois; Stahl, David A.

2008-04-26

Little is known about the long-term impacts of metal contamination on the microbiota of anoxic lake sediments. In this study, we examined microbial biomass and metals (arsenic, cadmium, chromium, copper, iron, lead, manganese, and zinc) in the sediments of Lake DePue, a backwater lake located near a former zinc smelter. Sediment core samples were examined using two independent measures for microbial biomass (total microscopic counts and total phospholipid-phosphate concentrations), and for various fractions of each metal (pore water extracts, sequential extractions, and total extracts of all studied metals and zinc speciation by X-ray absorption fine structure (XAFS). Zinc concentrations were up to 1000 times higher than reported for sediments in the adjacent Illinois River, and ranged from 21,400 mg/kg near the source to 1,680 mg/kg near the river. However, solid metal fractions were not well correlated with pore water concentrations, and were not good predictors of biomass concentrations. Instead, biomass, which varied among sites by as much as two-times, was inversely correlated with concentrations of pore water zinc and arsenic as established by multiple linear regression. Monitoring of other parameters known to naturally influence biomass in sediments (e.g., organic carbon concentrations, nitrogen concentrations, pH, sediment texture, and macrophytes) revealed no differences that could explain observed biomass trends. This study provides strong support for control of microbial abundance by pore water metal concentrations in contaminated freshwater sediments.

Harnessing a methane-fueled, sediment-free mixed microbial community for utilization of distributed sources of natural gas.

Science.gov (United States)

Marlow, Jeffrey J; Kumar, Amit; Enalls, Brandon C; Reynard, Linda M; Tuross, Noreen; Stephanopoulos, Gregory; Girguis, Peter

2018-06-01

Harnessing the metabolic potential of uncultured microbial communities is a compelling opportunity for the biotechnology industry, an approach that would vastly expand the portfolio of usable feedstocks. Methane is particularly promising because it is abundant and energy-rich, yet the most efficient methane-activating metabolic pathways involve mixed communities of anaerobic methanotrophic archaea and sulfate reducing bacteria. These communities oxidize methane at high catabolic efficiency and produce chemically reduced by-products at a comparable rate and in near-stoichiometric proportion to methane consumption. These reduced compounds can be used for feedstock and downstream chemical production, and at the production rates observed in situ they are an appealing, cost-effective prospect. Notably, the microbial constituents responsible for this bioconversion are most prominent in select deep-sea sediments, and while they can be kept active at surface pressures, they have not yet been cultured in the lab. In an industrial capacity, deep-sea sediments could be periodically recovered and replenished, but the associated technical challenges and substantial costs make this an untenable approach for full-scale operations. In this study, we present a novel method for incorporating methanotrophic communities into bioindustrial processes through abstraction onto low mass, easily transportable carbon cloth artificial substrates. Using Gulf of Mexico methane seep sediment as inoculum, optimal physicochemical parameters were established for methane-oxidizing, sulfide-generating mesocosm incubations. Metabolic activity required >∼40% seawater salinity, peaking at 100% salinity and 35 °C. Microbial communities were successfully transferred to a carbon cloth substrate, and rates of methane-dependent sulfide production increased more than threefold per unit volume. Phylogenetic analyses indicated that carbon cloth-based communities were substantially streamlined and were

Tofu wastewater treatment by sediment microbial fuel cells

Science.gov (United States)

Rinaldi, W.; Abubakar; Rahmi, R. F.; Silmina

2018-03-01

This research aimed to measure power density generated by sediment microbial fuel cells (SMFCs) by varying anode position and wastewater concentration. Anode position was varied at 2 cm and 4 cm under the surface of sediment, while wastewater concentration varied into 25%, 50%, 75% and 100%. The electrodes employed was stainless steel mesh, while the organic subtrate source was taken from wastewater of soybean washing and boiling process. The sediment was taken from the Lamnyong River around the outlet of tofu industry wastewater. SMFCs was run until the power density was relatively small. The produced electricity represented in power density. The results of this research showed that power density was decreased over time. Generated power density by varying 2 cm and 4 cm position of anode under the sediment surface was not significantly different, while the lowest wastewater concentration, 25%, gave the highest power density.

Microbial diversity in oiled and un-oiled shoreline sediments in the Norwegian Arctic

International Nuclear Information System (INIS)

Grossman, M.J.; Prince, R.C.; Garrett, R.M.; Garrett, K.K.; Bare, R.E.; O'Neil, K.R.; Sowlay, M.R.; Hinton, S.M.; Lee, K.; Sergy, G.A.; Guenette, C.C.

2000-01-01

Field trials were conducted at an oiled shoreline on the island of Spitsbergen to examine the effect of nutrient addition on the metabolic status, potential for aromatic hydrocarbon degradation, and the phylogenetic diversity of the microbial community in oiled Arctic shoreline sediments. IF-30 intermediate fuel grade oil was applied to the shoreline which was then divided into four plots. One was left untreated and two were tilled. Four applications of fertilizer were applied over a two-month period. Phospholipid fatty acid (PLFA), gene probe and 16S microbial community analysis suggested that bioremediation stimulated the metabolic activity, increased microbial biomass and genetic potential for aromatic hydrocarbon degradation, and increased the population of hydrocarbon degradation of an oiled Arctic shoreline microbial community. The results of this study are in agreement with the results from stimulation of oil biodegradation in temperate marine environments. It was concluded that biodegradation and fertilizer addition are feasible treatment methods for oil spills in Arctic regions. 31 refs., 3 tabs., 3 figs

Effects of light and microbial activity on the degradation of two fluoroquinolone antibiotics in pond water and sediment.

Science.gov (United States)

Lin, Juo-Shan; Pan, Hung-Yu; Liu, Shiu-Mei; Lai, Hong-Thih

2010-07-01

Enrofloxacin (ENR) and ciprofloxacin (CIP) are two fluoroquinolone (FQ) antibiotics widely used to treat diseases of human beings and cultured animals. These two FQs are usually detected in the effluent of municipal sewage plants and related aquatic environments. The purpose of this study was to understand the fates of ENR and CIP in aquaculture pond water and a sediment slurry in a laboratory-scale experiment. Effects of light and microbial activity on the degradation of these two FQs were investigated. Results indicated that natural irradiation plays a major role in the degradation of ENR and CIP in pond water and the sediment slurry. The 50 % dissipation times (DT(50)) with non-sterile treatment were 0.01 and 18.4 d for ENR, and 0.04 and 17.3 d for CIP in the water and sediment slurry, respectively. On the other hand, the degradation of ENR and CIP under dark conditions was slow or even hindered, and all of their DT(50) values exceeded 100 d. These two FQs degraded faster in the sediment slurry than in pond water under dark conditions. Artificial ultraviolet (UV) and fluorescence light had similar effects on the degradation of ENR in the pond water and sediment slurry. Degradation of CIP was faster with UV than with fluorescence light treatment, while no such difference was found for ENR degradation. CIP was a degradation product of ENR under both light and dark conditions, and DT(50) values for both compounds were shorter in the presence of light. The phenomenon of biodegradation was observed during degradation of CIP in the sediment slurry under natural light.

Evidence of in situ microbial activity and sulphidogenesis in perennially sub-0 °C and hypersaline sediments of a high Arctic permafrost spring.

Science.gov (United States)

Lamarche-Gagnon, Guillaume; Comery, Raven; Greer, Charles W; Whyte, Lyle G

2015-01-01

The lost hammer (LH) spring perennially discharges subzero hypersaline reducing brines through thick layers of permafrost and is the only known terrestrial methane seep in frozen settings on Earth. The present study aimed to identify active microbial communities that populate the sediments of the spring outlet, and verify whether such communities vary seasonally and spatially. Microcosm experiments revealed that the biological reduction of sulfur compounds (SR) with hydrogen (e.g., sulfate reduction) was potentially carried out under combined hypersaline and subzero conditions, down to -20 °C, the coldest temperature ever recorded for SR. Pyrosequencing analyses of both 16S rRNA (i.e., cDNA) and 16S rRNA genes (i.e., DNA) of sediments retrieved in late winter and summer indicated fairly stable bacterial and archaeal communities at the phylum level. Potentially active bacterial and archaeal communities were dominated by clades related to the T78 Chloroflexi group and Halobacteria species, respectively. The present study indicated that SR, hydrogenotrophy (possibly coupled to autotrophy), and short-chain alkane degradation (other than methane), most likely represent important, previously unaccounted for, metabolic processes carried out by LH microbial communities. Overall, the obtained findings provided additional evidence that the LH system hosts active communities of anaerobic, halophilic, and cryophilic microorganisms despite the extreme conditions in situ.

Sediment microbial fuel cells for wastewater treatment: challenges and opportunities

OpenAIRE

Xu, Bojun; Ge, Zheng; He, Zhen

2015-01-01

Sediment microbial fuel cells (SMFCs) have been intensively investigated for the harvest of energy from natural sediment, but studies of their application for wastewater treatment mainly occurred in the past 2-3 years. SMFCs with simple structures can generate electrical energy while decontaminating wastewater. Most SMFCs used for wastewater treatment contain plants to mimic constructed wetlands. Both synthetic and real wastewaters have been used as substrates in SMFCs that achieved satisfact...

The Link between Microbial Diversity and Nitrogen Cycling in Marine Sediments Is Modulated by Macrofaunal Bioturbation.

Science.gov (United States)

Yazdani Foshtomi, Maryam; Braeckman, Ulrike; Derycke, Sofie; Sapp, Melanie; Van Gansbeke, Dirk; Sabbe, Koen; Willems, Anne; Vincx, Magda; Vanaverbeke, Jan

2015-01-01

The marine benthic nitrogen cycle is affected by both the presence and activity of macrofauna and the diversity of N-cycling microbes. However, integrated research simultaneously investigating macrofauna, microbes and N-cycling is lacking. We investigated spatio-temporal patterns in microbial community composition and diversity, macrofaunal abundance and their sediment reworking activity, and N-cycling in seven subtidal stations in the Southern North Sea. Our results indicated that bacteria (total and β-AOB) showed more spatio-temporal variation than archaea (total and AOA) as sedimentation of organic matter and the subsequent changes in the environment had a stronger impact on their community composition and diversity indices in our study area. However, spatio-temporal patterns of total bacterial and β-AOB communities were different and related to the availability of ammonium for the autotrophic β-AOB. Highest bacterial richness and diversity were observed in June at the timing of the phytoplankton bloom deposition, while richness of β-AOB as well as AOA peaked in September. Total archaeal community showed no temporal variation in diversity indices. Distance based linear models revealed that, independent from the effect of grain size and the quality and quantity of sediment organic matter, nitrification and N-mineralization were affected by respectively the diversity of metabolically active β-AOB and AOA, and the total bacteria, near the sediment-water interface. Separate models demonstrated a significant and independent effect of macrofaunal activities on community composition and richness of total bacteria, and diversity indices of metabolically active AOA. Diversity of β-AOB was significantly affected by macrofaunal abundance. Our results support the link between microbial biodiversity and ecosystem functioning in marine sediments, and provided broad correlative support for the hypothesis that this relationship is modulated by macrofaunal activity. We

The Link between Microbial Diversity and Nitrogen Cycling in Marine Sediments Is Modulated by Macrofaunal Bioturbation.

Directory of Open Access Journals (Sweden)

Maryam Yazdani Foshtomi

Full Text Available The marine benthic nitrogen cycle is affected by both the presence and activity of macrofauna and the diversity of N-cycling microbes. However, integrated research simultaneously investigating macrofauna, microbes and N-cycling is lacking. We investigated spatio-temporal patterns in microbial community composition and diversity, macrofaunal abundance and their sediment reworking activity, and N-cycling in seven subtidal stations in the Southern North Sea.Our results indicated that bacteria (total and β-AOB showed more spatio-temporal variation than archaea (total and AOA as sedimentation of organic matter and the subsequent changes in the environment had a stronger impact on their community composition and diversity indices in our study area. However, spatio-temporal patterns of total bacterial and β-AOB communities were different and related to the availability of ammonium for the autotrophic β-AOB. Highest bacterial richness and diversity were observed in June at the timing of the phytoplankton bloom deposition, while richness of β-AOB as well as AOA peaked in September. Total archaeal community showed no temporal variation in diversity indices.Distance based linear models revealed that, independent from the effect of grain size and the quality and quantity of sediment organic matter, nitrification and N-mineralization were affected by respectively the diversity of metabolically active β-AOB and AOA, and the total bacteria, near the sediment-water interface. Separate models demonstrated a significant and independent effect of macrofaunal activities on community composition and richness of total bacteria, and diversity indices of metabolically active AOA. Diversity of β-AOB was significantly affected by macrofaunal abundance. Our results support the link between microbial biodiversity and ecosystem functioning in marine sediments, and provided broad correlative support for the hypothesis that this relationship is modulated by macrofaunal

In-Well Sediment Incubators to Evaluate Microbial Community Stability and Dynamics following Bioimmobilization of Uranium

International Nuclear Information System (INIS)

Baldwin, Brett R.; Peacock, Aaron D.; Gan, M.; Resch, Charles T.; Arntzen, Evan V.; Smithgall, A.N.; Pfiffner, S.; Freifeld, Barry M.; White, D.C.; Long, Philip E.

2009-01-01

An in-situ incubation device (ISI) was developed in order to investigate the stability and dynamics of sediment associated microbial communities to prevailing subsurface oxidizing or reducing conditions. Here we describe the use of these devices at the Old Rifle Uranium Mill Tailings Remedial Action (UMTRA) site. During the 7 month deployment oxidized Rifle aquifer background sediments (RABS) were deployed in previously biostimulated wells under iron reducing conditions, cell densities of known iron reducing bacteria including Geobacteraceae increased significantly showing the microbial community response to local subsurface conditions. PLFA profiles of RABS following in situ deployment were strikingly similar to those of adjacent sediment cores suggesting ISI results could be extrapolated to the native material of the test plots. Results for ISI deployed reduced sediments showed only slight changes in community composition and pointed toward the ability of the ISIs to monitor microbial community stability and response to subsurface conditions.

Microbial diversity in the hydrate-containing and -free surface sediments in the Shenhu area, South China Sea

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Lu Jiao

2015-07-01

Full Text Available Microbial diversity in the hydrate-containing (sites SH3B and SH7B and -free (sites SH1B, SH5B, SH5C sediments collected from the Shenhu area of the South China Sea (SCS was investigated using 16S rRNA gene phylogenetic analysis. The phylogenetic results indicate difference in microbial communities between hydrate-containing and -free sediments. At the gas hydrate-containing sites, bacterial communities were dominated by Deltaproteobacteria (30.5%, and archaeal communities were dominated by Miscellaneous Crenarchaeotic Group (33.8%; In contrast, Planctomycetes was the major group (43.9% in bacterial communities, while Marine Benthic Group-D (MBG-D (32.4% took up the largest proportion in the archaeal communities. Moreover, the microbial communities have characteristics different from those in other hydrate-related sediments around the world, indicating that the presence of hydrates can affect the microbial distribution. In addition, the microbial community composition in the studied sediments has its own uniqueness, which may result from co-effect of geochemical characteristics and presence/absence of hydrate.

Diversity and function of the microbial community on anodes of sediment microbial fuel cells fueled by root exudates

Energy Technology Data Exchange (ETDEWEB)

Cabezas da Rosa, Angela

2010-11-26

our study on identifying the bacteria capable of rice root exudate assimilation on anodes of planted SMFCs. Using stable isotope probing (SIP) with {sup 13}C-CO{sub 2} combined with high throughput sequencing, we detected that labeled bacteria belonged to {beta}-proteobacteria and Anaerolineae indicating their relevance in root exudate degradation. The main current producing bacteria, belonging to {delta}-proteobacteria were not able to assimilate root exudates. A microbial ''food chain'' combining activities of anode reducing bacteria with root exudate degrading bacteria is necessary for current production. However, we cannot dismiss the possibility that some bacteria might be able to directly use root exudates for current production. In the last part, we found that by submerging an anode into rice field soil up to 50% methane emission was reduced compared with open circuit controls. This mitigation could not only be explained by competition for common electron donors like acetate. We suggest that the anode, even in non-current controls, can be used as electron acceptor capturing electrons and transferring them from one part of the sediment to a spatially distant one, communicating biogeochemical processes occurring in different parts of the sediment. Our work is a first approach in understanding the microbial diversity on anodes of SMFCs fueled by rice root exudation and their potential as methane emission mitigation strategy. (orig.)

Potential sources of hydrocarbons and their microbial degradation in sediments from the deep geothermal Lusi site, Indonesia

Science.gov (United States)

Krueger, Martin; Mazzini, Adriano; Scheeder, Georg; Blumenberg, Martin

2017-04-01

The Lusi eruption represents one of the largest ongoing sedimentary hosted geothermal systems, which started in 2006 following an earthquake on Java Island. Since then it has been continuously producing hot and hydrocarbon rich mud from a central crater with peaks reaching 180.000 m3 per day. Numerous investigations focused on the study of microbial communities which thrive at offshore methane and oil seeps and mud volcanoes, however very little has been done on onshore seeping structures. Lusi represents a unique opportunity to complete a comprehensive study of onshore microbial communities fed by the seepage of CH4 as well as of liquid hydrocarbons originating from one or more km below the surface. While the source of the methane at Lusi is unambiuous, the origin of the seeping oil is still discussed. Both, source and maturity estimates from biomarkers, are in favor of a type II/III organic matter source. Likely the oils were formed from the studied black shales (deeper Ngimbang Fm.) which contained a Type III component in the Type II predominated organic matter. In all samples large numbers of active microorganisms were present. Rates for aerobic methane oxidation were high, as was the potential of the microbial communities to degrade different hydrocarbons. The data suggests a transition of microbial populations from an anaerobic, hydrocarbon-driven metabolism in fresher samples from center or from small seeps to more generalistic, aerobic microbial communities in older, more consolidated sediments. Ongoing microbial activity in crater sediment samples under high temperatures (80-95C) indicate a deep origin of the involved microorganisms. First results of molecular analyses of the microbial community compositions confirm the above findings. This study represents an initial step to better understand onshore seepage systems and provides an ideal analogue for comparison with the better investigated offshore structures.

Microbial processes and communities in sediment samples along a transect across the Lusi mud volcano, Indonesia

Science.gov (United States)

Krueger, Martin; Straaten, Nontje; Mazzini, Adriano

2015-04-01

The Lusi eruption represents one of the largest ongoing sedimentary hosted geothermal systems. This eruption started in 2006 following to a 6.3 M earthquake that stroke Java Island. Since then it has been spewing boiling mud from a central crater with peaks reaching 180.000 m3 per day. Today an area of about 8 km2 is covered by locally dried mud breccia where a network of hundreds of satellite seeping pools is active. Numerous investigations focused on the study of offshore microbial colonies that commonly thrive at offshore methane seeps and mud volcanoes, however very little has been done for onshore seeping structures. Lusi represents a unique opportunity to complete a comprehensive study of onshore microbial communities fed by the seepage of CH4 and CO2 as well as of heavier liquid hydrocarbons originating from several km below the surface. We conducted a sampling campaign at the Lusi site collecting samples of fresh mud close to the erupting crater using a remote controlled drone. In addition we completed a transect towards outer parts of the crater to collect older, weathered samples for comparison. In all samples active microorganisms were present. The highest activities for CO2 and CH4 production as well as for CH4 oxidation and hydrocarbon degradation were observed in medium-age mud samples collected roughly in the middle of the transect. Rates for aerobic methane oxidation were high, as was the potential of the microbial communities to degrade hydrocarbons (oils, alkanes, BTEX tested). The data suggests a transition of microbial populations from an anaerobic, hydrocarbon-driven metabolism in fresher samples from center or from small seeps to more generalistic, aerobic microbial communities in older, more consolidated sediments. Currently, the microbial communities in the different sediment samples are analyzed using quantitative PCR and T-RFLP combined with MiSeq sequencing. This study represents an initial step to better understand onshore seepage

Exploring the Impacts of Anthropogenic Disturbance on Seawater and Sediment Microbial Communities in Korean Coastal Waters Using Metagenomics Analysis

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Nam-Il Won

2017-01-01

Full Text Available The coastal ecosystems are considered as one of the most dynamic and vulnerable environments under various anthropogenic developments and the effects of climate change. Variations in the composition and diversity of microbial communities may be a good indicator for determining whether the marine ecosystems are affected by complex forcing stressors. DNA sequence-based metagenomics has recently emerged as a promising tool for analyzing the structure and diversity of microbial communities based on environmental DNA (eDNA. However, few studies have so far been performed using this approach to assess the impacts of human activities on the microbial communities in marine systems. In this study, using metagenomic DNA sequencing (16S ribosomal RNA gene, we analyzed and compared seawater and sediment communities between sand mining and control (natural sites in southern coastal waters of Korea to assess whether anthropogenic activities have significantly affected the microbial communities. The sand mining sites harbored considerably lower levels of microbial diversities in the surface seawater community during spring compared with control sites. Moreover, the sand mining areas had distinct microbial taxonomic group compositions, particularly during spring season. The microbial groups detected solely in the sediment load/dredging areas (e.g., Marinobacter, Alcanivorax, Novosphingobium are known to be involved in degradation of toxic chemicals such as hydrocarbon, oil, and aromatic compounds, and they also contain potential pathogens. This study highlights the versatility of metagenomics in monitoring and diagnosing the impacts of human disturbance on the environmental health of marine ecosystems from eDNA.

Microbial diversity in methane hydrate-bearing deep marine sediments core preserved in the original pressure.

Science.gov (United States)

Takahashi, Y.; Hata, T.; Nishida, H.

2017-12-01

In normal coring of deep marine sediments, the sampled cores are exposed to the pressure of the atmosphere, which results in dissociation of gas-hydrates and might change microbial diversity. In this study, we analyzed microbial composition in methane hydrate-bearing sediment core sampled and preserved by Hybrid-PCS (Pressure Coring System). We sliced core into three layers; (i) outside layer, which were most affected by drilling fluids, (ii) middle layer, and (iii) inner layer, which were expected to be most preserved as the original state. From each layer, we directly extracted DNA, and amplified V3-V4 region of 16S rRNA gene. We determined at least 5000 of nucleotide sequences of the partial 16S rDNA from each layer by Miseq (Illumina). In the all layers, facultative anaerobes, which can grow with or without oxygen because they can metabolize energy aerobically or anaerobically, were detected as majority. However, the genera which are often detected anaerobic environment is abundant in the inner layer compared to the outside layer, indicating that condition of drilling and preservation affect the microbial composition in the deep marine sediment core. This study was conducted as a part of the activity of the Research Consortium for Methane Hydrate Resources in Japan [MH21 consortium], and supported by JOGMEC (Japan Oil, Gas and Metals National Corporation). The sample was provided by AIST (National Institute of Advanced Industrial Science and Technology).

Influence of Wastewater Discharge on the Metabolic Potential of the Microbial Community in River Sediments.

Science.gov (United States)

Li, Dong; Sharp, Jonathan O; Drewes, Jörg E

2016-01-01

To reveal the variation of microbial community functions during water filtration process in river sediments, which has been utilized widely in natural water treatment systems, this study investigates the influence of municipal wastewater discharge to streams on the phylotype and metabolic potential of the microbiome in upstream and particularly various depths of downstream river sediments. Cluster analyses based on both microbial phylogenetic and functional data collectively revealed that shallow upstream sediments grouped with those from deeper subsurface downstream regions. These sediment samples were distinct from those found in shallow downstream sediments. Functional genes associated with carbohydrate, xenobiotic, and certain amino acid metabolisms were overrepresented in upstream and deep downstream samples. In contrast, the more immediate contact with wastewater discharge in shallow downstream samples resulted in an increase in the relative abundance of genes associated with nitrogen, sulfur, purine and pyrimidine metabolisms, as well as restriction-modification systems. More diverse bacterial phyla were associated with upstream and deep downstream sediments, mainly including Actinobacteria, Planctomycetes, and Firmicutes. In contrast, in shallow downstream sediments, genera affiliated with Betaproteobacteria and Gammaproteobacteria were enriched with putative functions that included ammonia and sulfur oxidation, polyphosphate accumulation, and methylotrophic bacteria. Collectively, these results highlight the enhanced capabilities of microbial communities residing in deeper stream sediments for the transformation of water contaminants and thus provide a foundation for better design of natural water treatment systems to further improve the removal of contaminants.

Analysis of effect of nicotine on microbial community structure in sediment using PCR-DGGE fingerprinting

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Ai-dong Ruan

2015-10-01

Full Text Available Solid or liquid waste containing a high concentration of nicotine can pollute sediment in rivers and lakes, and may destroy the ecological balance if it is directly discharged into the environment without any treatment. In this study, the polymerase chain reaction (PCR and denaturing gradient gel electrophoresis (DGGE method was used to analyze the variation of the microbial community structure in the control and nicotine-contaminated sediment samples with nicotine concentration and time of exposure. The results demonstrated that the growth of some bacterial species in the nicotine-contaminated sediment samples was inhibited during the exposure. Some bacteria decreased in species diversity and in quantity with the increase of nicotine concentration or time of exposure, while other bacteria were enriched under the effect of nicotine, and their DGGE bands changed from undertones to deep colors. The microbial community structure, however, showed a wide variation in the nicotine-contaminated sediment samples, especially in the sediment samples treated with high-concentration nicotine. The Jaccard index was only 35.1% between the initial sediment sample and the sediment sample with a nicotine concentration of 0.030 μg/g after 28 d of exposure. Diversity indices showed that the contaminated groups had a similar trend over time. The diversity indices of contaminated groups all decreased in the first 7 d after exposure, then increased until day 42. It has been found that nicotine decreased the diversity of the microbial community in the sediment.

Analysis of effect of nicotine on microbial community structure in sediment using PCR-DGGE fingerprinting

Directory of Open Access Journals (Sweden)

Ai-dong Ruan

2015-10-01

Full Text Available Solid or liquid waste containing a high concentration of nicotine can pollute sediment in rivers and lakes, and may destroy the ecological balance if it is directly discharged into the environment without any treatment. In this study, the polymerase chain reaction (PCR and denaturing gradient gel electrophoresis (DGGE method was used to analyze the variation of the microbial community structure in the control and nicotine-contaminated sediment samples with nicotine concentration and time of exposure. The results demonstrated that the growth of some bacterial species in the nicotine-contaminated sediment samples was inhibited during the exposure. Some bacteria decreased in species diversity and in quantity with the increase of nicotine concentration or time of exposure, while other bacteria were enriched under the effect of nicotine, and their DGGE bands changed from undertones to deep colors. The microbial community structure, however, showed a wide variation in the nicotine-contaminated sediment samples, especially in the sediment samples treated with high-concentration nicotine. The Jaccard index was only 35.1% between the initial sediment sample and the sediment sample with a nicotine concentration of 0.030 μg/g after 28 d of exposure. Diversity indices showed that the contaminated groups had a similar trend over time. The diversity indices of contaminated groups all decreased in the first 7 d after exposure, then increased until day 42. It has been found that nicotine decreased the diversity of the microbial community in the sediment.

Influence of Wastewater Discharge on the Metabolic Potential of the Microbial Community in River Sediments

KAUST Repository

Li, Dong

2015-09-24

To reveal the variation of microbial community functions during water filtration process in river sediments, which has been utilized widely in natural water treatment systems, this study investigates the influence of municipal wastewater discharge to streams on the phylotype and metabolic potential of the microbiome in upstream and particularly various depths of downstream river sediments. Cluster analyses based on both microbial phylogenetic and functional data collectively revealed that shallow upstream sediments grouped with those from deeper subsurface downstream regions. These sediment samples were distinct from those found in shallow downstream sediments. Functional genes associated with carbohydrate, xenobiotic, and certain amino acid metabolisms were overrepresented in upstream and deep downstream samples. In contrast, the more immediate contact with wastewater discharge in shallow downstream samples resulted in an increase in the relative abundance of genes associated with nitrogen, sulfur, purine and pyrimidine metabolisms, as well as restriction–modification systems. More diverse bacterial phyla were associated with upstream and deep downstream sediments, mainly including Actinobacteria, Planctomycetes, and Firmicutes. In contrast, in shallow downstream sediments, genera affiliated with Betaproteobacteria and Gammaproteobacteria were enriched with putative functions that included ammonia and sulfur oxidation, polyphosphate accumulation, and methylotrophic bacteria. Collectively, these results highlight the enhanced capabilities of microbial communities residing in deeper stream sediments for the transformation of water contaminants and thus provide a foundation for better design of natural water treatment systems to further improve the removal of contaminants. © 2015, Springer Science+Business Media New York.

Nitrogen cycling processes and microbial community composition in bed sediments in the Yukon River at Pilot Station

Science.gov (United States)

Repert, Deborah A.; Underwood, Jennifer C.; Smith, Richard L.; Song, Bongkeun

2014-01-01

Information on the contribution of nitrogen (N)-cycling processes in bed sediments to river nutrient fluxes in large northern latitude river systems is limited. This study examined the relationship between N-cycling processes in bed sediments and N speciation and loading in the Yukon River near its mouth at the Bering Sea. We conducted laboratory bioassays to measure N-cycling processes in sediment samples collected over distinct water cycle seasons. In conjunction, the microbial community composition in the bed sediments using genes involved in N-cycling (narG, napA, nosZ, and amoA) and 16S rRNA gene pyrosequences was examined. Temporal variation was observed in net N mineralization, nitrate uptake, and denitrification rate potentials and correlated strongly with sediment carbon (C) and extractable N content and microbial community composition rather than with river water nutrient concentrations. The C content of the bed sediment was notably impacted by the spring flood, ranging from 1.1% in the midst of an ice-jam to 0.1% immediately after ice-out, suggesting a buildup of organic material (OM) prior to scouring of the bed sediments during ice break up. The dominant members of the microbial community that explained differences in N-processing rates belonged to the genera Crenothrix,Flavobacterium, and the family of Comamonadaceae. Our results suggest that biogeochemical processing rates in the bed sediments appear to be more coupled to hydrology, nutrient availability in the sediments, and microbial community composition rather than river nutrient concentrations at Pilot Station.

CoBOP: Microbial Biofilms: A Parameter Altering the Apparent Optical Properties of Sediments, Seagrasses and Surfaces

Science.gov (United States)

2002-09-30

CoBOP: Microbial Biofilms: A Parameter Altering the Apparent Optical Properties of Sediments, Seagrasses and Surfaces Alan W. Decho Department...TITLE AND SUBTITLE CoBOP: Microbial Biofilms: A Parameter Altering the Apparent Optical Properties of Sediments, Seagrasses and Surfaces 5a. CONTRACT...structures produced by bacteria. Their growth appears to depend on biofilm processes and light distributions ( photosynthesis ). Therefore, the data acquired

Seasonal Changes in Microbial Community Structure in Freshwater Stream Sediment in a North Carolina River Basin

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John P. Bucci

2014-01-01

Full Text Available This study examined seasonal differences in microbial community structure in the sediment of three streams in North Carolina’s Neuse River Basin. Microbes that reside in sediment are at the base of the food chain and have a profound influence on the health of freshwater stream environments. Terminal-Restriction Fragment Length Polymorphism (T-RFLP, molecular fingerprint analysis of 16S rRNA genes was used to examine the diversity of bacterial species in stream sediment. Sediment was sampled in both wet and dry seasons from an agricultural (Bear, mixed urban (Crabtree and forested (Marks Creek, and the microbiota examined. Gamma, Alpha and Beta proteobacteria were prevalent species of microbial taxa represented among all sites. Actinobacteria was the next most prevalent species observed, with greater occurrence in dry compared to the wet season. Discernable clustering was observed of Marks and Bear Creek samples collected during the wetter period (September–April, which corresponded with a period of higher precipitation and cooler surface water temperatures. Although not statistically significant, microbial community structure appeared different between season (ANOSIM, R = 0.60; p < 0.10. Principal components analysis confirmed this pattern and showed that the bacterial groups were separated by wet and dry seasonal periods. These results suggest seasonal differences among the microbial community structure in sediment of freshwater streams and that these communities may respond to changes in precipitation during wetter periods.

Metal-macrofauna interactions determine microbial community structure and function in copper contaminated sediments.

Science.gov (United States)

Mayor, Daniel J; Gray, Nia B; Elver-Evans, Joanna; Midwood, Andrew J; Thornton, Barry

2013-01-01

Copper is essential for healthy cellular functioning, but this heavy metal quickly becomes toxic when supply exceeds demand. Marine sediments receive widespread and increasing levels of copper contamination from antifouling paints owing to the 2008 global ban of organotin-based products. The toxicity of copper will increase in the coming years as seawater pH decreases and temperature increases. We used a factorial mesocosm experiment to investigate how increasing sediment copper concentrations and the presence of a cosmopolitan bioturbating amphipod, Corophium volutator, affected a range of ecosystem functions in a soft sediment microbial community. The effects of copper on benthic nutrient release, bacterial biomass, microbial community structure and the isotopic composition of individual microbial membrane [phospholipid] fatty acids (PLFAs) all differed in the presence of C. volutator. Our data consistently demonstrate that copper contamination of global waterways will have pervasive effects on the metabolic functioning of benthic communities that cannot be predicted from copper concentrations alone; impacts will depend upon the resident macrofauna and their capacity for bioturbation. This finding poses a major challenge for those attempting to manage the impacts of copper contamination on ecosystem services, e.g. carbon and nutrient cycling, across different habitats. Our work also highlights the paucity of information on the processes that result in isotopic fractionation in natural marine microbial communities. We conclude that the assimilative capacity of benthic microbes will become progressively impaired as copper concentrations increase. These effects will, to an extent, be mitigated by the presence of bioturbating animals and possibly other processes that increase the influx of oxygenated seawater into the sediments. Our findings support the move towards an ecosystem approach for environmental management.

Metal-macrofauna interactions determine microbial community structure and function in copper contaminated sediments.

Directory of Open Access Journals (Sweden)

Daniel J Mayor

Full Text Available Copper is essential for healthy cellular functioning, but this heavy metal quickly becomes toxic when supply exceeds demand. Marine sediments receive widespread and increasing levels of copper contamination from antifouling paints owing to the 2008 global ban of organotin-based products. The toxicity of copper will increase in the coming years as seawater pH decreases and temperature increases. We used a factorial mesocosm experiment to investigate how increasing sediment copper concentrations and the presence of a cosmopolitan bioturbating amphipod, Corophium volutator, affected a range of ecosystem functions in a soft sediment microbial community. The effects of copper on benthic nutrient release, bacterial biomass, microbial community structure and the isotopic composition of individual microbial membrane [phospholipid] fatty acids (PLFAs all differed in the presence of C. volutator. Our data consistently demonstrate that copper contamination of global waterways will have pervasive effects on the metabolic functioning of benthic communities that cannot be predicted from copper concentrations alone; impacts will depend upon the resident macrofauna and their capacity for bioturbation. This finding poses a major challenge for those attempting to manage the impacts of copper contamination on ecosystem services, e.g. carbon and nutrient cycling, across different habitats. Our work also highlights the paucity of information on the processes that result in isotopic fractionation in natural marine microbial communities. We conclude that the assimilative capacity of benthic microbes will become progressively impaired as copper concentrations increase. These effects will, to an extent, be mitigated by the presence of bioturbating animals and possibly other processes that increase the influx of oxygenated seawater into the sediments. Our findings support the move towards an ecosystem approach for environmental management.

Water level changes affect carbon turnover and microbial community composition in lake sediments.

Science.gov (United States)

Weise, Lukas; Ulrich, Andreas; Moreano, Matilde; Gessler, Arthur; Kayler, Zachary E; Steger, Kristin; Zeller, Bernd; Rudolph, Kristin; Knezevic-Jaric, Jelena; Premke, Katrin

2016-05-01

Due to climate change, many lakes in Europe will be subject to higher variability of hydrological characteristics in their littoral zones. These different hydrological regimes might affect the use of allochthonous and autochthonous carbon sources. We used sandy sediment microcosms to examine the effects of different hydrological regimes (wet, desiccating, and wet-desiccation cycles) on carbon turnover. (13)C-labelled particulate organic carbon was used to trace and estimate carbon uptake into bacterial biomass (via phospholipid fatty acids) and respiration. Microbial community changes were monitored by combining DNA- and RNA-based real-time PCR quantification and terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA. The shifting hydrological regimes in the sediment primarily caused two linked microbial effects: changes in the use of available organic carbon and community composition changes. Drying sediments yielded the highest CO2 emission rates, whereas hydrological shifts increased the uptake of allochthonous organic carbon for respiration. T-RFLP patterns demonstrated that only the most extreme hydrological changes induced a significant shift in the active and total bacterial communities. As current scenarios of climate change predict an increase of drought events, frequent variations of the hydrological regimes of many lake littoral zones in central Europe are anticipated. Based on the results of our study, this phenomenon may increase the intensity and amplitude in rates of allochthonous organic carbon uptake and CO2 emissions. © FEMS 2016.

Salinity shapes microbial diversity and community structure in surface sediments of the Qinghai-Tibetan Lakes.

Science.gov (United States)

Yang, Jian; Ma, Li'an; Jiang, Hongchen; Wu, Geng; Dong, Hailiang

2016-04-26

Investigating microbial response to environmental variables is of great importance for understanding of microbial acclimatization and evolution in natural environments. However, little is known about how microbial communities responded to environmental factors (e.g. salinity, geographic distance) in lake surface sediments of the Qinghai-Tibetan Plateau (QTP). In this study, microbial diversity and community structure in the surface sediments of nine lakes on the QTP were investigated by using the Illumina Miseq sequencing technique and the resulting microbial data were statistically analyzed in combination with environmental variables. The results showed total microbial community of the studied lakes was significantly correlated (r = 0.631, P diversity and community structure in the studied samples. In addition, the abundant and rare taxa (OTUs with relative abundance higher than 1% and lower than 0.01% within one sample, respectively) were significantly (P < 0.05) correlated (r = 0.427 and 0.783, respectively) with salinity, suggesting rare taxa might be more sensitive to salinity than their abundant counterparts, thus cautions should be taken in future when evaluating microbial response (abundant vs. rare sub-communities) to environmental conditions.

Mineralization of PAHs in coal-tar impacted aquifer sediments and associated microbial community structure investigated with FISH

Energy Technology Data Exchange (ETDEWEB)

Rogers, S W; Ong, S K; Moorman, T B [Iowa State University, Ames, IA (USA)

2007-11-15

The microbial community structure and mineralization of polycyclic aromatic hydrocarbons (PAHs) in a coal-tar contaminated aquifer were investigated spatially using fluorescence in situ hybridization (FISH) and in laboratory-scale incubations of the aquifer sediments. DAPI-detected microbial populations in the contaminated sediments were three orders of magnitude greater than nearby uncontaminated sediments, suggesting growth on coal-tar constituents in situ. Actinobacteria, {beta}- and {gamma}-Proteobacteria, and Flavobacteria dominated the in situ aerobic (> 1 mg l{sup -1} dissolved oxygen) microbial community, whereas sulfate-reducing bacteria comprised 37% of the microbial community in the sulfidogenic region of the aquifer. Rapid mineralization of naphthalene and phenanthrene were observed in aerobic laboratory microcosms and resulted in significant enrichment of {beta}- and {gamma}-Proteobacteria potentially explaining their elevated presence in situ. Nitrate- and sulfate-limited mineralization of naphthalene in laboratory microcosms occurred to a small degree in aquifer sediments from locations where groundwater chemistry indicated nitrate- and sulfate-reduction, respectively. The results of this study suggest that FISH may be a useful tool for providing a link between laboratory microcosms and groundwater measurements made in situ necessary to better demonstrate the potential for natural attenuation at complex PAH contaminated sites.

Structural stability, microbial biomass and community composition of sediments affected by the hydric dynamics of an urban stormwater infiltration basin. Dynamics of physical and microbial characteristics of stormwater sediment.

Science.gov (United States)

Badin, Anne Laure; Monier, Armelle; Volatier, Laurence; Geremia, Roberto A; Delolme, Cécile; Bedell, Jean-Philippe

2011-05-01

The sedimentary layer deposited at the surface of stormwater infiltration basins is highly organic and multicontaminated. It undergoes considerable moisture content fluctuations due to the drying and inundation cycles (called hydric dynamics) of these basins. Little is known about the microflora of the sediments and its dynamics; hence, the purpose of this study is to describe the physicochemical and biological characteristics of the sediments at different hydric statuses of the infiltration basin. Sediments were sampled at five time points following rain events and dry periods. They were characterized by physical (aggregation), chemical (nutrients and heavy metals), and biological (total, bacterial and fungal biomasses, and genotypic fingerprints of total bacterial and fungal communities) parameters. Data were processed using statistical analyses which indicated that heavy metal (1,841 μg/g dry weight (DW)) and organic matter (11%) remained stable through time. By contrast, aggregation, nutrient content (NH₄⁺, 53-717 μg/g DW), pH (6.9-7.4), and biological parameters were shown to vary with sediment water content and sediment biomass, and were higher consecutive to stormwater flows into the basin (up to 7 mg C/g DW) than during dry periods (0.6 mg C/g DW). Coinertia analysis revealed that the structure of the bacterial communities is driven by the hydric dynamics of the infiltration basin, although no such trend was found for fungal communities. Hydric dynamics more than rain events appear to be more relevant for explaining variations of aggregation, microbial biomass, and shift in the microbial community composition. We concluded that the hydric dynamics of stormwater infiltration basins greatly affects the structural stability of the sedimentary layer, the biomass of the microbial community living in it and its dynamics. The decrease in aggregation consecutive to rewetting probably enhances access to organic matter (OM), explaining the consecutive release

Spatial structure and activity of sedimentary microbial communities underlying a Beggiatoa spp. mat in a Gulf of Mexico hydrocarbon seep.

Directory of Open Access Journals (Sweden)

Karen G Lloyd

Full Text Available BACKGROUND: Subsurface fluids from deep-sea hydrocarbon seeps undergo methane- and sulfur-cycling microbial transformations near the sediment surface. Hydrocarbon seep habitats are naturally patchy, with a mosaic of active seep sediments and non-seep sediments. Microbial community shifts and changing activity patterns on small spatial scales from seep to non-seep sediment remain to be examined in a comprehensive habitat study. METHODOLOGY/PRINCIPAL FINDINGS: We conducted a transect of biogeochemical measurements and gene expression related to methane- and sulfur-cycling at different sediment depths across a broad Beggiatoa spp. mat at Mississippi Canyon 118 (MC118 in the Gulf of Mexico. High process rates within the mat ( approximately 400 cm and approximately 10 cm from the mat's edge contrasted with sharply diminished activity at approximately 50 cm outside the mat, as shown by sulfate and methane concentration profiles, radiotracer rates of sulfate reduction and methane oxidation, and stable carbon isotopes. Likewise, 16S ribosomal rRNA, dsrAB (dissimilatory sulfite reductase and mcrA (methyl coenzyme M reductase mRNA transcripts of sulfate-reducing bacteria (Desulfobacteraceae and Desulfobulbaceae and methane-cycling archaea (ANME-1 and ANME-2 were prevalent at the sediment surface under the mat and at its edge. Outside the mat at the surface, 16S rRNA sequences indicated mostly aerobes commonly found in seawater. The seep-related communities persisted at 12-20 cm depth inside and outside the mat. 16S rRNA transcripts and V6-tags reveal that bacterial and archaeal diversity underneath the mat are similar to each other, in contrast to oxic or microoxic habitats that have higher bacterial diversity. CONCLUSIONS/SIGNIFICANCE: The visual patchiness of microbial mats reflects sharp discontinuities in microbial community structure and activity over sub-meter spatial scales; these discontinuities have to be taken into account in geochemical and

A comparison of microbial communities in deep-sea polymetallic nodules and the surrounding sediments in the Pacific Ocean

Science.gov (United States)

Wu, Yue-Hong; Liao, Li; Wang, Chun-Sheng; Ma, Wei-Lin; Meng, Fan-Xu; Wu, Min; Xu, Xue-Wei

2013-09-01

Deep-sea polymetallic nodules, rich in metals such as Fe, Mn, and Ni, are potential resources for future exploitation. Early culturing and microscopy studies suggest that polymetallic nodules are at least partially biogenic. To understand the microbial communities in this environment, we compared microbial community composition and diversity inside nodules and in the surrounding sediments. Three sampling sites in the Pacific Ocean containing polymetallic nodules were used for culture-independent investigations of microbial diversity. A total of 1013 near full-length bacterial 16S rRNA gene sequences and 640 archaeal 16S rRNA gene sequences with ~650 bp from nodules and the surrounding sediments were analyzed. Bacteria showed higher diversity than archaea. Interestingly, sediments contained more diverse bacterial communities than nodules, while the opposite was detected for archaea. Bacterial communities tend to be mostly unique to sediments or nodules, with only 13.3% of sequences shared. The most abundant bacterial groups detected only in nodules were Pseudoalteromonas and Alteromonas, which were predicted to play a role in building matrix outside cells to induce or control mineralization. However, archaeal communities were mostly shared between sediments and nodules, including the most abundant OTU containing 290 sequences from marine group I Thaumarchaeota. PcoA analysis indicated that microhabitat (i.e., nodule or sediment) seemed to be a major factor influencing microbial community composition, rather than sampling locations or distances between locations.

Microbial activity in the marine deep biosphere: progress and prospects.

Science.gov (United States)

Orcutt, Beth N; Larowe, Douglas E; Biddle, Jennifer F; Colwell, Frederick S; Glazer, Brian T; Reese, Brandi Kiel; Kirkpatrick, John B; Lapham, Laura L; Mills, Heath J; Sylvan, Jason B; Wankel, Scott D; Wheat, C Geoff

2013-01-01

The vast marine deep biosphere consists of microbial habitats within sediment, pore waters, upper basaltic crust and the fluids that circulate throughout it. A wide range of temperature, pressure, pH, and electron donor and acceptor conditions exists-all of which can combine to affect carbon and nutrient cycling and result in gradients on spatial scales ranging from millimeters to kilometers. Diverse and mostly uncharacterized microorganisms live in these habitats, and potentially play a role in mediating global scale biogeochemical processes. Quantifying the rates at which microbial activity in the subsurface occurs is a challenging endeavor, yet developing an understanding of these rates is essential to determine the impact of subsurface life on Earth's global biogeochemical cycles, and for understanding how microorganisms in these "extreme" environments survive (or even thrive). Here, we synthesize recent advances and discoveries pertaining to microbial activity in the marine deep subsurface, and we highlight topics about which there is still little understanding and suggest potential paths forward to address them. This publication is the result of a workshop held in August 2012 by the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI) "theme team" on microbial activity (www.darkenergybiosphere.org).

Sediment nitrogen cycling rates and microbial abundance along a submerged vegetation gradient in a eutrophic lake.

Science.gov (United States)

Yao, Lu; Chen, Chengrong; Liu, Guihua; Liu, Wenzhi

2018-03-01

Decline of submerged vegetation is one of the most serious ecological problems in eutrophic lakes worldwide. Although restoration of submerged vegetation is widely assumed to enhance ecological functions (e.g., nitrogen removal) and aquatic biodiversity, the evidence for this assumption is very limited. Here, we investigated the spatio-temporal patterns of sediment potential nitrification, unamended denitrification and N 2 O production rates along a vegetation gradient in the Lake Honghu, where submerged vegetation was largely restored by prohibiting net-pen aquaculture. We also used five functional genes as markers to quantify the abundance of sediment nitrifying and denitrifying microorganisms. Results showed that unvegetated sediments supported greater nitrification rates than rhizosphere sediments of perennial or seasonal vegetation. However, the absence of submerged vegetation had no significant effect on denitrification and N 2 O production rates. Additionally, the abundance of functional microorganisms in sediments was not significantly different among vegetation types. Season had a strong effect on both nitrogen cycling processes and microbial abundances. The highest nitrification rates were observed in September, while the highest denitrification rates occurred in December. The temporal variation of sediment nitrification, denitrification and N 2 O production rates could be due to changes in water quality and sediment properties rather than submerged vegetation and microbial abundances. Our findings highlight that vegetation restoration in eutrophic lakes improves water quality but does not enhance sediment nitrogen removal rates and microbial abundances. Therefore, for reducing the N level in eutrophic lakes, major efforts should be made to control nutrients export from terrestrial ecosystems. Copyright © 2017 Elsevier B.V. All rights reserved.

Adaption of the microbial community to continuous exposures of multiple residual antibiotics in sediments from a salt-water aquacultural farm.

Science.gov (United States)

Xi, Xiuping; Wang, Min; Chen, Yongshan; Yu, Shen; Hong, Youwei; Ma, Jun; Wu, Qian; Lin, Qiaoyin; Xu, Xiangrong

2015-06-15

Residual antibiotics from aquacultural farming may alter microbial community structure in aquatic environments in ways that may adversely or positively impact microbially-mediated ecological functions. This study investigated 26 ponds (26 composited samples) used to produce fish, razor clam and shrimp (farming and drying) and 2 channels (10 samples) in a saltwater aquacultural farm in southern China to characterize microbial community structure (represented by phospholipid fatty acids) in surface sediments (0-10 cm) with long-term exposure to residual antibiotics. 11 out of 14 widely-used antibiotics were quantifiable at μg kg(-1) levels in sediments but their concentrations did not statistically differ among ponds and channels, except norfloxacin in drying shrimp ponds and thiamphenicol in razor clam ponds. Concentrations of protozoan PLFAs were significantly increased in sediments from razor clam ponds while other microbial groups were similar among ponds and channels. Both canonical-correlation and stepwise-multiple-regression analyses on microbial community and residual antibiotics suggested that roxithromycin residuals were significantly related to shifts in microbial community structure in sediments. This study provided field evidence that multiple residual antibiotics at low environmental levels from aquacultural farming do not produce fundamental shifts in microbial community structure. Copyright © 2015 Elsevier B.V. All rights reserved.

High arsenic (As concentrations in the shallow groundwaters of southern Louisiana: Evidence of microbial controls on As mobilization from sediments

Directory of Open Access Journals (Sweden)

Ningfang Yang

2016-03-01

Full Text Available Study region: The Mississippi Delta in southern Louisiana, United States. Study focus: The probable role that microbial respiration plays in As release from the shallow aquifer sediments. New hydrological insights for the region: Shallow groundwaters in southern Louisiana have been reported to contain elevated As concentrations, whereas mechanisms responsible for As release from sediments have rarely been studied in this region. Microbial respiration is generally considered the main mechanism controlling As release in reducing anoxic aquifers such as the shallow aquifers in southern Louisiana and those of the Bengal basin. This study investigates the role microbial respiration plays in As release from shallow aquifer sediments in southern Louisiana through sediment incubation experiments and porewater analysis. Arsenic concentrations were the lowest in the sterilized control experiments, slightly higher in the un-amended experiments, and the highest in the experiments amended with acetate, and especially those amended with both acetate and AQDS (9,10-anthraquinone-2,6-disulfonic acid. Although Fe and Mn generally decreased at the beginning of all the experiments, they did follow a similar trend to As after the decrease. Porewater analysis showed that As and Fe concentrations were generally positively correlated and were higher in the coarse-grained sediments than in the fine-grained sediments. Results of the investigation are consistent with microbial respiration playing a key role in As release from the shallow aquifers sediments in southern Louisiana. Keywords: Groundwater, Arsenic, Microbial respiration

Shifts in coastal sediment oxygenation cause pronounced changes in microbial community composition and associated metabolism

DEFF Research Database (Denmark)

Broman, Elias; Sjöstedt, Johanna; Pinhassi, Jarone

2017-01-01

. In particular, the intermediate site sediments responded differently upon oxygenation compared to the anoxic and oxic site sediments. This included a microbial community composition with more habitat generalists, lower amounts of RNA transcripts attributed to methane oxidation, and a reduced rate of organic...... efforts, depend largely on the oxygenation history of sites. Furthermore, it was shown that re-oxygenation efforts to remediate dead zones could ultimately be facilitated by in situ microbial molecular mechanisms involved in removal of toxic H2S and the potent greenhouse gas methane....

Final report - Microbial pathways for the reduction of mercury in saturated subsurface sediments

Energy Technology Data Exchange (ETDEWEB)

Tamar barkay; Lily Young; Gerben Zylstra

2009-08-25

Mercury is a component of mixed wastes that have contaminated vast areas of the deep subsurface as a result of nuclear weapon and energy production. While this mercury is mostly bound to soil constituents episodes of groundwater contamination are known in some cases resulting in potable water super saturated with Hg(0). Microbial processes that reduce Hg(II) to the elemental form Hg(0) in the saturated subsurface sediments may contribute to this problem. When we started the project, only one microbial pathway for the reduction of Hg(II), the one mediated by the mer operon in mercury resistant bacteria was known. As we had previously demonstrated that the mer mediated process occurred in highly contaminated environments (Schaefer et al., 2004), and mercury concentrations in the subsurface were reported to be low (Krabbenhoft and Babiarz, 1992), we hypothesized that other microbial processes might be active in reducing Hg(II) to Hg(0) in saturated subsurface environments. The specific goals of our projects were: (1) Investigating the potential for Hg(II) reduction under varying electron accepting conditions in subsurface sediments and relating these potential to mer gene distribution; and (2) Examining the physiological and biochemical characteristics of the interactions of anaerobic bacteria with mercury. The results are briefly summarized with references to published papers and manuscripts in preparation where details about our research can be found. Additional information may be found in copies of our published manuscripts and conference proceedings, and our yearly reports that were submitted through the RIMS system.

Diversity and activity of benthic microbial communities at the North Alex mud volcano, Eastern Mediterranean

Science.gov (United States)

Makarow, Dorothee; Feseker, Tomas; Schmitz, Ruth; Treude, Tina

2010-05-01

North Alex mud volcano, located on the upper slope of the western Nile deep-sea fan, is characterized by an active seepage center transporting pore fluids, hydrocarbons and gases from deep subsurface sources to the sediment-water interface. Surface sediments feature steep temperature gradient of 8.5°C m-1. We sampled the top 40 cm of the sediments at different locations between the center and rim of the mud volcano to study the diversity, activity, and physiological characteristics of benthic microorganisms. The sediments revealed the activity of anaerobic oxidation of methane coupled to sulfate reduction with a mesophilic temperature optimum. Organisms involved in the process include consortia of methanotrophic archaea (ANME-2 group) and an unknown bacterial partner. Besides methanotrophic organisms the sediments harbored a variety of other bacterial and archaeal groups - including potentially thermophilic bacteria that could be involved in sulfur cycling. This poster presentation will provide an overview of microbial activities and community compositions of North Alex mud volcano sediments.

Present and past microbial life in continental salt pan sediments in Southern Africa

Science.gov (United States)

Genderjahn, Steffi; Mangelsdorf, Kai; Alawi, Mashal; Kallmeyer, Jens; Wagner, Dirk

2015-04-01

The southwestern African region is characterized by strong climate variability. To get a better understanding on the climate evolution and environmental condition in Namibia and South Africa, terrestrial climate archives are investigated. Since there are almost no lakes, continental salt pans represent the only terrestrial geoarchives with the potential to preserve climate signals during sediment deposition. Climate has a strong impact on the salt pan ecosystem, causing adaptation of salt pan microorganisms to varying temperature, precipitation and salinity conditions. To reconstruct climate variability during the Holocene, the composition, diversity and abundance of indigenous microbial communities with depth and related to different soil parameters are investigated. We are using a combined approach of microbiological and lipid biomarker analyses to demonstrate the response of the microbial communities due to environmental changes. For microbiological analyses outcrops were conducted or short cores (0-100 cm) were drilled at four different salt pans in Aminuis, Koes and Witpan region having rather different geochemical properties. The current work focused on changes within the microbial communities due to the impact of long-term climate variation and the associated environmental changes and is part of the project 'Signals of climate and landscape change preserved in southern African GeoArchives' in the scope of the SPACES program, which is funded by the German Federal Ministry of Education and Research (BMBF). For a quantitative characterization of microbial communities molecular techniques such as polymerase chain reaction (PCR) and real-time quantitative PCR (qPCR) based on the 16S rRNA genes are used. Moreover, 454 sequencing technique is utilized to describe the diversity and abundance of microorganisms in detail. Soil parameters are described by standard soil scientific methods. Furthermore, microbial lipid biomarker analyses were done to characterize living

Batteryless, wireless sensor powered by a sediment microbial fuel cell.

Science.gov (United States)

Donovan, Conrad; Dewan, Alim; Heo, Deukhyoun; Beyenal, Haluk

2008-11-15

Sediment microbial fuel cells (SMFCs) are considered to be an alternative renewable power source for remote monitoring. There are two main challenges to using SMFCs as power sources: 1) a SMFC produces a low potential at which most sensor electronics do not operate, and 2) a SMFC cannot provide continuous power, so energy from the SMFC must be stored and then used to repower sensor electronics intermittently. In this study, we developed a SMFC and a power management system (PMS) to power a batteryless, wireless sensor. A SMFC operating with a microbial anode and cathode, located in the Palouse River, Pullman, Washington, U.S.A., was used to demonstrate the utility of the developed system. The designed PMS stored microbial energy and then started powering the wireless sensor when the SMFC potential reached 320 mV. It continued powering until the SMFC potential dropped below 52 mV. The system was repowered when the SMFC potential increased to 320 mV, and this repowering continued as long as microbial reactions continued. We demonstrated that a microbial fuel cell with a microbial anode and cathode can be used as an effective renewable power source for remote monitoring using custom-designed electronics.

Evidence of synsedimentary microbial activity and iron deposition in ferruginous crusts of the Late Cenomanian Utrillas Formation (Iberian Basin, central Spain)

Science.gov (United States)

García-Hidalgo, José F.; Elorza, Javier; Gil-Gil, Javier; Herrero, José M.; Segura, Manuel

2018-02-01

Ferruginous sandstones and crusts are prominent sedimentary features throughout the continental (braided)-coastal siliciclastic (estuarine-tidal) wedges of the Late Cenomanian Utrillas Formation in the Iberian Basin. Crust types recognized are: Ferruginous sandy crusts (Fsc) with oxides-oxyhydroxides (hematite and goethite) concentrated on sandstone tops presenting a fibro-radial internal structure reminding organic structures that penetrate different mineral phases, suggesting the existence of bacterial activity in crust development; Ferruginous muddy crusts (Fmc) consisting of wavy, laminated, microbial mats, being composed mainly of hematite. On the other hand, a more dispersed and broader mineralization included as Ferruginous sandstones with iron oxides and oxyhydroxides (hematite and goethite) representing a limited cement phase on these sediments. The presence of microbial remains, ferruginous minerals, Microbially-induced sedimentary structures, microbial laminites and vertebrate tracks preserved due to the presence of biofilms suggest firstly a direct evidence of syn-depositional microbial activity in these sediments; and, secondly, that iron accumulation and ferruginous crusts development occurred immediately after deposition of the host, still soft sediments. Ferruginous crusts cap sedimentary cycles and they represent the gradual development of hard substrate conditions, and the development of a discontinuity surface at the top of the parasequence sets, related to very low sedimentary rates; the overlying sediments record subsequent flooding of underlying shallower environments; crusts are, consequently, interpreted as boundaries for these higher-order cycles in the Iberian Basin.

Bacterial abundance and activity in deep-sea sediments from the eastern North Atlantic

Science.gov (United States)

Eardly, D. F.; Carton, M. W.; Gallagher, J. M.; Patching, J. W.

Results are presented from four cruises to the Porcupine Abyssal Plain (PAP site) that took place during the BENGAL project from September 1996 to March 1998, and two cruises to the PAP and an oligotrophic site (EUMELI) that took place during the DEEPSEAS project between September 1993 and March 1994. Bacterial abundances in sediment and sediment contact water were measured by epifluorescence microscopy. Bacterial activity was determined by 3H-thymidine incorporation as a measure of DNA synthesis, and by 3H-leucine incorporation as a measure of protein synthesis. Activities were measured under atmospheric and in situ pressures and temperatures. Bacterial activity was usually higher in samples incubated at in situ pressure than those incubated at atmospheric pressure indicating that a barophilic community was dominant. Inter-cruise comparisons of abundance and activity during the BENGAL project showed no firm evidence of there being a seasonal response in the benthic microbial community to any episodic phytodetritus event. This was probably because of inter-annual variations in the quality and quantity of phytodetritus deposition at the PAP site, the rapid remineralization of fresh organic material by the microbial communities and the timing of cruises to the study area. 3H-thymidine and 3H-leucine incorporation in sediments was higher during the BENGAL period than the DEEPSEAS programme. A methodological change in the 3H-thymidine incorporation technique for sediments may explain the differences in DNA synthesis observed between the two projects, whereas the lower levels of protein synthesis observed during the DEEPSEAS programme probably reflected both inter-annual variations in activity at the PAP site and the lower productivity that prevailed at surface at the EUMELI oligotrophic site. Rates of 3H-thymidine incorporation in sediment contact water were similar during both projects.

Microbial activity in the marine deep biosphere: Progress and prospects

Directory of Open Access Journals (Sweden)

Beth N Orcutt

2013-07-01

Full Text Available The vast marine deep biosphere consists of microbial habitats within sediment, pore waters, upper basaltic crust and the fluids that circulate throughout it. A wide range of temperature, pressure, pH, and electron donor and acceptor conditions exists – all of which can combine to affect carbon and nutrient cycling and result in gradients on spatial scales ranging from millimeters to kilometers. Diverse and mostly uncharacterized microorganisms live in these habitats, and potentially play a role in mediating global scale biogeochemical processes. Quantifying the rates at which microbial activity in the subsurface occurs is a challenging endeavor, yet developing an understanding of these rates is essential to determine the impact of subsurface life on Earth's global biogeochemical cycles, and for understanding how microorganisms in these "extreme" environments survive (or even thrive. Here, we synthesize recent advances and discoveries pertaining to microbial activity in the marine deep subsurface, and we highlight topics about which there is still little understanding and suggest potential paths forward to address them. This publication is the result of a workshop held in August 2012 by the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI "theme team" on microbial activity (www.darkenergybiosphere.org.

Microbial activity in the marine deep biosphere: progress and prospects

Science.gov (United States)

Orcutt, Beth N.; LaRowe, Douglas E.; Biddle, Jennifer F.; Colwell, Frederick S.; Glazer, Brian T.; Reese, Brandi Kiel; Kirkpatrick, John B.; Lapham, Laura L.; Mills, Heath J.; Sylvan, Jason B.; Wankel, Scott D.; Wheat, C. Geoff

2013-01-01

The vast marine deep biosphere consists of microbial habitats within sediment, pore waters, upper basaltic crust and the fluids that circulate throughout it. A wide range of temperature, pressure, pH, and electron donor and acceptor conditions exists—all of which can combine to affect carbon and nutrient cycling and result in gradients on spatial scales ranging from millimeters to kilometers. Diverse and mostly uncharacterized microorganisms live in these habitats, and potentially play a role in mediating global scale biogeochemical processes. Quantifying the rates at which microbial activity in the subsurface occurs is a challenging endeavor, yet developing an understanding of these rates is essential to determine the impact of subsurface life on Earth's global biogeochemical cycles, and for understanding how microorganisms in these “extreme” environments survive (or even thrive). Here, we synthesize recent advances and discoveries pertaining to microbial activity in the marine deep subsurface, and we highlight topics about which there is still little understanding and suggest potential paths forward to address them. This publication is the result of a workshop held in August 2012 by the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI) “theme team” on microbial activity (www.darkenergybiosphere.org). PMID:23874326

Functional structure of laminated microbial sediments from a supratidal sandy beach of the German Wadden Sea (St. Peter-Ording)

Science.gov (United States)

Bühring, Solveig I.; Kamp, Anja; Wörmer, Lars; Ho, Stephanie; Hinrichs, Kai-Uwe

2014-01-01

Hidden for the untrained eye through a thin layer of sand, laminated microbial sediments occur in supratidal beaches along the North Sea coast. The inhabiting microbial communities organize themselves in response to vertical gradients of light, oxygen or sulfur compounds. We performed a fine-scale investigation on the vertical zonation of the microbial communities using a lipid biomarker approach, and assessed the biogeochemical processes using a combination of microsensor measurements and a 13C-labeling experiment. Lipid biomarker fingerprinting showed the overarching importance of cyanobacteria and diatoms in these systems, and heterocyst glycolipids revealed the presence of diazotrophic cyanobacteria even in 9 to 20 mm depth. High abundance of ornithine lipids (OL) throughout the system may derive from sulfate reducing bacteria, while a characteristic OL profile between 5 and 8 mm may indicate presence of purple non-sulfur bacteria. The fate of 13C-labeled bicarbonate was followed by experimentally investigating the uptake into microbial lipids, revealing an overarching importance of cyanobacteria for carbon fixation. However, in deeper layers, uptake into purple sulfur bacteria was evident, and a close microbial coupling could be shown by uptake of label into lipids of sulfate reducing bacteria in the deepest layer. Microsensor measurements in sediment cores collected at a later time point revealed the same general pattern as the biomarker analysis and the labeling experiments. Oxygen and pH-microsensor profiles showed active photosynthesis in the top layer. The sulfide that diffuses from deeper down and decreases just below the layer of active oxygenic photosynthesis indicates the presence of sulfur bacteria, like anoxygenic phototrophs that use sulfide instead of water for photosynthesis.

Potential Activity of Subglacial Microbiota Transported to Anoxic River Delta Sediments

DEFF Research Database (Denmark)

Cameron, Karen A.; Stibal, Marek; Olsen, Nikoline S.

2017-01-01

-related organisms. Later, a reduction in methane was observed to be paired with the depletion of sulphate, and we hypothesise that sulphate reduction out competed hydrogenotrophic methanogenesis. The structure and diversity of the original CO2/H2-amended incubation communities changed dramatically with a major......The Watson River drains a portion of the SW Greenland ice sheet, transporting microbial communities from subglacial environments to a delta at the head of Søndre Strømfjord. This study investigates the potential activity and community shifts of glacial microbiota deposited and buried under layers...... of sediments within the river delta. A long-term (12-month) incubation experiment was established using Watson River delta sediment under anaerobic conditions, with and without CO2/H2 enrichment. Within CO2/H2-amended incubations, sulphate depletion and a shift in the microbial community to a 52% predominance...

DEEP BIOSPHERE. Exploring deep microbial life in coal-bearing sediment down to ~2.5 km below the ocean floor.

Science.gov (United States)

Inagaki, F; Hinrichs, K-U; Kubo, Y; Bowles, M W; Heuer, V B; Hong, W-L; Hoshino, T; Ijiri, A; Imachi, H; Ito, M; Kaneko, M; Lever, M A; Lin, Y-S; Methé, B A; Morita, S; Morono, Y; Tanikawa, W; Bihan, M; Bowden, S A; Elvert, M; Glombitza, C; Gross, D; Harrington, G J; Hori, T; Li, K; Limmer, D; Liu, C-H; Murayama, M; Ohkouchi, N; Ono, S; Park, Y-S; Phillips, S C; Prieto-Mollar, X; Purkey, M; Riedinger, N; Sanada, Y; Sauvage, J; Snyder, G; Susilawati, R; Takano, Y; Tasumi, E; Terada, T; Tomaru, H; Trembath-Reichert, E; Wang, D T; Yamada, Y

2015-07-24

Microbial life inhabits deeply buried marine sediments, but the extent of this vast ecosystem remains poorly constrained. Here we provide evidence for the existence of microbial communities in ~40° to 60°C sediment associated with lignite coal beds at ~1.5 to 2.5 km below the seafloor in the Pacific Ocean off Japan. Microbial methanogenesis was indicated by the isotopic compositions of methane and carbon dioxide, biomarkers, cultivation data, and gas compositions. Concentrations of indigenous microbial cells below 1.5 km ranged from <10 to ~10(4) cells cm(-3). Peak concentrations occurred in lignite layers, where communities differed markedly from shallower subseafloor communities and instead resembled organotrophic communities in forest soils. This suggests that terrigenous sediments retain indigenous community members tens of millions of years after burial in the seabed. Copyright © 2015, American Association for the Advancement of Science.

The microbial nitrogen cycling potential in marine sediments is impacted by polyaromatic hydrocarbon pollution

Directory of Open Access Journals (Sweden)

Nicole M Scott

2014-03-01

Full Text Available During petroleum hydrocarbon exposure the composition and functional dynamics of marine microbial communities are altered, favoring bacteria that can utilize this rich carbon source. Initial exposure of high levels of hydrocarbons in aerobic surface sediments can enrich growth of heterotrophic microorganisms having hydrocarbon degradation capacity. As a result, there can be a localized reduction in oxygen potential, if the sediments are aerobic, within the surface layer of marine sediments resulting in anaerobic zones. We hypothesized that increasing exposure to elevated hydrocarbon concentrations would positively correlate with an increase in denitrification processes and the net accumulation of dinitrogen. This hypothesis was tested by comparing the relative abundance of genes associated with nitrogen metabolism and nitrogen cycling identified in 6 metagenomes from sediments contaminated by polyaromatic hydrocarbons from the Deepwater Horizon oil spill in the Gulf of Mexico, and 3 metagenomes from sediments associated with natural oil seeps in the Santa Barbara Channel. An additional 8 metagenomes from uncontaminated sediments from the Gulf of Mexico were analyzed for comparison. We predicted relative changes in metabolite turnover as a function of the differential microbial gene abundances, which showed predicted accumulation of metabolites associated with denitrification processes, including anammox, in the contaminated samples compared to uncontaminated sediments, with the magnitude of this change being positively correlated to the hydrocarbon concentration and exposure duration. These data highlight the potential impact of hydrocarbon inputs on N cycling processes in marine sediments and provide information relevant for system scale models of nitrogen metabolism in affected ecosystems.

Influence of microbiological activity on the mobility of redoxsensitive radionuclides in sediments

International Nuclear Information System (INIS)

Stroetmann, I.; Kaempfer, P.; Dott, W.; Schuele, J.; Sokotnejat, R.; Winkler, A.; Pekdeger, A.

1994-01-01

The influence of microbial activity on the transport and migration behaviour of redox-sensitive radionuclides (e.g. Technetium (T c ) and Selenium (Se)) in groundwater environment were investigated within an interdisciplinary research program. Soil material and sediments were investigated with batch- and recirculation column experiments. The number of microorganisms in the water was determined by counting the colony forming units (CFU) on R2A agar at regular periods. The results of sterile and non sterile recirculation column experiments showed within 80 days a high fixation of the radionuclides in the unsterile samples (80% of T c , 50% of Se compared with the initial concentration A 0 ), and no fixation in the sterile samples. There was no difference in the redox values. It could be shown that the immobilisation of the redox-sensitive elements T c and Se are strongly determined by microbial activity, depending on the different sediments and their microbial live stock. There are indications that the microorganisms found in the non sterile columns are allochthonous bacteria which were dragged into the experimental systems and samples during laboratory work and sampling. The composition of the microbial flora was shown to be very heterogeneous and different in each individual column and within the same column at different times. Thus these columns might have been contaminated with microorganisms during sampling and handling of the experimental systems under non sterile conditions, as done generally in most laboratories

D:L-Amino Acid Modeling Reveals Fast Microbial Turnover of Days to Months in the Subsurface Hydrothermal Sediment of Guaymas Basin.

Science.gov (United States)

Møller, Mikkel H; Glombitza, Clemens; Lever, Mark A; Deng, Longhui; Morono, Yuki; Inagaki, Fumio; Doll, Mechthild; Su, Chin-Chia; Lomstein, Bente A

2018-01-01

We investigated the impact of temperature on the microbial turnover of organic matter (OM) in a hydrothermal vent system in Guaymas Basin, by calculating microbial bio- and necromass turnover times based on the culture-independent D:L-amino acid model. Sediments were recovered from two stations near hydrothermal mounds (community of microorganisms in the hydrothermal sediment demonstrated short turnover times. The modeled turnover times of microbial bio- and necromass in the hydrothermal sediments were notably faster (biomass: days to months; necromass: up to a few hundred years) than in the cold sediments (biomass: tens of years; necromass: thousands of years), suggesting that temperature has a significant influence on the microbial turnover rates. We suggest that short biomass turnover times are necessary for maintance of essential cell funtions and to overcome potential damage caused by the increased temperature.The reduced OM quality at the hyrothemal sites might thus only allow for a small population size of microorganisms.

The Diffusive Boundary-Layer of Sediments - Oxygen Microgradients Over a Microbial Mat

DEFF Research Database (Denmark)

JØRGENSEN, BB; MARAIS, DJD

1990-01-01

Oxygen microelectrodes were used to analyze the distribution of the diffusive boundary layer (DBL) at the sedimen-water interface in relation to surface topography and flow velocity. The sediment, collected from saline ponds, was covered by a microbial mat that had high oxygen consumption rate...

Seasonal and spatial variations in microbial activity at various phylogenetic resolutions at a groundwater – surface water interface

DEFF Research Database (Denmark)

Yu, Ran; Smets, Barth F.; Gan, Ping

2014-01-01

analysis. Consistently higher microbial activities with less variation in depth were measured in the AIMC traps than in the ambient sediments. Flood disturbance appeared to control AIMC activity distributions at the gradually elevated GSI. The highest AIMC activities were generally obtained from locations...... closest to the free surface water boundary except during the dry season when microbial activities were similar across the entire GSI. A clone library of AIMC 16S rRNA genes was constructed, and it confirmed the predominant role of the targeted alphaproteobacterial group in AIMC activity and composition...... phylogenetically related to putative IOB, supporting the occurrence and persistence of active microbial iron oxidation across the studied iron-rich GSI ecosystem....

Uranium Biomineralization by Natural Microbial Phosphatase Activities in the Subsurface

Energy Technology Data Exchange (ETDEWEB)

Sobecky, Patricia A. [Univ. of Alabama, Tuscaloosa, AL (United States)

2015-04-06

In this project, inter-disciplinary research activities were conducted in collaboration among investigators at The University of Alabama (UA), Georgia Institute of Technology (GT), Lawrence Berkeley National Laboratory (LBNL), Brookhaven National Laboratory (BNL), the DOE Joint Genome Institute (JGI), and the Stanford Synchrotron Radiation Light source (SSRL) to: (i) confirm that phosphatase activities of subsurface bacteria in Area 2 and 3 from the Oak Ridge Field Research Center result in solid U-phosphate precipitation in aerobic and anaerobic conditions; (ii) investigate the eventual competition between uranium biomineralization via U-phosphate precipitation and uranium bioreduction; (iii) determine subsurface microbial community structure changes of Area 2 soils following organophosphate amendments; (iv) obtain the complete genome sequences of the Rahnella sp. Y9-602 and the type-strain Rahnella aquatilis ATCC 33071 isolated from these soils; (v) determine if polyphosphate accumulation and phytate hydrolysis can be used to promote U(VI) biomineralization in subsurface sediments; (vi) characterize the effect of uranium on phytate hydrolysis by a new microorganism isolated from uranium-contaminated sediments; (vii) utilize positron-emission tomography to label and track metabolically-active bacteria in soil columns, and (viii) study the stability of the uranium phosphate mineral product. Microarray analyses and mineral precipitation characterizations were conducted in collaboration with DOE SBR-funded investigators at LBNL. Thus, microbial phosphorus metabolism has been shown to have a contributing role to uranium immobilization in the subsurface.

Uranium Biomineralization by Natural Microbial Phosphatase Activities in the Subsurface

International Nuclear Information System (INIS)

Sobecky, Patricia A.

2015-01-01

In this project, inter-disciplinary research activities were conducted in collaboration among investigators at The University of Alabama (UA), Georgia Institute of Technology (GT), Lawrence Berkeley National Laboratory (LBNL), Brookhaven National Laboratory (BNL), the DOE Joint Genome Institute (JGI), and the Stanford Synchrotron Radiation Light source (SSRL) to: (i) confirm that phosphatase activities of subsurface bacteria in Area 2 and 3 from the Oak Ridge Field Research Center result in solid U-phosphate precipitation in aerobic and anaerobic conditions; (ii) investigate the eventual competition between uranium biomineralization via U-phosphate precipitation and uranium bioreduction; (iii) determine subsurface microbial community structure changes of Area 2 soils following organophosphate amendments; (iv) obtain the complete genome sequences of the Rahnella sp. Y9-602 and the type-strain Rahnella aquatilis ATCC 33071 isolated from these soils; (v) determine if polyphosphate accumulation and phytate hydrolysis can be used to promote U(VI) biomineralization in subsurface sediments; (vi) characterize the effect of uranium on phytate hydrolysis by a new microorganism isolated from uranium-contaminated sediments; (vii) utilize positron-emission tomography to label and track metabolically-active bacteria in soil columns, and (viii) study the stability of the uranium phosphate mineral product. Microarray analyses and mineral precipitation characterizations were conducted in collaboration with DOE SBR-funded investigators at LBNL. Thus, microbial phosphorus metabolism has been shown to have a contributing role to uranium immobilization in the subsurface.

Are Microbial Nanowires Responsible for Geoelectrical Changes at Hydrocarbon Contaminated Sites?

Science.gov (United States)

Hager, C.; Atekwana, E. A.; Gorby, Y. A.; Duris, J. W.; Allen, J. P.; Atekwana, E. A.; Ownby, C.; Rossbach, S.

2007-05-01

Significant advances in near-surface geophysics and biogeophysics in particular, have clearly established a link between geoelectrical response and the growth and enzymatic activities of microbes in geologic media. Recent studies from hydrocarbon contaminated sites suggest that the activities of distinct microbial populations, specifically syntrophic, sulfate reducing, and dissimilatory iron reducing microbial populations are a contributing factor to elevated sediment conductivity. However, a fundamental mechanistic understanding of the processes and sources resulting in the measured electrical response remains uncertain. The recent discovery of bacterial nanowires and their electron transport capabilities suggest that if bacterial nanowires permeate the subsurface, they may in part be responsible for the anomalous conductivity response. In this study we investigated the microbial population structure, the presence of nanowires, and microbial-induced alterations of a hydrocarbon contaminated environment and relate them to the sediments' geoelectrical response. Our results show that microbial communities varied substantially along the vertical gradient and at depths where hydrocarbons saturated the sediments, ribosomal intergenic spacer analysis (RISA) revealed signatures of microbial communities adapted to hydrocarbon impact. In contrast, RISA profiles from a background location showed little community variations with depth. While all sites showed evidence of microbial activity, a scanning electron microscope (SEM) study of sediment from the contaminated location showed pervasive development of "nanowire-like structures" with morphologies consistent with nanowires from laboratory experiments. SEM analysis suggests extensive alteration of the sediments by microbial Activity. We conclude that, excess organic carbon (electron donor) but limited electron acceptors in these environments cause microorganisms to produce nanowires to shuttle the electrons as they seek for

ACTIVIDAD MICROBIANA EN SEDIMENTOS SUPERFICIALES DEL BOSQUE DE MANGLAR (Rhizophora mangle DE LA BAHÍA DE PERTIGALETE (ANZOÁTEGUI, VENEZUELA, DURANTE LOS PERÍODOS DE SURGENCIA Y TRANSICIÓN | MICROBIAL ACTIVITY IN SURFACE SEDIMENTS OF MANGROVE FOREST OF PERTIGALETE BAY (ANZOÁTEGUI, VENEZUELA, DURING THE UP WELLING AND TRANSITION PERIODS

Directory of Open Access Journals (Sweden)

Meximara Rodríguez

2016-08-01

Full Text Available The Pertigalete Bay is bordered by an extensive mangrove zone and it is affected by an intense boating and sailing traffic, the pouring of the waste water coming from the nearing population and effluent from the company Cements of Venezuela. The objective of this research was to determinate the microbial activity and the possible anthropogenic impact in surface sediments of mangrove zones in the Pertigalete Bay during the up welling and transition periods. The microbial biomass (Cmic, the basal respiration (RB, dehydrogenases activity (DHS, fluorescein diacetate hydrolysis (HDAF and the metabolic quotient (qCO2 were used in the determination of the microbial activity. In three zones of the bay three transects of 30 m of length were established with a separation of 10 m among them. In each transect, three sampling points were placed and triplicate samples of the surface sediments were taken from each. The results showed that during the up welling period there is a higher Cmic in the three selected zones: 851.01; 539.87 and 533.66 mg Cmic kg-1 sediment in zones I, II and III, respectively. The DHS indicated that there is a predominance of the anaerobic heterotrophic population during this period. The HDAF confirmed that there is a higher heterotrophic activity during the up welling and the qCO2 indicated a greater efficiency in the use of carbon by the microorganism present in the sediments. The results showed that the predominance of the microbial flora and its activity in the sediments is mainly determined by the up welling and transition periods, especially in the zone I, which is less exposed to the anthropogenic action.

Microbial Biomass and Activity in Geomorphic Features in Forested and Urban Restored and Degraded Streams

Science.gov (United States)

Geomorphic spatial heterogeneity affects sediment denitrification, an anaerobic microbial process that results in the loss of nitrogen (N), and other anaerobic microbial processes such as methanogenesis in urban streams. We measured sediment denitrification potential (DEA), metha...

Molecular fossils of prokaryotes in ancient authigenic minerals: archives of microbial activity in reefs and mounds?

Science.gov (United States)

Heindel, Katrin; Birgel, Daniel; Richoz, Sylvain; Westphal, Hildegard; Peckmann, Jörn

2016-04-01

Molecular fossils (lipid biomarkers) are commonly used as proxies in organic-rich sediments of various sources, including eukaryotes and prokaryotes. Usually, molecular fossils of organisms transferred from the water column to the sediment are studied to monitor environmental changes (e.g., temperature, pH). Apart from these 'allochthonous' molecular fossils, prokaryotes are active in sediments and mats on the seafloor and leave behind 'autochthonous' molecular fossils in situ. In contrast to many phototrophic organisms, most benthic sedimentary prokaryotes are obtaining their energy from oxidation or reduction of organic or inorganic substrates. A peculiarity of some of the sediment-thriving prokaryotes is their ability to trigger in situ mineral precipitation, often but not only due to metabolic activity, resulting in authigenic rocks (microbialites). During that process, prokaryotes are rapidly entombed in the mineral matrix, where the molecular fossils are protected from early (bio)degradation. In contrast to other organic compounds (DNA, proteins etc.), molecular fossils can be preserved over very long time periods (millions of years). Thus, molecular fossils in authigenic mineral phases are perfectly suitable to trace microbial activity back in time. Among the best examples of molecular fossils, which are preserved in authigenic rocks are various microbialites, forming e.g. in phototrophic microbial mats and at cold seeps. Microbialite formation is reported throughout earth history. We here will focus on reefal microbialites form the Early Triassic and the Holocene. After the End-Permian mass extinction, microbialites covered wide areas on the ocean margins. In microbialites from the Griesbachian in Iran and Turkey (both Neotethys), molecular fossils of cyanobacteria, archaea, anoxygenic phototrophs, and sulphate-reducing bacteria indicate the presence of layered microbial mats on the seafloor, in which carbonate precipitation was induced. In association with

Microbial Communities and Organic Matter Composition in Surface and Subsurface Sediments of the Helgoland Mud Area, North Sea

Science.gov (United States)

Oni, Oluwatobi E.; Schmidt, Frauke; Miyatake, Tetsuro; Kasten, Sabine; Witt, Matthias; Hinrichs, Kai-Uwe; Friedrich, Michael W.

2015-01-01

The role of microorganisms in the cycling of sedimentary organic carbon is a crucial one. To better understand relationships between molecular composition of a potentially bioavailable fraction of organic matter and microbial populations, bacterial and archaeal communities were characterized using pyrosequencing-based 16S rRNA gene analysis in surface (top 30 cm) and subsurface/deeper sediments (30–530 cm) of the Helgoland mud area, North Sea. Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR MS) was used to characterize a potentially bioavailable organic matter fraction (hot-water extractable organic matter, WE-OM). Algal polymer-associated microbial populations such as members of the Gammaproteobacteria, Bacteroidetes, and Verrucomicrobia were dominant in surface sediments while members of the Chloroflexi (Dehalococcoidales and candidate order GIF9) and Miscellaneous Crenarchaeota Groups (MCG), both of which are linked to degradation of more recalcitrant, aromatic compounds and detrital proteins, were dominant in subsurface sediments. Microbial populations dominant in subsurface sediments (Chloroflexi, members of MCG, and Thermoplasmata) showed strong correlations to total organic carbon (TOC) content. Changes of WE-OM with sediment depth reveal molecular transformations from oxygen-rich [high oxygen to carbon (O/C), low hydrogen to carbon (H/C) ratios] aromatic compounds and highly unsaturated compounds toward compounds with lower O/C and higher H/C ratios. The observed molecular changes were most pronounced in organic compounds containing only CHO atoms. Our data thus, highlights classes of sedimentary organic compounds that may serve as microbial energy sources in methanic marine subsurface environments. PMID:26635758

Marine Microbial Gene Abundance and Community Composition in Response to Ocean Acidification and Elevated Temperature in Two Contrasting Coastal Marine Sediments

Directory of Open Access Journals (Sweden)

Ashleigh R. Currie

2017-08-01

Full Text Available Marine ecosystems are exposed to a range of human-induced climate stressors, in particular changing carbonate chemistry and elevated sea surface temperatures as a consequence of climate change. More research effort is needed to reduce uncertainties about the effects of global-scale warming and acidification for benthic microbial communities, which drive sedimentary biogeochemical cycles. In this research, mesocosm experiments were set up using muddy and sandy coastal sediments to investigate the independent and interactive effects of elevated carbon dioxide concentrations (750 ppm CO2 and elevated temperature (ambient +4°C on the abundance of taxonomic and functional microbial genes. Specific quantitative PCR primers were used to target archaeal, bacterial, and cyanobacterial/chloroplast 16S rRNA in both sediment types. Nitrogen cycling genes archaeal and bacterial ammonia monooxygenase (amoA and bacterial nitrite reductase (nirS were specifically targeted to identify changes in microbial gene abundance and potential impacts on nitrogen cycling. In muddy sediment, microbial gene abundance, including amoA and nirS genes, increased under elevated temperature and reduced under elevated CO2 after 28 days, accompanied by shifts in community composition. In contrast, the combined stressor treatment showed a non-additive effect with lower microbial gene abundance throughout the experiment. The response of microbial communities in the sandy sediment was less pronounced, with the most noticeable response seen in the archaeal gene abundances in response to environmental stressors over time. 16S rRNA genes (amoA and nirS were lower in abundance in the combined stressor treatments in sandy sediments. Our results indicated that marine benthic microorganisms, especially in muddy sediments, are susceptible to changes in ocean carbonate chemistry and seawater temperature, which ultimately may have an impact upon key benthic biogeochemical cycles.

Sedimentological imprint on subseafloor microbial communities in Western Mediterranean Sea Quaternary sediments

Science.gov (United States)

Ciobanu, M.-C.; Rabineau, M.; Droz, L.; Révillon, S.; Ghiglione, J.-F.; Dennielou, B.; Jorry, S.-J.; Kallmeyer, J.; Etoubleau, J.; Pignet, P.; Crassous, P.; Vandenabeele-Trambouze, O.; Laugier, J.; Guégan, M.; Godfroy, A.; Alain, K.

2012-09-01

An interdisciplinary study was conducted to evaluate the relationship between geological and paleoenvironmental parameters and the bacterial and archaeal community structure of two contrasting subseafloor sites in the Western Mediterranean Sea (Ligurian Sea and Gulf of Lion). Both depositional environments in this area are well-documented from paleoclimatic and paleooceanographic point of views. Available data sets allowed us to calibrate the investigated cores with reference and dated cores previously collected in the same area, and notably correlated to Quaternary climate variations. DNA-based fingerprints showed that the archaeal diversity was composed by one group, Miscellaneous Crenarchaeotic Group (MCG), within the Gulf of Lion sediments and of nine different lineages (dominated by MCG, South African Gold Mine Euryarchaeotal Group (SAGMEG) and Halobacteria) within the Ligurian Sea sediments. Bacterial molecular diversity at both sites revealed mostly the presence of the classes Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria within Proteobacteria phylum, and also members of Bacteroidetes phylum. The second most abundant lineages were Actinobacteria and Firmicutes at the Gulf of Lion site and Chloroflexi at the Ligurian Sea site. Various substrates and cultivation conditions allowed us to isolate 75 strains belonging to four lineages: Alpha-, Gammaproteobacteria, Firmicutes and Actinobacteria. In molecular surveys, the Betaproteobacteria group was consistently detected in the Ligurian Sea sediments, characterized by a heterolithic facies with numerous turbidites from a deep-sea levee. Analysis of relative betaproteobacterial abundances and turbidite frequency suggested that the microbial diversity was a result of main climatic changes occurring during the last 20 ka. Statistical direct multivariate canonical correspondence analyses (CCA) showed that the availability of electron acceptors and the quality of electron donors (indicated by age

Response of core microbial consortia to hydrocarbon contaminations in coastal sediment habitats

Directory of Open Access Journals (Sweden)

Mathilde Jeanbille

2016-10-01

Full Text Available Traditionally, microbial surveys investigating the effect of chronic anthropogenic pressure such as polyaromatic hydrocarbons (PAHs contaminations consider just the alpha and beta diversity and ignore the interactions among the different taxa forming the microbial community. Here, we investigated the ecological relationships between the three domains of life (i.e. Bacteria, Archaea and Eukarya using 454 pyrosequencing data of the 16S rRNA and 18S rRNA genes from chronically impacted and pristine sediments, along the coasts of the Mediterranean Sea (Gulf of Lion, Vermillion coast, Corsica, Bizerte lagoon and Lebanon and the French Atlantic Ocean (Bay of Biscay and English Channel. Our approach provided a robust ecological framework for the partition of the taxa abundance distribution into 859 core OTUs and 6629 satellite OTUs. OTUs forming the core microbial community showed the highest sensitivity to changes in environmental and contaminant variations, with salinity, latitude, temperature, particle size distribution, total organic carbon (TOC and PAH concentrations as main drivers of community assembly. The core communities were dominated by Gammaproteobacteria and Deltaproteobacteria for Bacteria, by Thaumarchaeota, Bathyarchaeota and Thermoplasmata for Archaea and Metazoa and Dinoflagellata for Eukarya. In order to find associations among microorganisms, we generated a co-occurrence network in which PAHs were found to impact significantly the potential predator – prey relationship in one microbial consortium composed of ciliates and Actinobacteria. Comparison of network topological properties between contaminated and non-contaminated samples showed substantial differences in the structure of the network and indicated a higher vulnerability to environmental perturbations in the contaminated sediments.

Microbial degradation. Mass transfer in the system pollutant - water - sediment; Mikrobieller Abbau. Massentransfer im System Schadstoff - Wasser - Sediment

Energy Technology Data Exchange (ETDEWEB)

Tiehm, Andreas [Technologiezentrum Wasser (TZW), Karlsruhe (Germany). Abt. Umweltbiotechnologie und Altlasten; Kranzioch, Irene; Stoll, Claudia

2011-09-15

The microbial degradation of pollutants in the aquatic environment essentially is influenced by the prevailing redox conditions and mass exchange processes (bioavailability). Within a new project, the Technologiezentrum Wasser TZW (Karlsruhe, Federal Republic of Germany) deals with the microbial conversion under dynamic conditions such as those expected in the area of the Three Gorges Dam at the Yangtze River. In particular, molecular-biological methods (PCR, polymerase chain reaction and DGGE Denatured gradient gel electrophoresis) are used for a targeted monitoring and further developed. The focus of the investigation initially focuses on the degradation of halogenated substances which are used as main substances for understanding the mass exchange between sediment and water as well as the microbial conversion processes. An enhanced understanding of the process and the compilation of the dynamic sales performance can be defined as a target.

Shifts in identity and activity of methanotrophs in arctic lake sediments in response to temperature changes

Science.gov (United States)

He, Ruo; Wooller, Matthew J.; Pohlman, John W.; Quensen, John; Tiedje, James M.; Leigh, Mary Beth

2012-01-01

Methane (CH4) flux to the atmosphere is mitigated via microbial CH4 oxidation in sediments and water. As arctic temperaturesincrease, understanding the effects of temperature on the activity and identity of methanotrophs in arctic lake sediments is importantto predicting future CH4 emissions. We used DNA-based stable-isotope probing (SIP), quantitative PCR (Q-PCR), andpyrosequencing analyses to identify and characterize methanotrophic communities active at a range of temperatures (4°C, 10°C,and 21°C) in sediments (to a depth of 25 cm) sampled from Lake Qalluuraq on the North Slope of Alaska. CH4 oxidation activitywas measured in microcosm incubations containing sediments at all temperatures, with the highest CH4 oxidation potential of37.5 mol g1 day1 in the uppermost (depth, 0 to 1 cm) sediment at 21°C after 2 to 5 days of incubation. Q-PCR of pmoA and ofthe 16S rRNA genes of type I and type II methanotrophs, and pyrosequencing of 16S rRNA genes in 13C-labeled DNA obtained bySIP demonstrated that the type I methanotrophs Methylobacter, Methylomonas, and Methylosoma dominated carbon acquisitionfrom CH4 in the sediments. The identity and relative abundance of active methanotrophs differed with the incubation temperature.Methylotrophs were also abundant in the microbial community that derived carbon from CH4, especially in the deeper sediments(depth, 15 to 20 cm) at low temperatures (4°C and 10°C), and showed a good linear relationship (R0.82) with the relativeabundances of methanotrophs in pyrosequencing reads. This study describes for the first time how methanotrophiccommunities in arctic lake sediments respond to temperature variations.

Anaerobic Methane-Oxidizing Microbial Community in a Coastal Marine Sediment: Anaerobic Methanotrophy Dominated by ANME-3.

Science.gov (United States)

Bhattarai, Susma; Cassarini, Chiara; Gonzalez-Gil, Graciela; Egger, Matthias; Slomp, Caroline P; Zhang, Yu; Esposito, Giovanni; Lens, Piet N L

2017-10-01

The microbial community inhabiting the shallow sulfate-methane transition zone in coastal sediments from marine Lake Grevelingen (The Netherlands) was characterized, and the ability of the microorganisms to carry out anaerobic oxidation of methane coupled to sulfate reduction was assessed in activity tests. In vitro activity tests of the sediment with methane and sulfate demonstrated sulfide production coupled to the simultaneous consumption of sulfate and methane at approximately equimolar ratios over a period of 150 days. The maximum sulfate reduction rate was 5 μmol sulfate per gram dry weight per day during the incubation period. Diverse archaeal and bacterial clades were retrieved from the sediment with the majority of them clustered with Euryarchaeota, Thaumarcheota, Bacteroidetes, and Proteobacteria. The 16S rRNA gene sequence analysis showed that the sediment from marine Lake Grevelingen contained anaerobic methanotrophic Archaea (ANME) and methanogens as archaeal clades with a role in the methane cycling. ANME at the studied site mainly belong to the ANME-3 clade. This study provides one of the few reports for the presence of ANME-3 in a shallow coastal sediment. Sulfate-reducing bacteria from Desulfobulbus clades were found among the sulfate reducers, however, with very low relative abundance. Desulfobulbus has previously been commonly found associated with ANME, whereas in our study, ANME-3 and Desulfobulbus were not observed simultaneously in clusters, suggesting the possibility of independent AOM by ANME-3.

The microbial degradation of polycyclic aromatic hydrocarbons in soils and sediments. Der mikrobielle Abbau polyzyklischer aromatischer Kohlenwasserstoffe (PAK) in Boeden und Sedimenten: Mineralisierung, Metabolitenbildung und Entstehung gebundener Rueckstaende

Energy Technology Data Exchange (ETDEWEB)

Mahro, B; Kaestner, M [Technische Univ. Hamburg-Harburg (Germany). Arbeitsbereich Biotechnologie 2

1993-02-01

The microbial degradation of polycylic aromatic hydrocarbons in soils and sediments: mineralization, metabolite excretion and the formation of bound residues microorganisms degrade polycyclic aromatic hydrocarbons (PAH) via three different metabolic pathways: mineralization, cometabolic oxidation or an unspecific triggering of radical reactions. As a result of these microbial transformation processes PAH may be converted to CO[sub 2] and biomass or partially oxidized metabolites. The possible fate of these presumed metabolites in the soil matrix is analyzed. It is pointed out that the formation of humus bound residues, stimulated by microbial exoenzyme activities, may contribute to significant extent to the disappearance of PAHs in soils and sediments. The relevance of this fact for the biological remediation of contaminated soils is discussed. (orig.).

Cellular content of biomolecules in sub-seafloor microbial communities

DEFF Research Database (Denmark)

Braun, Stefan; Morono, Yuki; Becker, Kevin W.

2016-01-01

the lifetime of their microbial sources. Here we provide for the first time measurements of the cellular content of biomolecules in sedimentary microbial cells. We separated intact cells from sediment matrices in samples from surficial, deeply buried, organic-rich, and organic-lean marine sediments by density...... content. We find that the cellular content of biomolecules in the marine subsurface is up to four times lower than previous estimates. Our approach will facilitate and improve the use of biomolecules as proxies for microbial abundance in environmental samples and ultimately provide better global estimates......Microbial biomolecules, typically from the cell envelope, can provide crucial information about distribution, activity, and adaptations of sub-seafloor microbial communities. However, when cells die these molecules can be preserved in the sediment on timescales that are likely longer than...

Effects of zinc pyrithione and copper pyrithione on microbial community function and structure in sediments

DEFF Research Database (Denmark)

Petersen, DG; Dahllof, I.; Nielsen, LP

2004-01-01

The effects of the new antifouling biocides, zinc pyrithione (ZPT) and copper pyrithione (CPT), on microbial communities in estuarine sediments were studied in microcosms. As functional endpoints, fluxes of nutrients (NO3-, NH4+, HPO42-, Si(OH)(4)) and protein synthesis ([C-14] leucine incorporat......The effects of the new antifouling biocides, zinc pyrithione (ZPT) and copper pyrithione (CPT), on microbial communities in estuarine sediments were studied in microcosms. As functional endpoints, fluxes of nutrients (NO3-, NH4+, HPO42-, Si(OH)(4)) and protein synthesis ([C-14] leucine...... DNA content, whereas the LOEC for CPT was 0.1 nmol/g dry sediment for the nitrate flux and total DNA content. Nitrate fluxes increased significantly following additions of both ZPT and CPT, whereas ammonium fluxes decreased significantly after ZPT addition, suggesting changes in the nitrification...... and denitrification processes. The total DNA content decreased significantly following addition of both ZPT and CPT, but at the highest addition of ZPT (10 nmol ZPT/g dry sediment), an increase in total DNA content was found. Increased protein synthesis and bacterial diversity were also observed at this concentration...

Microbial transformation of uranium in wastes

International Nuclear Information System (INIS)

Francis, A.J.; Dodge, C.J.; Gillow, J.B.; Cline, J.E.

1989-01-01

Contamination of soils, water, and sediments by radionuclides and toxic metals from the disposal of uranium processing wastes is a major national concern. Although much is known about the physico- chemical aspects of U, we have little information on the effects of aerobic and anaerobic microbial activities on the mobilization or immobilization of U and other toxic metals in mixed wastes. In order to understand the mechanisms of microbial transformations of uranium, we examined a contaminated pond sediment and a sludge sample from the uranium processing facility at Y-12 Plant, Oak Ridge, TN. The uranium concentration in the sediment and sludge samples was 923 and 3080 ug/g dry wt, respectively. In addition to U, the sediment and sludge samples contained high levels of toxic metals such as Cd, Cr, Cu, Hg, Pb, Ni, and Zn. The association of uranium with the various mineral fractions of the sediment and sludge was determined by selective chemical extraction techniques. Uranium was associated to varying degrees with the exchangeable carbonate, iron oxide, organic, and inert fractions in both samples. Initial results in samples amended with carbon and nitrogen indicate immobilization of U due to enhanced indigenous microbial activity under anaerobic conditions. 23 refs., 4 figs., 5 tabs

To prevent the occurrence of black water agglomerate through delaying decomposition of cyanobacterial bloom biomass by sediment microbial fuel cell.

Science.gov (United States)

Zhou, Yan-Li; Jiang, He-Long; Cai, Hai-Yuan

2015-04-28

Settlement of cyanobacterial bloom biomass (CBB) into sediments in eutrophic lakes often induced the occurrence of black water agglomerate and then water quality deterioration. This study investigated the effect of sediment microbial fuel cell (SMFC) on CBB removal in sediments and related water pollution. Sediment bulking and subsequent black water from decomposition of settled CBB happened without SMFC, but were not observed over 100-day experiments with SMFC employment. While CBB in sediments improved power production from SMFC, the removal efficiency of organic matters in CBB-amended sediments with SMFC was significantly lower than that without SMFC. Pyrosequencing analysis showed higher abundances of the fermentative Clostridium and acetoclastic methanogen in CBB-amended bulk sediments without SMFC than with SMFC at the end of experiments. Obviously, SMFC operation changed the microbial community in CBB-amended sediments, and delayed the CBB degradation against sediment bulking. Thus, SMFC could be potentially applied as pollution prevention in CBB-settled and sensitive zones in shallow lakes. Copyright © 2015 Elsevier B.V. All rights reserved.

The Diffusive Boundary-Layer of Sediments - Oxygen Microgradients Over a Microbial Mat

DEFF Research Database (Denmark)

JØRGENSEN, BB; MARAIS, DJD

1990-01-01

Oxygen microelectrodes were used to analyze the distribution of the diffusive boundary layer (DBL) at the sedimen-water interface in relation to surface topography and flow velocity. The sediment, collected from saline ponds, was covered by a microbial mat that had high oxygen consumption rate...... and well-defined surface structure. Diffusion through the DBL constituted an important rate limitation to the oxygen uptake of the sediment. The mean effective DBL thickness decreased from 0.59 to 0.16 mm as the flow velocity of the overlying water was increased from 0.3 to 7.7 cm s-1 (measured 1 cm above...

Shift in the microbial community composition of surface water and sediment along an urban river.

Science.gov (United States)

Wang, Lan; Zhang, Jing; Li, Huilin; Yang, Hong; Peng, Chao; Peng, Zhengsong; Lu, Lu

2018-06-15

Urban rivers represent a unique ecosystem in which pollution occurs regularly, leading to significantly altered of chemical and biological characteristics of the surface water and sediments. However, the impact of urbanization on the diversity and structure of the river microbial community has not been well documented. As a major tributary of the Yangtze River, the Jialing River flows through many cities. Here, a comprehensive analysis of the spatial microbial distribution in the surface water and sediments in the Nanchong section of Jialing River and its two urban branches was conducted using 16S rRNA gene-based Illumina MiSeq sequencing. The results revealed distinct differences in surface water bacterial composition along the river with a differential distribution of Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes and Acidobacteria (P urban water. PICRUSt metabolic inference analysis revealed a growing number of genes associated with xenobiotic metabolism and nitrogen metabolism in the urban water, indicating that urban discharges might act as the dominant selective force to alter the microbial communities. Redundancy analysis suggested that the microbial community structure was influenced by several environmental factors. TP (P urban river. These results highlight that river microbial communities exhibit spatial variation in urban areas due to the joint influence of chemical variables associated with sewage discharging and construction of hydropower stations. Copyright © 2018 Elsevier B.V. All rights reserved.

Deep subsurface microbial processes

Science.gov (United States)

Lovley, D.R.; Chapelle, F.H.

1995-01-01

Information on the microbiology of the deep subsurface is necessary in order to understand the factors controlling the rate and extent of the microbially catalyzed redox reactions that influence the geophysical properties of these environments. Furthermore, there is an increasing threat that deep aquifers, an important drinking water resource, may be contaminated by man's activities, and there is a need to predict the extent to which microbial activity may remediate such contamination. Metabolically active microorganisms can be recovered from a diversity of deep subsurface environments. The available evidence suggests that these microorganisms are responsible for catalyzing the oxidation of organic matter coupled to a variety of electron acceptors just as microorganisms do in surface sediments, but at much slower rates. The technical difficulties in aseptically sampling deep subsurface sediments and the fact that microbial processes in laboratory incubations of deep subsurface material often do not mimic in situ processes frequently necessitate that microbial activity in the deep subsurface be inferred through nonmicrobiological analyses of ground water. These approaches include measurements of dissolved H2, which can predict the predominant microbially catalyzed redox reactions in aquifers, as well as geochemical and groundwater flow modeling, which can be used to estimate the rates of microbial processes. Microorganisms recovered from the deep subsurface have the potential to affect the fate of toxic organics and inorganic contaminants in groundwater. Microbial activity also greatly influences 1 the chemistry of many pristine groundwaters and contributes to such phenomena as porosity development in carbonate aquifers, accumulation of undesirably high concentrations of dissolved iron, and production of methane and hydrogen sulfide. Although the last decade has seen a dramatic increase in interest in deep subsurface microbiology, in comparison with the study of

Sedimentological imprint on subseafloor microbial communities in Western Mediterranean Sea Quaternary sediments

Directory of Open Access Journals (Sweden)

M.-C. Ciobanu

2012-09-01

Full Text Available An interdisciplinary study was conducted to evaluate the relationship between geological and paleoenvironmental parameters and the bacterial and archaeal community structure of two contrasting subseafloor sites in the Western Mediterranean Sea (Ligurian Sea and Gulf of Lion. Both depositional environments in this area are well-documented from paleoclimatic and paleooceanographic point of views. Available data sets allowed us to calibrate the investigated cores with reference and dated cores previously collected in the same area, and notably correlated to Quaternary climate variations. DNA-based fingerprints showed that the archaeal diversity was composed by one group, Miscellaneous Crenarchaeotic Group (MCG, within the Gulf of Lion sediments and of nine different lineages (dominated by MCG, South African Gold Mine Euryarchaeotal Group (SAGMEG and Halobacteria within the Ligurian Sea sediments. Bacterial molecular diversity at both sites revealed mostly the presence of the classes Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria within Proteobacteria phylum, and also members of Bacteroidetes phylum. The second most abundant lineages were Actinobacteria and Firmicutes at the Gulf of Lion site and Chloroflexi at the Ligurian Sea site. Various substrates and cultivation conditions allowed us to isolate 75 strains belonging to four lineages: Alpha-, Gammaproteobacteria, Firmicutes and Actinobacteria. In molecular surveys, the Betaproteobacteria group was consistently detected in the Ligurian Sea sediments, characterized by a heterolithic facies with numerous turbidites from a deep-sea levee. Analysis of relative betaproteobacterial abundances and turbidite frequency suggested that the microbial diversity was a result of main climatic changes occurring during the last 20 ka. Statistical direct multivariate canonical correspondence

Shifts among Eukaryota, Bacteria, and Archaea define the vertical organization of a lake sediment.

Science.gov (United States)

Wurzbacher, Christian; Fuchs, Andrea; Attermeyer, Katrin; Frindte, Katharina; Grossart, Hans-Peter; Hupfer, Michael; Casper, Peter; Monaghan, Michael T

2017-04-08

Lake sediments harbor diverse microbial communities that cycle carbon and nutrients while being constantly colonized and potentially buried by organic matter sinking from the water column. The interaction of activity and burial remained largely unexplored in aquatic sediments. We aimed to relate taxonomic composition to sediment biogeochemical parameters, test whether community turnover with depth resulted from taxonomic replacement or from richness effects, and to provide a basic model for the vertical community structure in sediments. We analyzed four replicate sediment cores taken from 30-m depth in oligo-mesotrophic Lake Stechlin in northern Germany. Each 30-cm core spanned ca. 170 years of sediment accumulation according to 137 Cs dating and was sectioned into layers 1-4 cm thick. We examined a full suite of biogeochemical parameters and used DNA metabarcoding to examine community composition of microbial Archaea, Bacteria, and Eukaryota. Community β-diversity indicated nearly complete turnover within the uppermost 30 cm. We observed a pronounced shift from Eukaryota- and Bacteria-dominated upper layers (14 cm) dominated by enigmatic Archaea that typically occur in deep-sea sediments. Taxonomic replacement was the prevalent mechanism in structuring the community composition and was linked to parameters indicative of microbial activity (e.g., CO 2 and CH 4 concentration, bacterial protein production). Richness loss played a lesser role but was linked to conservative parameters (e.g., C, N, P) indicative of past conditions. By including all three domains, we were able to directly link the exponential decay of eukaryotes with the active sediment microbial community. The dominance of Archaea in deeper layers confirms earlier findings from marine systems and establishes freshwater sediments as a potential low-energy environment, similar to deep sea sediments. We propose a general model of sediment structure and function based on microbial characteristics and

Variation in PAH inputs and microbial community in surface sediments of Hamilton Harbour: Implications to remediation and monitoring

International Nuclear Information System (INIS)

Slater, G.F.; Cowie, B.R.; Harper, N.; Droppo, I.G.

2008-01-01

Variations in concentrations of polycyclic aromatic hydrocarbons (PAHs) and microbial community indicators were investigated in representative highly contaminated and less contaminated surface sediment sites of Hamilton Harbour. Inputs of PAH to the upper 3 cm of sediments up to four times the average upper sediment concentrations were observed. Associated PAH fingerprint profiles indicated that the source was consistent with the PAH source to the industrial region of the harbour. Increased PAH loadings were associated with decreased bacterial populations as indicated by phospholipid fatty acid (PLFA) concentrations. However, relatively minor impacts on overall community composition were indicated. Porewater methane concentrations and isotopic data indicated a difference in the occurrence of methane oxidation between the two sites. This study confirms temporally limited transport of contaminants from highly impacted regions as a vector for contaminants within the harbour and the impact on microbial carbon cycling and bed stability. - Variations in PAH inputs to harbour sediments have implications to implementation and monitoring of mitigation/remediation efforts

Microbial response to oil enrichment in Gulf of Mexico sediment measured using a novel long-term benthic lander system

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Beth N. Orcutt

2017-04-01

Full Text Available Weathered crude oil sank to the seafloor following the 'Deepwater Horizon' disaster in 2010, removing this oil from further physical and photo-chemical degradation processes and leaving benthic processes as the mechanisms for altering and remediating this hydrocarbon source. To quantify potential microbial oil degradation rates at the seafloor, and associated changes in sediment microbial community structure and pore fluid composition, we used a benthic lander system to deploy novel sediment flow-through chambers at a natural hydrocarbon seep in the Gulf of Mexico (at a depth of 1226 m in lease block GC600 roughly 265 km southwest of the 'Deepwater Horizon' wellhead (at 1500 m depth. Sediment amended with 20% unweathered crude oil had elevated rates of sulfate reduction over the course of the 5-month-long experiment as compared to an unamended control, yielding potential rates of sulfate reduction (600–800 mmol m–2 d–1 among the highest measured in hydrocarbon-influenced seafloor sediment. Oil amendment also stimulated methane production towards the end of the experiment, and led to slightly higher cell densities without significant changes in microbial community structure, based on 16S rRNA gene sequence libraries and fatty acid profiles. Assuming a link between sulfate reduction and hydrocarbon degradation, these results suggest that electron acceptor availability may become limiting in heavily oiled deep-sea environments, resulting in minimal degradation of deposited oil. This study provides unique data on seafloor sediment responses to oil deposition, and reveals the value of using observatories to fill the gap in understanding deep-sea microbial processes, especially for ephemeral and stochastic events such as oil spills.

Quantitative microbial risk assessment (QMRA) shows increased public health risk associated with exposure to river water under conditions of riverbed sediment resuspension.

Science.gov (United States)

Abia, Akebe Luther King; Ubomba-Jaswa, Eunice; Genthe, Bettina; Momba, Maggy Ndombo Benteke

2016-10-01

Although higher microbial concentrations have been reported in sediments than in the overlying water column, most quantitative microbial risk assessment (QMRA) studies have not clearly indicated the contribution of sediment-borne pathogens to estimated risks. Thus, the present study aimed at determining the public health risk associated with exposure to pathogenic bacteria in polluted river water under undisturbed conditions and conditions of sediment resuspension in the Apies River, Gauteng, South Africa. Microbial pathogens were isolated and identified using culture and molecular methods. The beta-Poisson dose-response model was used to estimate the probability of infection (Pi) with the various pathogens, following accidental/intentional ingestion of 1mL or 100mL (or 50mL) of untreated river water. Mean wet season Escherichia coli counts ranged between 5.8E+01 and 8.8E+04MPN/100mL (water column) and between 2.40E+03 and 1.28E+05MPN/100mL (sediments). Mean dry season E. coli counts ranged between 5.11E+00 and 3.40E+03MPN/100mL (water column) and between 5.09E+00 and 6.30E+03MPN/100mL (sediments). Overall (water and sediments) Vibrio cholerae was the most detected pathogen (58.8%) followed by Salmonella spp. (23.9%) and Shigella (10.1%). Ingestion of 1mL of river water could lead to 0%-4% and 1%-74% Pi with E. coli during the dry and wet season, respectively. During the dry season, the Pi with V. cholerae, Salmonella spp. and Shigella spp. were 0%-1.39%, 0%-4.11% and 0%-0.16% respectively, depending on volume of water ingested. The risks of infections with all microorganisms increased during the wet season. A 2-log increase in water E. coli count following sediments disturbance led to approximately 10 times higher Pi with E. coli than when sediments were undisturbed. Therefore, the use of the untreated water from the Apies River for drinking, household purposes or recreational activities poses a potential health risk to the users of the river. Copyright © 2016

D:L-Amino Acid Modeling Reveals Fast Microbial Turnover of Days to Months in the Subsurface Hydrothermal Sediment of Guaymas Basin

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Mikkel H. Møller

2018-05-01

Full Text Available We investigated the impact of temperature on the microbial turnover of organic matter (OM in a hydrothermal vent system in Guaymas Basin, by calculating microbial bio- and necromass turnover times based on the culture-independent D:L-amino acid model. Sediments were recovered from two stations near hydrothermal mounds (<74°C and from one cold station (<9°C. Cell abundance at the two hydrothermal stations dropped from 108 to 106 cells cm-3 within ∼5 m of sediment depth resulting in a 100-fold lower cell number at this depth than at the cold site where numbers remained constant at 108 cells cm-3 throughout the recovered sediment. There were strong indications that the drop in cell abundance was controlled by decreasing OM quality. The quality of the sedimentary OM was determined by the diagenetic indicators %TAAC (percentage of total organic carbon present as amino acid carbon, %TAAN (percentage of total nitrogen present as amino acid nitrogen, aspartic acid:β-alanine ratios, and glutamic acid:γ-amino butyric acid ratios. All parameters indicated that the OM became progressively degraded with increasing sediment depth, and the OM in the hydrothermal sediment was more degraded than in the uniformly cold sediment. Nonetheless, the small community of microorganisms in the hydrothermal sediment demonstrated short turnover times. The modeled turnover times of microbial bio- and necromass in the hydrothermal sediments were notably faster (biomass: days to months; necromass: up to a few hundred years than in the cold sediments (biomass: tens of years; necromass: thousands of years, suggesting that temperature has a significant influence on the microbial turnover rates. We suggest that short biomass turnover times are necessary for maintance of essential cell funtions and to overcome potential damage caused by the increased temperature.The reduced OM quality at the hyrothemal sites might thus only allow for a small population size of microorganisms.

Microbial reductive transformation of phyllosilicate Fe(III) and U(VI) in fluvial subsurface sediments.

Science.gov (United States)

Lee, Ji-Hoon; Fredrickson, James K; Kukkadapu, Ravi K; Boyanov, Maxim I; Kemner, Kenneth M; Lin, Xueju; Kennedy, David W; Bjornstad, Bruce N; Konopka, Allan E; Moore, Dean A; Resch, Charles T; Phillips, Jerry L

2012-04-03

The microbial reduction of Fe(III) and U(VI) was investigated in shallow aquifer sediments collected from subsurface flood deposits near the Hanford Reach of the Columbia River in Washington State. Increases in 0.5 N HCl-extractable Fe(II) were observed in incubated sediments and (57)Fe Mössbauer spectroscopy revealed that Fe(III) associated with phyllosilicates and pyroxene was reduced to Fe(II). Aqueous uranium(VI) concentrations decreased in subsurface sediments incubated in sulfate-containing synthetic groundwater with the rate and extent being greater in sediment amended with organic carbon. X-ray absorption spectroscopy of bioreduced sediments indicated that 67-77% of the U signal was U(VI), probably as an adsorbed species associated with a new or modified reactive mineral phase. Phylotypes within the Deltaproteobacteria were more common in Hanford sediments incubated with U(VI) than without, and in U(VI)-free incubations, members of the Clostridiales were dominant with sulfate-reducing phylotypes more common in the sulfate-amended sediments. These results demonstrate the potential for anaerobic reduction of phyllosilicate Fe(III) and sulfate in Hanford unconfined aquifer sediments and biotransformations involving reduction and adsorption leading to decreased aqueous U concentrations.

Effects of shelter and enrichment on the ecology and nutrient cycling of microbial communities of subtidal carbonate sediments.

Science.gov (United States)

Forehead, Hugh I; Kendrick, Gary A; Thompson, Peter A

2012-04-01

The interactions between physical disturbances and biogeochemical cycling are fundamental to ecology. The benthic microbial community controls the major pathway of nutrient recycling in most shallow-water ecosystems. This community is strongly influenced by physical forcing and nutrient inputs. Our study tests the hypotheses that benthic microbial communities respond to shelter and enrichment with (1) increased biomass, (2) change in community composition and (3) increased uptake of inorganic nutrients from the water column. Replicate in situ plots were sheltered from physical disturbance and enriched with inorganic nutrients or left without additional nutrients. At t(0) and after 10 days, sediment-water fluxes of nutrients, O(2) and N(2) , were measured, the community was characterized with biomarkers. Autochthonous benthic microalgal (BMA) biomass increased 30% with shelter and a natural fivefold increase in nutrient concentration; biomass did not increase with greater enrichment. Diatoms remained the dominant taxon of BMA, suggesting that the sediments were not N or Si limited. Bacteria and other heterotrophic organisms increased with enrichment and shelter. Daily exchanges of inorganic nutrients between sediments and the water column did not change in response to shelter or nutrient enrichment. In these sediments, physical disturbance, perhaps in conjunction with nutrient enrichment, was the primary determinant of microbial biomass. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Influence of biological activity on sorption by using 65Zn and 109Cd into mangrove sediment

International Nuclear Information System (INIS)

Sondermann, Melissa N.; Barros, Joanna F.; Suzuki, Katia N.; Bellido, Alfredo V.B.; Lopes, Ricardo T.

2015-01-01

Evaluation of the chemical behavior of zinc and cadmium as well as the influence of biological activity in the sorption kinetics under microcosm experiments by mangrove sediments collected in Sepetiba Bay - Rio de Janeiro was carried out. The mentioned area was well contaminated due to the leaching from the tailing pile by the abandoned zinc processing company Inga Mercantil. Radiotracer 65 Zn and 109 Cd were used to follow their exchange across water-sediment interfaces up to 48 hours experiments in six mangrove sediment cores. To determine the benthic activity index (BAI) the cores were treated with formaldehyde (biocide) and it was found that the presence of the radiotracers in the deeper layers of sediment without formaldehyde treatment showed clearly the influence of benthic activity retention (benthic faunal and microbial effects), since the same pattern was not found in the treated sediment. The activity values obtained for 65 Zn and 109 Cd in the untreated sediment with formaldehyde on the first centimeter were 53.79±0.28 % and 67.34±0.16 % respectively, whereas for the treated ones, were 98.72 ± 0.29 % and 98.31 ± 0.24 % respectively. Thus, it was demonstrated that the use of formaldehyde, as biological activity inhibitor, ceases the bioturbation process and allowed the accumulation along the sediment. (author)

Bacterial diversity is strongly associated with historical penguin activity in an Antarctic lake sediment profile.

Science.gov (United States)

Zhu, Renbin; Shi, Yu; Ma, Dawei; Wang, Can; Xu, Hua; Chu, Haiyan

2015-11-25

Current penguin activity in Antarctica affects the geochemistry of sediments and their microbial communities; the effects of historical penguin activity are less well understood. Here, bacterial diversity in ornithogenic sediment was investigated using high-throughput pyrosequencing. The relative abundances of dominant phyla were controlled by the amount of historical penguin guano deposition. Significant positive correlations were found between both the bacterial richness and diversity, and the relative penguin number (p penguin activity drove the vertical distribution of the bacterial communities. The lowest relative abundances of individual phyla corresponded to lowest number of penguin population at 1,800-2,300 yr BP during a drier and colder period; the opposite was observed during a moister and warmer climate (1,400-1,800 yr BP). This study shows that changes in the climate over millennia affected penguin populations and the outcomes of these changes affect the sediment bacterial community today.

Diversity of Microbial Communities and Quantitative Chemodiversity in Layers of Marine Sediment Cores from a Causeway (Kaichu-Doro) in Okinawa Island, Japan.

Science.gov (United States)

Soliman, Taha; Reimer, James D; Yang, Sung-Yin; Villar-Briones, Alejandro; Roy, Michael C; Jenke-Kodama, Holger

2017-01-01

Microbial community diversity and chemodiversity were investigated in marine sediments adjacent to the Okinawan "Kaichu-Doro" Causeway, which was constructed 46 years ago to connect a group of four islands (Henza-jima, Miyagi-jima, Ikei-jima, Hamahiga-jima) to the Okinawan main island. This causeway was not built on pilings, but by land reclamation; hence, it now acts as a long, thin peninsula. The construction of this causeway was previously shown to have influenced the surrounding marine ecosystem, causing ecosystem fragmentation and loss of water circulation. In this study, we collected sediment cores ( n = 10) from five paired sites in 1 m water depths. Each pair of sites consisted of one site each on the immediate north and south sides of the causeway. Originally the members of each pair were much closer to each other (microbial communities and chemical compounds to determine the correlation between chemodiversity and microbial communities among marine sediment cores and layers. Principal coordinate analyses (PCoA) of detected compounds and of bacterial and archaeal operational taxonomic units (OTUs) revealed that the north and south sides of the causeway are relatively isolated, with each side having unique microbial OTUs. Additionally, some bacterial families (e.g., Acidaminobacteraceae, Rhizobiaceae, and Xanthomonadaceae) were found only on the south side of Kaichu-Doro. Interestingly, we found that the relative abundance of OTUs for some microbial families increased from top to bottom, but this was reversed in some other families. We conclude that the causeway has altered microbial community composition and metabolite profiles in marine sediments.

Carbon and nitrogen assimilation in deep subseafloor microbial cells

OpenAIRE

Morono, Yuki; Terada, Takeshi; Nishizawa, Manabu; Ito, Motoo; Hillion, François; Takahata, Naoto; Sano, Yuji; Inagaki, Fumio

2011-01-01

Remarkable numbers of microbial cells have been observed in global shallow to deep subseafloor sediments. Accumulating evidence indicates that deep and ancient sediments harbor living microbial life, where the flux of nutrients and energy are extremely low. However, their physiology and energy requirements remain largely unknown. We used stable isotope tracer incubation and nanometer-scale secondary ion MS to investigate the dynamics of carbon and nitrogen assimilation activities in individua...

Hourly and daily variation of sediment redox potential in tidal wetland sediments

Science.gov (United States)

Catallo, W. James

1999-01-01

Variation of electrochemical oxidation-reduction (redox) potential was examined in surface salt march sediments under conditions of flooding and tidal simulation in mesocosms and field sites. Time series were generated of redox potential measured in sediment profiles at 2-10 cm depth using combination Pt-Ag/AgCl (ORP) electrodes. Redox potential data were acquired at rapid rates (1-55 samples/h) over extended periods (3-104 days) along with similar times series of temperature (water, air, soil) and pH. It was found that redox potential vaired as a result of water level changes and was unrelated to diurnal changes in temperature or pH, the latter of which changed by 370 mV redox potential decrease in under 48 hours). Attenuatoin of microbial activity by [gamma] y-radiation and toxic chemicals elimintated this response. In tidal salt marsh mesocosms where the sediment-plant assemblages were exposed to a simulated diurnal tide, redox potenial oscillations of 40-300 mV amplitude were recoded that has the same periodicity as the flood-drain cycle. Periodic redoc potential time series were observed repeatedly in sediments receiving tidal pulsing but not in those sediments exposed to static hydrological conditions. Data collected over 12 days from a coastal marsh site experiencing diurnal tides showed similar fluctuations in redox potential. Data from the experimentents indicated that (a) redox potential can be a dynamic, nonlinear variable in coastal and estuarine wetland sediments over hourly and daily scales, and the designs of biogeochemical experiments should reflect this, (b) redox potential can change rapidly and signigicantly in coastal wetland sediments in response of flooding and draining, (c) microbial community processes are primarily determinants of the time course of redox potential in wetland sediments, and elimination of inhibition of microbial activity (e.g. by pollutants) can significantly alter that behavior, and (d) fast redox potential dynamics appear

Diatom-driven recolonization of microbial mat-dominated siliciclastic tidal flat sediments.

Science.gov (United States)

Pan, Jerónimo; Cuadrado, Diana G; Bournod, Constanza N

2017-10-01

Modern microbial mats and biofilms play a paramount role in sediment biostabilization. When sporadic storms affect tidal flats of Bahía Blanca Estuary, the underlying siliciclastic sediment is exposed by physical disruption of the mat, and in a few weeks' lapse, a microbial community re-establishes. With the objective of studying colonization patterns and the ecological succession of microorganisms at the scale of these erosional structures, these were experimentally made and their biological recolonization followed for 8 weeks, with replication in winter and spring. Motile pennate diatoms led the initial colonization following two distinct patterns: a dominance by Cylindrotheca closterium in winter and by naviculoid and nitzschioid diatoms in spring. During the first 7 days, cell numbers increased 2- to 17-fold. Cell densities further increased exhibiting sigmoidal community growth, reaching 2.9-8.9 × 106 cells cm-3 maxima around day 30; centric diatoms maintained low densities throughout. In 56 days after removal of the original mat, filamentous cyanobacteria that dominate mature mats did not establish a significant biomass, leading to the rejection of the hypothesis that cyanobacteria would drive the colonization. The observed dominance of pennate diatoms is attributed to extrinsic factors determined by tidal flooding, and intrinsic ones, e.g. motility, nutrient affinity and high growth rate. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

The Importance of Microbial Iron Sulfide Oxidation for Nitrate Depletion in Anoxic Danish Sediments

DEFF Research Database (Denmark)

Vaclavkova, Sarka; Jacobsen, Ole Stig; Jørgensen, Christian Juncher

2014-01-01

of organic carbon in the sediment. An apparent salinity limitation to MISON was observed in the most brackish environment. Addition of high surface area synthetically precipitated iron sulfide (FeS x ) to the aquifer sediment with the lowest natural FeS x reactivity increased both the relative fraction of NO......Nitrate (NO3 −) reduction processes are important for depleting the NO3 − load from agricultural source areas before the discharge water reaches surface waters or groundwater aquifers. In this study, we experimentally demonstrate the co-occurrence of microbial iron sulfide oxidation by NO3 − (MISON......) and other NO3 −-depleting processes in a range of contrasting sediment types: sandy groundwater aquifer, non-managed minerotrophic freshwater peat and two brackish muddy sediments. Approximately 1/3 of the net NO3 − reduction was caused by MISON in three of the four environments despite the presence...

Microbial and biochemical alterations due to storage of deep-sea sediments under ambient tropical conditions

Digital Repository Service at National Institute of Oceanography (India)

Das, A.; Fernandes, C.E.G.; Naik, S.S.; Mourya, B.S.; Sujith, P.P.; Sharma, R; LokaBharathi, P.A.

-tight polythene containers. Changes in microbial and biochemical parameters were monitored once in every two months for a year. Bacterial counts and ATP decreased from ~108 to ~107 g-1 and ~103 to ~101 ng g-1 dry sediment respectively, within 8-10 months before...

Culture-Dependent and Independent Studies of Microbial Diversity in Highly Copper-Contaminated Chilean Marine Sediments

NARCIS (Netherlands)

Besaury, L.; Marty, F.; Buquet, S.; Mesnage, V.; Muijzer, G.; Quillet, L.

2013-01-01

Cultivation and molecular-based approaches were used to study microbial diversity in two Chilean marine sediments contaminated with high (835 ppm) and very high concentrations of copper (1,533 ppm). The diversity of cultivable bacteria resistant to copper was studied at oxic and anoxic conditions,

Multitaxon activity profiling reveals differential microbial response to reduced seawater pH and oil pollution.

Science.gov (United States)

Coelho, Francisco J R C; Cleary, Daniel F R; Costa, Rodrigo; Ferreira, Marina; Polónia, Ana R M; Silva, Artur M S; Simões, Mário M Q; Oliveira, Vanessa; Gomes, Newton C M

2016-09-01

There is growing concern that predicted changes to global ocean chemistry will interact with anthropogenic pollution to significantly alter marine microbial composition and function. However, knowledge of the compounding effects of climate change stressors and anthropogenic pollution is limited. Here, we used 16S and 18S rRNA (cDNA)-based activity profiling to investigate the differential responses of selected microbial taxa to ocean acidification and oil hydrocarbon contamination under controlled laboratory conditions. Our results revealed that a lower relative abundance of sulphate-reducing bacteria (Desulfosarcina/Desulfococcus clade) due to an adverse effect of seawater acidification and oil hydrocarbon contamination (reduced pH-oil treatment) may be coupled to changes in sediment archaeal communities. In particular, we observed a pronounced compositional shift and marked reduction in the prevalence of otherwise abundant operational taxonomic units (OTUs) belonging to the archaeal Marine Benthic Group B and Marine Hydrothermal Vent Group (MHVG) in the reduced pH-oil treatment. Conversely, the abundance of several putative hydrocarbonoclastic fungal OTUs was higher in the reduced pH-oil treatment. Sediment hydrocarbon profiling, furthermore, revealed higher concentrations of several alkanes in the reduced pH-oil treatment, corroborating the functional implications of the structural changes to microbial community composition. Collectively, our results advance the understanding of the response of a complex microbial community to the interaction between reduced pH and anthropogenic pollution. In future acidified marine environments, oil hydrocarbon contamination may alter the typical mixotrophic and k-/r-strategist composition of surface sediment microbiomes towards a more heterotrophic state with lower doubling rates, thereby impairing the ability of the ecosystem to recover from acute oil contamination events. © 2016 John Wiley & Sons Ltd.

Microbial Sulfate Reduction in Deep-Sea Sediments at the Guaymas Basin - Hydrothermal Vent Area - Influence of Temperature and Substrates

DEFF Research Database (Denmark)

ELSGAARD, L.; ISAKSEN, MF; JØRGENSEN, BB

1994-01-01

Microbial sulfate reduction was studied by a S-35 tracer technique in sediments from the hydrothermal vent site in Guaymas Basin, Gulf of California, Mexico. In situ temperatures ranged from 2.7-degrees-C in the overlying seawater to > 120-degrees-C at 30 cm depth in the hydrothermal sediment...

Methane emission in a specific riparian-zone sediment decreased with bioelectrochemical manipulation and corresponded to the microbial community dynamics

Directory of Open Access Journals (Sweden)

Elliot S. Friedman

2016-01-01

Full Text Available Dissimilatory metal-reducing bacteria are widespread in terrestrial ecosystems, especially in anaerobic soils and sediments. Thermodynamically, dissimilatory metal reduction is more favorable than sulfate reduction and methanogenesis but less favorable than denitrification and aerobic respiration. It is critical to understand the complex relationships, including the absence or presence of terminal electron acceptors, that govern microbial competition and coexistence in anaerobic soils and sediments, because subsurface microbial processes can effect greenhouse gas emissions from soils, possibly resulting in impacts at the global scale. Here, we elucidated the effect of an inexhaustible, ferrous-iron and humic-substance mimicking terminal electron acceptor by deploying potentiostatically poised electrodes in the sediment of a very specific stream riparian zone in Upstate New York state. At two sites within the same stream riparian zone during the course of six weeks in the spring of 2013, we measured CH4 and N2/N2O emissions from soil chambers containing either poised or unpoised electrodes, and we harvested biofilms from the electrodes to quantify microbial community dynamics. At the upstream site, which had a lower vegetation cover and highest soil temperatures, the poised electrodes inhibited CH4 emissions by ~45% (when normalized to remove temporal effects. CH4 emissions were not significantly impacted at the downstream site. N2/N2O emissions were generally low at both sites and were not impacted by poised electrodes. We did not find a direct link between bioelectrochemical treatment and microbial community membership; however, we did find a correspondence between environment/function and microbial community dynamics.

Determinants of the microbial community structure of eutrophic, hyporheic river sediments polluted with chlorinated aliphatic hydrocarbons

NARCIS (Netherlands)

Hamonts, K.; Ryngaert, A.; Smidt, H.; Springael, D.; Dejonghe, W.

2014-01-01

Chlorinated aliphatic hydrocarbons (CAHs) often discharge into rivers as contaminated groundwater baseflow. As biotransformation of CAHs in the impacted river sediments might be an effective remediation strategy, we investigated the determinants of the microbial community structure of eutrophic,

Marine Subsurface Microbial Communities Across a Hydrothermal Gradient in Okinawa Trough Sediments

Science.gov (United States)

Brandt, L. D.; Hser Wah Saw, J.; Ettema, T.; House, C. H.

2015-12-01

IODP Expedition 331 to the Okinawa backarc basin provided an opportunity to study the microbial stratigraphy within the sediments surrounding a hydrothermal vent. The Okinawa backarc basin is a sedimented region of the seafloor located on a continental margin, and also hosts a hydrothermal network within the subsurface. Site C0014 within the Iheya North hydrothermal field is located 450 m east of the active vent and has a surface temperature of 5°C with no evidence of hydrothermal alteration within the top 10 meters below sea floor (mbsf). Temperature increases with depth at an estimated rate of 3°C/m and transitions from non-hydrothermal margin sediments to a hydrothermally altered regime below 10 mbsf. In this study, we utilized deep 16S rRNA sequencing of DNA from IODP Expedition 331 Site C0014 sediment horizons in order to assess diversity throughout the sediment column as well as determine the potential limits of the biosphere. Analysis of the amplicon data shows a shift over 15 mbsf from a heterogeneous community of cosmopolitan marine subsurface taxa toward an archaeal-dominated community in the deepest horizons of the predicted biosphere. Notably, the phylum Chloroflexi represents a substantial taxon through most horizons, where it appears to be replaced below 10 mbsf by punctuations of thermophilic and methanotrophic Archaea and Miscellaneous Crenarchaeotic Group abundances. DNA from the aforementioned transition horizons was further analyzed using metagenomic sequencing. Preliminary taxonomic analysis of the metagenomic data agrees well with amplicon data in capturing the shift in relative abundance of Archaea increasing with depth. Additionally, reverse gyrase, a gene found exclusively in hyperthermophilic microorganisms, was recovered only in the metagenome of the deepest horizon. A BLAST search of this protein sequence against the GenBank non-redudnant protein database produced top hits with reverse gyrase from Thermococcus and Pyrococcus, which are

Bacterial sulfur cycle shapes microbial communities in surface sediments of an ultramafic hydrothermal vent field

DEFF Research Database (Denmark)

Schauer, Regina; Røy, Hans; Augustin, Nico

2011-01-01

RNA sequence analysis, was characterized by the capability to metabolize sulfur components. High sulfate reduction rates as well as sulfide depleted in (34)S further confirmed the importance of the biogeochemical sulfur cycle. In contrast, methane was found to be of minor relevance for microbial life in mat......, these sediments were investigated in order to determine biogeochemical processes and key organisms relevant for primary production. Temperature profiling at two mat-covered sites showed a conductive heating of the sediments. Elemental sulfur was detected in the overlying mat and metal-sulfides in the upper...

Comparison in performance of sediment microbial fuel cells according to depth of embedded anode.

Science.gov (United States)

An, Junyeong; Kim, Bongkyu; Nam, Jonghyeon; Ng, How Yong; Chang, In Seop

2013-01-01

Five rigid graphite plates were embedded in evenly divided sections of sediment, ranging from 2 cm (A1) to 10 cm (A5) below the top sediment layer. The maximum power and current of the MFCs increased in depth order; however, despite the increase in the internal resistance, the power and current density of the A5 MFC were 2.2 and 3.5 times higher, respectively, than those of the A1 MFC. In addition, the anode open circuit potentials (OCPs) of the sediment microbial fuel cells (SMFCs) became more negative with sediment depth. Based on these results, it could be then concluded that as the anode-embedding depth increases, that the anode environment is thermodynamically and kinetically favorable to anodophiles or electrophiles. Therefore, the anode-embedding depth should be considered an important parameter that determines the performance of SMFCs, and we posit that the anode potential could be one indicator for selecting the anode-embedding depth. Copyright © 2012 Elsevier Ltd. All rights reserved.

Suitability of granular carbon as an anode material for sediment microbial fuel cells

Energy Technology Data Exchange (ETDEWEB)

Arends, Jan B.A.; Blondeel, Evelyne; Boon, Nico; Verstraete, Willy [Ghent Univ. (Belgium). Faculty of Bioscience Engineering; Tennison, Steve R. [Mast Carbon International Ltd., Basingstoke, Hampshire (United Kingdom)

2012-08-15

Purpose: Sediment microbial fuel cells (S-MFCs) are bio-electrochemical devices that are able to oxidize organic matter directly into harvestable electrical power. The flux of organic matter into the sediment is rather low; therefore, other researchers have introduced plants for a continuous supply of organic matter to the anode electrode. Until now only interconnected materials have been considered as anode materials in S-MFCs. Here, granular carbon materials were investigated for their suitability as an anode material in S-MFCs. Materials and methods: Laboratory microcosms with eight different electrode materials (granules, felts and cloths) were examined with controlled organic matter addition under brackish conditions. Current density, organic matter removal and microbial community composition were monitored using 16S rRNA gene PCR followed by denaturing gradient gel electrophoresis (DGGE). The main parameters investigated were the influence of the amount of electrode material applied to the sediment, the size of the granular material and the electrode configuration. Results and discussion: Felt material had an overall superior performance in terms of current density per amount of applied electrode material; felt and granular anode obtained similar current densities (approx. 50-60 mA m{sup -2}), but felt materials required 29 % less material to be applied. Yet, when growing plants, granular carbon is more suited because it is considered to restore, upon disturbance, the electrical connectivity within the anode compartment. Small granules (0.25-0.5 mm) gave the highest current density compared to larger granules (1-5 mm) of the same material. Granules with a rough surface had a better performance compared to smooth granules of the same size. The different granular materials lead to a selection of distinct microbial communities for each material, as shown by DGGE. Conclusions: Granular carbon is suitable as an anode material for S-MFCs. This opens the possibility

Diversity of Microbial Communities and Quantitative Chemodiversity in Layers of Marine Sediment Cores from a Causeway (Kaichu-Doro in Okinawa Island, Japan

Directory of Open Access Journals (Sweden)

Taha Soliman

2017-12-01

Full Text Available Microbial community diversity and chemodiversity were investigated in marine sediments adjacent to the Okinawan “Kaichu-Doro” Causeway, which was constructed 46 years ago to connect a group of four islands (Henza-jima, Miyagi-jima, Ikei-jima, Hamahiga-jima to the Okinawan main island. This causeway was not built on pilings, but by land reclamation; hence, it now acts as a long, thin peninsula. The construction of this causeway was previously shown to have influenced the surrounding marine ecosystem, causing ecosystem fragmentation and loss of water circulation. In this study, we collected sediment cores (n = 10 from five paired sites in 1 m water depths. Each pair of sites consisted of one site each on the immediate north and south sides of the causeway. Originally the members of each pair were much closer to each other (<150 m than to other pairs, but now the members of each pair are isolated by the causeway. Each core was 60–80 cm long and was divided into 15-cm layers. We examined the vertical diversity of microbial communities and chemical compounds to determine the correlation between chemodiversity and microbial communities among marine sediment cores and layers. Principal coordinate analyses (PCoA of detected compounds and of bacterial and archaeal operational taxonomic units (OTUs revealed that the north and south sides of the causeway are relatively isolated, with each side having unique microbial OTUs. Additionally, some bacterial families (e.g., Acidaminobacteraceae, Rhizobiaceae, and Xanthomonadaceae were found only on the south side of Kaichu-Doro. Interestingly, we found that the relative abundance of OTUs for some microbial families increased from top to bottom, but this was reversed in some other families. We conclude that the causeway has altered microbial community composition and metabolite profiles in marine sediments.

Temporal and Spatial Distribution of the Microbial Community of Winogradsky Columns.

Directory of Open Access Journals (Sweden)

David J Esteban

Full Text Available Winogradsky columns are model microbial ecosystems prepared by adding pond sediment to a clear cylinder with additional supplements and incubated with light. Environmental gradients develop within the column creating diverse niches that allow enrichment of specific bacteria. The enrichment culture can be used to study soil and sediment microbial community structure and function. In this study we used a 16S rRNA gene survey to characterize the microbial community dynamics during Winogradsky column development to determine the rate and extent of change from the source sediment community. Over a period of 60 days, the microbial community changed from the founding pond sediment population: Cyanobacteria, Chloroflexi, Nitrospirae, and Planctomycetes increased in relative abundance over time, while most Proteobacteria decreased in relative abundance. A unique, light-dependent surface biofilm community formed by 60 days that was less diverse and dominated by a few highly abundant bacteria. 67-72% of the surface community was comprised of highly enriched taxa that were rare in the source pond sediment, including the Cyanobacteria Anabaena, a member of the Gemmatimonadetes phylum, and a member of the Chloroflexi class Anaerolinea. This indicates that rare taxa can become abundant under appropriate environmental conditions and supports the hypothesis that rare taxa serve as a microbial seed bank. We also present preliminary findings that suggest that bacteriophages may be active in the Winogradsky community. The dynamics of certain taxa, most notably the Cyanobacteria, showed a bloom-and-decline pattern, consistent with bacteriophage predation as predicted in the kill-the-winner hypothesis. Time-lapse photography also supported the possibility of bacteriophage activity, revealing a pattern of colony clearance similar to formation of viral plaques. The Winogradsky column, a technique developed early in the history of microbial ecology to enrich soil

Radioactive tracers as a tool for the study of in situ meiofaunal-microbial trophic interactions in marine sediments

International Nuclear Information System (INIS)

Carman, K.R.

1989-01-01

Three methods of delivering labeled substrates to natural cores of sediments were compared. Slurried sediments disrupted the sedimentary structure and significantly altered uptake of labeled substrates by copepod species. Thus, disruption of sedimentary structure can significantly alter microbial-meiofaunal interactions and influence the results of grazing studies. The [ 3 H]-thymidine technique for measuring bacterial production was evaluated. The metabolic fate of labeled thymidine in a coastal marine sediment was not consistent with assumptions necessary for measuring bacterial production or its consumption by meiofauna. Microautoradiography was used to demonstrate the sedimentary microalgae and heterotrophic bacteria can be selectively labeled with [ 14 C]bicarbonate and labeled organic substrates, respectively. A study was performed to determine if radioactivity measured in copepods from grazing experiments was the result of ingestion of labeled microorganisms or the result of uptake by non-feeding processes. Uptake of label by copepods from [ 14 C]-bicarbonate was due almost exclusively to grazing on microalgae. Uptake of label by copepods from [ 14 C]-acetate, however, resulted from activity by epicuticular bacteria and was not due to ingestion of labeled bacteria

Influence of biological activity on sorption by using {sup 65}Zn and {sup 109}Cd into mangrove sediment

Energy Technology Data Exchange (ETDEWEB)

Sondermann, Melissa N.; Barros, Joanna F.; Suzuki, Katia N.; Bellido, Alfredo V.B., E-mail: melissa.sonder@gmail.com, E-mail: joanna_barros2@hotmail.com, E-mail: ksuzuki@id.uff.br, E-mail: alfredobellido@gmail.com [Universidade Federal Fluminense (UFF), Niteroi, RJ (Brazil). Instituto de Quimica. Pos-Graduacao em Geoquimica Ambiental; Bellido, Luis F., E-mail: lbellido@cnen.gov.br [Instituto de Radioprotecao e Dosimetria (IRD/CNEN-RJ), Rio de Janeiro, RJ (Brazil); Lopes, Ricardo T., E-mail: ricardo@lin.ufrj.br [Coordenacao dos Programas de Pos-Graduacao em Engenharia (COPPE/UFRJ), Rio de Janeiro, RJ (Brazil)

2015-07-01

Evaluation of the chemical behavior of zinc and cadmium as well as the influence of biological activity in the sorption kinetics under microcosm experiments by mangrove sediments collected in Sepetiba Bay - Rio de Janeiro was carried out. The mentioned area was well contaminated due to the leaching from the tailing pile by the abandoned zinc processing company Inga Mercantil. Radiotracer {sup 65}Zn and {sup 109}Cd were used to follow their exchange across water-sediment interfaces up to 48 hours experiments in six mangrove sediment cores. To determine the benthic activity index (BAI) the cores were treated with formaldehyde (biocide) and it was found that the presence of the radiotracers in the deeper layers of sediment without formaldehyde treatment showed clearly the influence of benthic activity retention (benthic faunal and microbial effects), since the same pattern was not found in the treated sediment. The activity values obtained for {sup 65}Zn and {sup 109}Cd in the untreated sediment with formaldehyde on the first centimeter were 53.79±0.28 % and 67.34±0.16 % respectively, whereas for the treated ones, were 98.72 ± 0.29 % and 98.31 ± 0.24 % respectively. Thus, it was demonstrated that the use of formaldehyde, as biological activity inhibitor, ceases the bioturbation process and allowed the accumulation along the sediment. (author)

Living microbial ecosystems within the active zone of catagenesis: Implications for feeding the deep biosphere

Science.gov (United States)

Horsfield, B.; Schenk, H. J.; Zink, K.; Ondrak, R.; Dieckmann, V.; Kallmeyer, J.; Mangelsdorf, K.; di Primio, R.; Wilkes, H.; Parkes, R. J.; Fry, J.; Cragg, B.

2006-06-01

Earth's largest reactive carbon pool, marine sedimentary organic matter, becomes increasingly recalcitrant during burial, making it almost inaccessible as a substrate for microorganisms, and thereby limiting metabolic activity in the deep biosphere. Because elevated temperature acting over geological time leads to the massive thermal breakdown of the organic matter into volatiles, including petroleum, the question arises whether microorganisms can directly utilize these maturation products as a substrate. While migrated thermogenic fluids are known to sustain microbial consortia in shallow sediments, an in situ coupling of abiotic generation and microbial utilization has not been demonstrated. Here we show, using a combination of basin modelling, kinetic modelling, geomicrobiology and biogeochemistry, that microorganisms inhabit the active generation zone in the Nankai Trough, offshore Japan. Three sites from ODP Leg 190 have been evaluated, namely 1173, 1174 and 1177, drilled in nearly undeformed Quaternary and Tertiary sedimentary sequences seaward of the Nankai Trough itself. Paleotemperatures were reconstructed based on subsidence profiles, compaction modelling, present-day heat flow, downhole temperature measurements and organic maturity parameters. Today's heat flow distribution can be considered mainly conductive, and is extremely high in places, reaching 180 mW/m 2. The kinetic parameters describing total hydrocarbon generation, determined by laboratory pyrolysis experiments, were utilized by the model in order to predict the timing of generation in time and space. The model predicts that the onset of present day generation lies between 300 and 500 m below sea floor (5100-5300 m below mean sea level), depending on well location. In the case of Site 1174, 5-10% conversion has taken place by a present day temperature of ca. 85 °C. Predictions were largely validated by on-site hydrocarbon gas measurements. Viable organisms in the same depth range have been

Metagenomic Signatures of Microbial Communities in Deep-Sea Hydrothermal Sediments of Azores Vent Fields.

Science.gov (United States)

Cerqueira, Teresa; Barroso, Cristina; Froufe, Hugo; Egas, Conceição; Bettencourt, Raul

2018-01-21

The organisms inhabiting the deep-seafloor are known to play a crucial role in global biogeochemical cycles. Chemolithoautotrophic prokaryotes, which produce biomass from single carbon molecules, constitute the primary source of nutrition for the higher organisms, being critical for the sustainability of food webs and overall life in the deep-sea hydrothermal ecosystems. The present study investigates the metabolic profiles of chemolithoautotrophs inhabiting the sediments of Menez Gwen and Rainbow deep-sea vent fields, in the Mid-Atlantic Ridge. Differences in the microbial community structure might be reflecting the distinct depth, geology, and distance from vent of the studied sediments. A metagenomic sequencing approach was conducted to characterize the microbiome of the deep-sea hydrothermal sediments and the relevant metabolic pathways used by microbes. Both Menez Gwen and Rainbow metagenomes contained a significant number of genes involved in carbon fixation, revealing the largely autotrophic communities thriving in both sites. Carbon fixation at Menez Gwen site was predicted to occur mainly via the reductive tricarboxylic acid cycle, likely reflecting the dominance of sulfur-oxidizing Epsilonproteobacteria at this site, while different autotrophic pathways were identified at Rainbow site, in particular the Calvin-Benson-Bassham cycle. Chemolithotrophy appeared to be primarily driven by the oxidation of reduced sulfur compounds, whether through the SOX-dependent pathway at Menez Gwen site or through reverse sulfate reduction at Rainbow site. Other energy-yielding processes, such as methane, nitrite, or ammonia oxidation, were also detected but presumably contributing less to chemolithoautotrophy. This work furthers our knowledge of the microbial ecology of deep-sea hydrothermal sediments and represents an important repository of novel genes with potential biotechnological interest.

Distribution, activity and function of short-chain alkane degrading phylotypes in hydrothermal vent sediments

Science.gov (United States)

Adams, M. M.; Joye, S. B.; Hoarfrost, A.; Girguis, P. R.

2012-12-01

hydrocarbon species characteristic of these metalliferous sediments. These systems are also characterized by sharp physicochemical gradients that have been shown to have a pronounced effect on microbial ecology and activity. Sediments were collected from a Middle Valley field with relatively high concentrations of short-chain alkanes and incubated in anaerobic batch reactors with each individual alkane (C1, C2, C3 and C4, respectively) at a range of temperatures (25, 55 and 75 °C) to mimic environmental physico-chemical conditions in a closed system. Stable carbon isotope ratios and radiotracer incubations provide clear evidence for C2-C4 alkane oxidation in the sediments over time. Upon identifying sediments with anaerobic alkane oxidation activity, microbial communities were screened via 16S rRNA pyrosequencing, and key phylotypes were then quantified using both molecular and microscopic methods. There were shifts in overall community composition and putative alkane-oxidizing phylotypes after the incubation period with the alkane substrates. These are the first evidence to date indicating that anaerobic C2-C4 alkane oxidation occurs across a broad range of temperatures in metalliferous sediments.

Microbial characterization of a radionuclide- and metal-contaminated waste site

International Nuclear Information System (INIS)

Bolton, H. Jr.; Lumppio, H.L.; Ainsworth, C.C.; Plymale, A.E.

1993-04-01

The operation of nuclear processing facilities and defense-related nuclear activities has resulted in contamination of near-surface and deep-subsurface sediments with both radionuclides and metals. The presence of mixed inorganic contaminants may result in undetectable microbial populations or microbial populations that are different from those present in uncontaminated sediments. To determine the impact of mixed radionuclide and metal contaminants on sediment microbial communities, we sampled a processing pond that was used from 1948 to 1975 for the disposal of radioactive and metal-contaminated wastewaters from laboratories and nuclear fuel fabrication facilities on the Hanford Site in Washington State. Because the Hanford Site is located in a semiarid environment with average rainfall of 159 mm/year, the pond dried and a settling basin remained after wastewater input into the pond ceased in 1975. This processing pond basin offered a unique opportunity to obtain near-surface sediments that had been contaminated with both radionuclides and metals for several decades. Our objectives were to determine the viable populations of microorganisms in the sediments and to test several hypotheses about how the addition of both radionuclides and metals influenced the microbial ecology of the sediments. Our first hypothesis was that viable populations of microorganisms would be lower in the more contaminated sediments. Second, we expected that long-term metal exposure would result in enhanced metal resistance. Finally, we hypothesized that microorganisms from the most radioactive sediments should have had enhanced radiation resistance

Spies and Bloggers: New Synthetic Biology Tools to Understand Microbial Processes in Soils and Sediments

Science.gov (United States)

Masiello, C. A.; Silberg, J. J.; Cheng, H. Y.; Del Valle, I.; Fulk, E. M.; Gao, X.; Bennett, G. N.

2017-12-01

Microbes can be programmed through synthetic biology to report on their behavior, informing researchers when their environment has triggered changes in their gene expression (e.g. in response to shifts in O2 or H2O), or when they have participated in a specific step of an elemental cycle (e.g. denitrification). This use of synthetic biology has the potential to significantly improve our understanding of microbes' roles in elemental and water cycling, because it allows reporting on the environment from the perspective of a microbe, matching the measurement scale exactly to the scale that a microbe experiences. However, synthetic microbes have not yet seen wide use in soil and sediment laboratory experiments because synthetic organisms typically report by fluorescing, making their signals difficult to detect outside the petri dish. We are developing a new suite of microbial programs that report instead by releasing easily-detected gases, allowing the real-time, noninvasive monitoring of behaviors in sediments and soils. Microbial biosensors can, in theory, be programmed to detect dynamic processes that contribute to a wide range of geobiological processes, including C cycling (biofilm production, methanogenesis, and synthesis of extracellular enzymes that degrade organic matter), N cycling (expression of enzymes that underlie different steps of the N cycle) and potentially S cycling. We will provide an overview of the potential uses of gas-reporting biosensors in soil and sediment lab experiments, and will report the development of the systematics of these sensors. Successful development of gas biosensors for laboratory use will require addressing issues including: engineering the intensity and selectivity of microbial gas production to maximize the signal to noise ratio; normalizing the gas reporter signal to cell population size, managing gas diffusion effects on signal shape; and developing multiple gases that can be used in parallel.

Biostimulation of Iron Reduction and Uranium Immobilization: Microbial and Mineralogical Controls

International Nuclear Information System (INIS)

Joel E. Kostka; Lainie Petrie; Nadia North; David L. Balkwill; Joseph W. Stucki; Lee Kerkhof

2004-01-01

The overall objective of our project is to understand the microbial and geochemical mechanisms controlling the reduction and immobilization of U(VI) during biostimulation in subsurface sediments of the Field Research Center (FRC) which are cocontaminated with uranium and nitrate. The focus will be on activity of microbial populations (metal- and nitrate-reducing bacteria) and iron minerals which are likely to make strong contributions to the fate of uranium during in situ bioremediation. The project will: (1) quantify the relationships between active members of the microbial communities, iron mineralogy, and nitrogen transformations in the field and in laboratory incubations under a variety of biostimulation conditions, (2) purify and physiologically characterize new model metal-reducing bacteria isolated from moderately acidophilic FRC subsurface sediments, and (3) elucidate the biotic and abiotic mechanisms by which FRC aluminosilicate clay minerals are reduced and dissolved under environmental conditions resembling those during biostimulation. Active microbial communities will be assessed using quantitative molecular techniques along with geochemical measurements to determine the different terminal-electron-accepting pathways. Iron minerals will be characterized using a suite of physical, spectroscopic, and wet chemical methods. Monitoring the activity and composition of the denitrifier community in parallel with denitrification intermediates during nitrate removal will provide a better understanding of the indirect effects of nitrate reduction on uranium speciation. Through quantification of the activity of specific microbial populations and an in-depth characterization of Fe minerals likely to catalyze U sorption/precipitation, we will provide important inputs for reaction-based biogeochemical models which will provide the basis for development of in situ U bioremediation strategies. In collaboration with Jack Istok and Lee Krumholz, we have begun to study the

Effects of deposition of heavy-metal-polluted harbor mud on microbial diversity and metal resistance in sandy marine sediments

DEFF Research Database (Denmark)

Toes, Ann-Charlotte M; Finke, Niko; Kuenen, J Gijs

2008-01-01

Deposition of dredged harbor sediments in relatively undisturbed ecosystems is often considered a viable option for confinement of pollutants and possible natural attenuation. This study investigated the effects of deposition of heavy-metal-polluted sludge on the microbial diversity of sandy...... the finding that some groups of clones were shared between the metal-impacted sandy sediment and the harbor control, comparative analyses showed that the two sediments were significantly different in community composition. Consequences of redeposition of metal-polluted sediment were primarily underlined...... with cultivation-dependent techniques. Toxicity tests showed that the percentage of Cd- and Cu-tolerant aerobic heterotrophs was highest among isolates from the sandy sediment with metal-polluted mud on top....

Early diagenesis in the sediments of the Congo deep-sea fan dominated by massive terrigenous deposits: Part III - Sulfate- and methane- based microbial processes

Science.gov (United States)

Pastor, L.; Toffin, L.; Decker, C.; Olu, K.; Cathalot, C.; Lesongeur, F.; Caprais, J.-C.; Bessette, S.; Brandily, C.; Taillefert, M.; Rabouille, C.

2017-08-01

Geochemical profiles (SO42-, H2S, CH4, δ13CH4) and phylogenetic diversity of Archaea and Bacteria from two oceanographic cruises dedicated to the lobes sediments of the Congo deep-sea fan are presented in this paper. In this area, organic-rich turbidites reach 5000 m and allow the establishment of patchy cold-seep-like habitats including microbial mats, reduced sediments, and vesicomyid bivalves assemblages. These bivalves live in endosymbiosis with sulfur-oxidizing bacteria and use sulfides to perform chemosynthesis. In these habitats, unlike classical abyssal sediments, anoxic processes are dominant. Total oxygen uptake fluxes and methane fluxes measured with benthic chambers are in the same range as those of active cold-seep environments, and oxygen is mainly used for reoxidation of reduced compounds, especially in bacterial mats and reduced sediments. High concentrations of methane and sulfate co-exist in the upper 20 cm of sediments, and evidence indicates that sulfate-reducing microorganisms and methanogens co-occur in the shallow layers of these sediments. Simultaneously, anaerobic oxidation of methane (AOM) with sulfate as the electron acceptor is evidenced by the presence of ANMEs (ANaerobic MEthanotroph). Dissolved sulfide produced through the reduction of sulfate is reoxidized through several pathways depending on the habitat. These pathways include vesicomyid bivalves uptake (adults or juveniles in the bacterial mats habitats), reoxidation by oxygen or iron phases within the reduced sediment, or reoxidation by microbial mats. Sulfide uptake rates by vesicomyids measured in sulfide-rich sea water (90±18 mmol S m-2 d-1) were similar to sulfide production rates obtained by modelling the sulfate profile with different bioirrigation constants, highlighting the major control of vesicomyids on sulfur cycle in their habitats.

Microbial functional genes enriched in the Xiangjiang River sediments with heavy metal contamination.

Science.gov (United States)

Jie, Shiqi; Li, Mingming; Gan, Min; Zhu, Jianyu; Yin, Huaqun; Liu, Xueduan

2016-08-08

Xiangjiang River (Hunan, China) has been contaminated with heavy metal for several decades by surrounding factories. However, little is known about the influence of a gradient of heavy metal contamination on the diversity, structure of microbial functional gene in sediment. To deeply understand the impact of heavy metal contamination on microbial community, a comprehensive functional gene array (GeoChip 5.0) has been used to study the functional genes structure, composition, diversity and metabolic potential of microbial community from three heavy metal polluted sites of Xiangjiang River. A total of 25595 functional genes involved in different biogeochemical processes have been detected in three sites, and different diversities and structures of microbial functional genes were observed. The analysis of gene overlapping, unique genes, and various diversity indices indicated a significant correlation between the level of heavy metal contamination and the functional diversity. Plentiful resistant genes related to various metal were detected, such as copper, arsenic, chromium and mercury. The results indicated a significantly higher abundance of genes involved in metal resistance including sulfate reduction genes (dsr) in studied site with most serious heavy metal contamination, such as cueo, mer, metc, merb, tehb and terc gene. With regard to the relationship between the environmental variables and microbial functional structure, S, Cu, Cd, Hg and Cr were the dominating factor shaping the microbial distribution pattern in three sites. This study suggests that high level of heavy metal contamination resulted in higher functional diversity and the abundance of metal resistant genes. These variation therefore significantly contribute to the resistance, resilience and stability of the microbial community subjected to the gradient of heavy metals contaminant in Xiangjiang River.

Isoprenoid quinones resolve the stratification of microbial redox processes in a biogeochemical continuum from the photic zone to deep anoxic sediments of the Black Sea.

Science.gov (United States)

Becker, Kevin W; Elling, Felix J; Schröder, Jan M; Lipp, Julius S; Goldhammer, Tobias; Zabel, Matthias; Elvert, Marcus; Overmann, Jörg; Hinrichs, Kai-Uwe

2018-03-09

of microorganisms and their metabolisms, as the majority remains uncultured. Thus, culture-independent approaches are critical for determining microbial diversity and active metabolic processes. In order to resolve the stratification of microbial communities in the Black Sea, we comprehensively analyzed redox process-specific isoprenoid quinone biomarkers in a unique continuous record from the photic zone through the chemocline into anoxic subsurface sediments. We describe an unprecedented quinone diversity that allowed us to detect distinct biogeochemical processes including oxygenic photosynthesis, archaeal ammonia oxidation, aerobic methanotrophy and anoxygenic photosynthesis in defined geochemical zones. Copyright © 2018 American Society for Microbiology.

Biostimulation induces syntrophic interactions that impact C, S and N cycling in a sediment microbial community

Energy Technology Data Exchange (ETDEWEB)

Handley, KM [University of California, Berkeley; Verberkmoes, Nathan C [ORNL; Steefel, Carl I [Lawrence Berkeley National Laboratory (LBNL); Sharon, I [University of California, Berkeley; Williams, Ken [Lawrence Berkeley National Laboratory (LBNL); Miller, CS [University of California, Berkeley; Frischkorn, Kyle C [University of California, Berkeley; Chourey, Karuna [ORNL; Thomas, Brian [University of California, Berkeley; Shah, Manesh B [ORNL; Long, Phil [Pacific Northwest National Laboratory (PNNL); Hettich, Robert {Bob} L [ORNL; Banfield, Jillian F. [University of California, Berkeley

2013-01-01

Stimulation of subsurface microorganisms to induce reductive immobilization of metals is a promising approach for bioremediation, yet the overall microbial community response is typically poorly understood. Here we used community proteogenomics to test the hypothesis that excess input of acetate activates syntrophic interactions among autotrophs and heterotrophs. A flow-through sediment column was incubated in a groundwater well of an acetate-amended aquifer. Genomic sequences from the community recovered during microbial sulfate reduction were used to econstruct, de novo, near-complete genomes for Desulfobacter (Deltaproteobacteria) and relatives of Sulfurovum and Sulfurimonas (Epsilonproteobacteria), and Bacteroidetes. Partial genomes were obtained for Clostridiales (Firmicutes) and Desulfuromonadales-like Deltaproteobacteria. The majority of proteins identified by mass spectrometry corresponded to Desulfobacter-like species, and demonstrate the role of this organism in sulfate reduction (Dsr and APS), nitrogen-fixation (Nif) and acetate oxidation to CO2 during amendment. Results suggest less abundant Desulfuromonadales and Bacteroidetes also actively contributed to CO2 production via the TCA cycle. Proteomic data indicate that sulfide was partially re-oxidized by Epsilonproteobacteria through nitrate-dependent sulfide oxidation (using Nap, Nir, Nos, SQR and Sox), with CO2 fixed using the reverse TCA cycle. Modeling shows that this reaction was thermodynamically possible, and kinetically favorable relative to acetate-dependent denitrification. We conclude that high-levels of carbon amendment aimed to stimulate anaerobic heterotrophy led to carbon fixation in co-dependent chemoautotrophs. These results have implications for understanding complex ecosystem behavior, and show that high levels of organic carbon supplementation can expand the range of microbial functionalities accessible for ecosystem manipulation.

Evidence for the Occurrence of Microbial Iron Reduction in Bulk Aerobic Unsaturated Sediments

Science.gov (United States)

Cooper, D. C.; Kukkadapu, R. K.; Smith, W. A.; Fox, D. T.; Plummer, M. A.; Hull, L. C.

2003-12-01

Radionuclide transport experiments conducted in a large, meso-scale column reactor (MSCR, 10 ft high x 3 ft dia) operated under unsaturated flow conditions with simulated rainwater influent provide evidence that microbial iron reduction can occur in bulk-aerobic vadose zone systems with a low organic carbon content (~0.5 wt%). Soil gas analyses indicate that CO2 varied between ~0.1% of soil gas (top) and 12% to 18% of soil gas (bottom). O2 varied inversely with CO2, and the ratio of (CO2 produced) / (O2 consumed) was 0.8 +/- 0.1. NO3- was present at high concentrations, and originated from soluble NO3- salts present in the packing material. Ammonia was present at low levels, and limited NO2- production was observed. There was no increase in aqueous iron, and methane and sulfide were not produced. M\\H{o}ssbauer analyses of sediment iron mineralogy indicate that the sedimentary iron in the packing material is 63% illite Fe(III), 16% illite Fe(II), 13% hematite, and 8% poorly-crystalline/small-particulate (pc/sp) iron oxide. Sediments collected from the lower portion of the column (5.5 fbs, feet below surface) still contain illite and hematite, but have lost the pc/sp iron oxide component. The Fe(III)/Fe(II) ratio of the illite appears to be unchanged at this depth. Analyses of sediment extractable DNA and cell number indicate that bacterial abundances increase from the surface to 0.5 fbs, and then remain constant with depth. Initial results from DGGE and 16s rDNA clone libraries indicate that microbial community structure alters with increasing depth, decreasing O2 content, and loss of pc/sp iron oxides. These data indicate a predominance of Clostridium at the column top, with Bacillus, Desulfobacterium, and Pseudomonas also providing a significant contribution. At 0.5 fbs, Clostridium represents a larger fraction of the total community with Desulfobacterium present as the second most abundant component. By 5.5 fbs, Clostridium is a minor component and the community

A comparative study of microbial diversity and community structure in marine sediments using poly(A tailing and reverse transcription PCR

Directory of Open Access Journals (Sweden)

Tatsuhiko eHoshino

2013-06-01

Full Text Available To obtain a better understanding of metabolically active microbial communities, we tested a molecular ecological approach using poly(A tailing of environmental 16S rRNA, followed by full-length complementary DNA (cDNA synthesis and sequencing to eliminate potential biases caused by mismatching of PCR primer sequences. The RNA pool tested was extracted from marine sediments of the Yonaguni Knoll IV hydrothermal field in the southern Okinawa Trough. The sequences obtained using the ploy(A tailing method were compared statistically and phylogenetically with those obtained using conventional reverse transcription-polymerase chain reaction (RT-PCR with published domain-specific primers. Both methods indicated that Deltaproteobacteria are predominant in sediment (>85% of the total sequence read. The poly(A tailing method indicated that Desulfobacterales were the predominant deltaproteobacteria, while most of the sequences in libraries constructed using RT-PCR were derived from Desulfuromonadales. This discrepancy may have been due to low coverage of Desulfobacterales by the primers used. A comparison of library diversity indices indicated that the poly(A tailing method retrieves more phylogenetically diverse sequences from the environment. The four archaeal 16S rRNA sequences that were obtained using the poly(A tailing method formed deeply branching lineages that were related to Candidatus Parvarchaeum and the Ancient Archaeal Group. These results clearly demonstrate that poly(A tailing followed by cDNA sequencing is a powerful and less biased molecular ecological approach for the study of metabolically active microbial communities.

Thalassic biogas production from sea wrack biomass using different microbial seeds: cow manure, marine sediment and sea wrack-associated microflora.

Science.gov (United States)

Marquez, Gian Powell B; Reichardt, Wolfgang T; Azanza, Rhodora V; Klocke, Michael; Montaño, Marco Nemesio E

2013-04-01

Sea wrack (dislodged sea grasses and seaweeds) was used in biogas production. Fresh water scarcity in island communities where sea wrack could accumulate led to seawater utilization as liquid substrate. Three microbial seeds cow manure (CM), marine sediment (MS), and sea wrack-associated microflora (SWA) were explored for biogas production. The average biogas produced were 2172±156 mL (MS), 1223±308 mL (SWA) and 551±126 mL (CM). Though methane potential (396.9 mL(CH4) g(-1) volatile solid) computed from sea wrack proximate values was comparable to other feedstocks, highest methane yield was low (MS=94.33 mL(CH4) g(-1) VS). Among the microbial seeds, MS proved the best microbial source in utilizing sea wrack biomass and seawater. However, salinity (MS=42‰) observed exceeded average seawater salinity (34‰). Hence, methanogenic activity could have been inhibited. This is the first report on sea wrack biomass utilization for thalassic biogas production. Copyright © 2013 Elsevier Ltd. All rights reserved.

Bioleaching of heavy metal polluted sediment: kinetics of leaching and microbial sulfur oxidation

Energy Technology Data Exchange (ETDEWEB)

Loeser, C. [Technische Universitaet Dresden, Institut fuer Lebenmitteltechnik und Bioverfahrenstechnik, D-01062 Dresden (Germany); Zehnsdorf, A. [UFZ-Umweltforschungszentrum Leipzig-Halle GmbH, Umwelt- und Biotechnologisches Zentrum (UBZ), Permoserstrasse 15, D-04318 Leipzig (Germany); Goersch, K.; Seidel, H. [UFZ-Umweltforschungszentrum Leipzig-Halle GmbH, Department Bioremediation, Permoserstrasse 15, D-04318 Leipzig (Germany)

2005-12-01

Remediation of heavy metal polluted sediment through bioleaching using elemental sulfur (S{sup 0}) as the leaching agent can be regarded as a two-step process: firstly, the microbial oxidation of the added S{sup 0} to sulfuric acid and, secondly, the reaction of the produced acid with the sediment. Here, both subprocesses were studied in detail independently: oxidized river sediment was either suspended in sulfuric acid of various strengths, or mixed with various amounts of finely ground S{sup 0} powder (diameter of the S{sup 0} particles between 1 and 175 {mu}m with a Rosin-Rammler-Sperling-Bennet (RRSB) distribution and an average diameter of 35 {mu}m) and suspended in water. The leaching process was observed by repeated analysis of the suspension concerning pH, soluble sulfate and metals, and remaining S{sup 0}. In the case of abiotic leaching with H{sub 2}SO{sub 4}, the reaction between the acid and the sediment resulted in a gradual increase in pH and a solubilization of sediment-borne heavy metals which required some time; 80 % of the finally solubilized heavy metals was dissolved after 1 h, 90 % after 10 h, and 100 % after 100 h. In the case of bioleaching, the rate of S{sup 0} oxidation was maximal at the beginning, gradually diminished with time, and was proportional to the initial amount of S{sup 0}. Due to its very low solubility in water, S{sup 0} is oxidized in a surface reaction catalyzed by attached bacteria. The oxidation let the particles shrink, their surface became smaller and, thus, the S{sup 0} oxidation rate gradually decreased. The shrinking rate was time-invariant and, at 30 C, amounted to 0.5 {mu}m/day (or 100 {mu}g/cm{sup 2}/day). Within 21 days, 90 % of the applied S{sup 0} was oxidized. Three models with a different degree of complexity have been developed that describe this S{sup 0} oxidation, assuming S{sup 0} particles of uniform size (I), using a measured particle size distribution (II), or applying an adapted RRSB distribution (III

Organic Matter Loading Modifies the Microbial Community Responsible for Nitrogen Loss in Estuarine Sediments.

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Babbin, Andrew R; Jayakumar, Amal; Ward, Bess B

2016-04-01

Coastal marine sediments, as locations of substantial fixed nitrogen loss, are very important to the nitrogen budget and to the primary productivity of the oceans. Coastal sediment systems are also highly dynamic and subject to periodic natural and anthropogenic organic substrate additions. The response to organic matter by the microbial community involved in nitrogen loss processes was evaluated using mesocosms of Chesapeake Bay sediments. Over the course of a 50-day incubation, rates of anammox and denitrification were measured weekly using (15)N tracer incubations, and samples were collected for genetic analysis. Rates of both nitrogen loss processes and gene abundances associated with them corresponded loosely, probably because heterogeneities in sediments obscured a clear relationship. The rates of denitrification were stimulated more, and the fraction of nitrogen loss attributed to anammox slightly reduced, by the higher organic matter addition. Furthermore, the large organic matter pulse drove a significant and rapid shift in the denitrifier community composition as determined using a nirS microarray, indicating that the diversity of these organisms plays an essential role in responding to anthropogenic inputs. We also suggest that the proportion of nitrogen loss due to anammox in these coastal estuarine sediments may be underestimated due to temporal dynamics as well as from methodological artifacts related to conventional sediment slurry incubation approaches.

Molecular characterization of organic matter mobilized from Bangladeshi aquifer sediment: tracking carbon compositional change during microbial utilization

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L. E. Pracht

2018-03-01

Full Text Available Bioavailable organic carbon in aquifer recharge waters and sediments can fuel microbial reactions with implications for groundwater quality. A previous incubation experiment showed that sedimentary organic carbon (SOC mobilized off sandy sediment collected from an arsenic-contaminated and methanogenic aquifer in Bangladesh was bioavailable; it was transformed into methane. We used high-resolution mass spectrometry to molecularly characterize this mobilized SOC, reference its composition against dissolved organic carbon (DOC in surface recharge water, track compositional changes during incubation, and advance understanding of microbial processing of organic carbon in anaerobic environments. Organic carbon mobilized off aquifer sediment was more diverse, proportionately larger, more aromatic, and more oxidized than DOC in surface recharge. Mobilized SOC was predominately composed of terrestrially derived organic matter and had characteristics signifying that it evaded microbial processing within the aquifer. Approximately 50 % of identified compounds in mobilized SOC and in DOC from surface recharge water contained sulfur. During incubation, after mobilized SOC was converted into methane, new organosulfur compounds with high S-to-C ratios and a high nominal oxidation state of carbon (NOSC were detected. We reason that these detected compounds formed abiotically following microbial reduction of sulfate to sulfide, which could have occurred during incubation but was not directly measured or that they were microbially synthesized. Most notably, microbes transformed all carbon types during incubation, including those currently considered thermodynamically unviable for microbes to degrade in anaerobic conditions (i.e., those with a low NOSC. In anaerobic environments, energy yields from redox reactions are small and the amount of energy required to remove electrons from highly reduced carbon substrates during oxidation decreases the thermodynamic

Molecular characterization of organic matter mobilized from Bangladeshi aquifer sediment: tracking carbon compositional change during microbial utilization

Science.gov (United States)

Pracht, Lara E.; Tfaily, Malak M.; Ardissono, Robert J.; Neumann, Rebecca B.

2018-03-01

Bioavailable organic carbon in aquifer recharge waters and sediments can fuel microbial reactions with implications for groundwater quality. A previous incubation experiment showed that sedimentary organic carbon (SOC) mobilized off sandy sediment collected from an arsenic-contaminated and methanogenic aquifer in Bangladesh was bioavailable; it was transformed into methane. We used high-resolution mass spectrometry to molecularly characterize this mobilized SOC, reference its composition against dissolved organic carbon (DOC) in surface recharge water, track compositional changes during incubation, and advance understanding of microbial processing of organic carbon in anaerobic environments. Organic carbon mobilized off aquifer sediment was more diverse, proportionately larger, more aromatic, and more oxidized than DOC in surface recharge. Mobilized SOC was predominately composed of terrestrially derived organic matter and had characteristics signifying that it evaded microbial processing within the aquifer. Approximately 50 % of identified compounds in mobilized SOC and in DOC from surface recharge water contained sulfur. During incubation, after mobilized SOC was converted into methane, new organosulfur compounds with high S-to-C ratios and a high nominal oxidation state of carbon (NOSC) were detected. We reason that these detected compounds formed abiotically following microbial reduction of sulfate to sulfide, which could have occurred during incubation but was not directly measured or that they were microbially synthesized. Most notably, microbes transformed all carbon types during incubation, including those currently considered thermodynamically unviable for microbes to degrade in anaerobic conditions (i.e., those with a low NOSC). In anaerobic environments, energy yields from redox reactions are small and the amount of energy required to remove electrons from highly reduced carbon substrates during oxidation decreases the thermodynamic favorability of

Molecular biological and isotopic biogeochemical prognoses of the nitrification-driven dynamic microbial nitrogen cycle in hadopelagic sediments.

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Nunoura, Takuro; Nishizawa, Manabu; Kikuchi, Tohru; Tsubouchi, Taishi; Hirai, Miho; Koide, Osamu; Miyazaki, Junichi; Hirayama, Hisako; Koba, Keisuke; Takai, Ken

2013-11-01

There has been much progress in understanding the nitrogen cycle in oceanic waters including the recent identification of ammonia-oxidizing archaea and anaerobic ammonia oxidizing (anammox) bacteria, and in the comprehensive estimation in abundance and activity of these microbial populations. However, compared with the nitrogen cycle in oceanic waters, there are fewer studies concerning the oceanic benthic nitrogen cycle. To further elucidate the dynamic nitrogen cycle in deep-sea sediments, a sediment core obtained from the Ogasawara Trench at a water depth of 9760 m was analysed in this study. The profiles obtained for the pore-water chemistry, and nitrogen and oxygen stable isotopic compositions of pore-water nitrate in the hadopelagic sediments could not be explained by the depth segregation of nitrifiers and nitrate reducers, suggesting the co-occurrence of nitrification and nitrate reduction in the shallowest nitrate reduction zone. The abundance of SSU rRNA and functional genes related to nitrification and denitrification are consistent with the co-occurrence of nitrification and nitrate reduction observed in the geochemical analyses. This study presents the first example of cooperation between aerobic and anaerobic nitrogen metabolism in the deep-sea sedimentary environments. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

Relationship of subseafloor microbial diversity to sediment age and organic carbon content

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Walsh, E. A.; Kirkpatrick, J. B.; Sogin, M. L.; D'Hondt, S. L.

2013-12-01

Our tag pyrosequencing investigation of four globally distant sites reveals sediment age and total organic carbon content to be significant components in understanding subseafloor diversity. Our sampling locations include two sites from high-productivity regions (Indian Ocean and Bering Sea) and two from moderate-productivity (eastern and central equatorial Pacific Ocean). Sediment from the high-productivity sites has much higher TOC than sediment from the moderate-productivity equatorial sites. We applied a high-resolution 16S V4-V6 tag pyrosequencing approach to 24 bacterial and 17 archaeal samples, totaling 602,502 reads. We identified1,291 archaeal and 15,910 bacterial OTUs (97%) from these reads. We analyzed bacterial samples from all four sites in addition to archaeal samples from our high productivity sites. These high productivity, high TOC sites have a pronounced methane-rich sulfate-free zone at depth from which archaea have been previously considered to dominate (Biddle et al., 2006). At all four locations, microbial diversity is highest near the seafloor and drops rapidly to low but stable values with increasing sediment depth. The depth at which diversity stabilizes varies greatly from site to site, but the age at which it stabilizes is relatively constant. At all four sites, diversity reaches low stable values a few hundred thousand years after sediment deposition. The sites with high total organic carbon (high productivity sites) generally exhibit higher diversity at each sediment age than the sites with lower total organic carbon (moderate-productivity sites). Archaeal diversity is lower than bacterial diversity at every sampled depth. Biddle, J.F., Lipp, J.S., Lever, M.A., Lloyd, K.G., Sørensen, K.B., Anderson, R. et al. (2006) Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru. PNAS 103: 3846-3851.

Applicability of API ZYM to capture seasonal and spatial variabilities in lake and river sediments.

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Patel, Drashti; Gismondi, Renee; Alsaffar, Ali; Tiquia-Arashiro, Sonia M

2018-05-02

Waters draining into a lake carry with them much of the suspended sediment that is transported by rivers and streams from the local drainage basin. The organic matter processing in the sediments is executed by heterotrophic microbial communities, whose activities may vary spatially and temporally. Thus, to capture and evaluate some of these variabilities in the sediments, we sampled six sites: three from the St. Clair River and three from Lake St. Clair in spring, summer, fall, and winter of 2016. At all sites and dates, we investigated the spatial and temporal variations in 19 extracellular enzyme activities using API ZYM. Our results indicated that a broad range of enzymes were found to be active in the sediments. Phosphatases, lipases, and esterases were synthesized most intensively by the sediment microbial communities. No consistent difference was found between the lake and sediment samples. Differences were more obvious between sites and seasons. Sites with the highest metabolic (enzyme) diversity reflected the capacity of the sediment microbial communities to breakdown a broader range of substrates and may be linked to differences in river and lake water quality. The seasonal variability of the enzymes activities was governed by the variations of environmental factors caused by anthropogenic and terrestrial inputs, and provides information for a better understanding of the dynamics of sediment organic matter of the river and lake ecosystems. The experimental results suggest that API ZYM is a simple and rapid enzyme assay procedure to evaluate natural processes in ecosystems and their changes.

A survey of microbial community diversity in marine sediments impacted by petroleum hydrocarbons from the Gulf of Mexico and Atlantic shorelines, Texas to Florida

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Lisle, John T.; Stellick, Sarah H.

2011-01-01

Microbial community genomic DNA was extracted from sediment samples collected along the Gulf of Mexico and Atlantic coasts from Texas to Florida. Sample sites were identified as being ecologically sensitive and (or) as having high potential of being impacted by Macondo-1 (M-1) well oil from the Deepwater Horizon blowout. The diversity within the microbial communities associated with the collected sediments provides a baseline dataset to which microbial community-diversity data from impacted sites could be compared. To determine the microbial community diversity in the samples, genetic fingerprints were generated and compared. Specific sequences within the community genomic DNA were first amplified using the polymerase chain reaction (PCR) with a primer set that provides possible resolution to the species level. A second nested PCR was performed on the primary PCR products using a primer set on which a GC-clamp was attached to one of the primers. The nested PCR products were separated using denaturing-gradient gel electrophoresis (DGGE) that resolves the nested PCR products based on sequence dissimilarities (or similarities), forming a genomic fingerprint of the microbial diversity within the respective samples. Samples with similar fingerprints were grouped and compared to oil-fingerprint data from the same sites (Rosenbauer and others, 2011). The microbial community fingerprints were generally grouped into sites that had been shown to contain background concentrations of non-Deepwater Horizon oil. However, these groupings also included sites where no oil signature was detected. This report represents some of the first information on naturally occurring microbial communities in sediment from shorelines along the Gulf of Mexico and Atlantic coasts from Texas to Florida.

Bioelectric production from sediment of pond fishing and molasses using microbial fuel cell (MFC) technology-base with the influence of substrate concentration variety

Science.gov (United States)

Syafitri, L. M.; Saputro, Y. A.; Hana, P. N.; Hardiani, D.; Raharjo, B.

2018-03-01

Indonesia is currently faced the problem of the need for electrical energy. MFC is a technology that can be used to generate electricity by utilizing microbial activity. The aims of this study is to manage the molasses waste and sediment of fishery as a substrate in the MFC system. The research method was performed by preparing anode and cathode connected by a salt bridge forming the system of MFC Double Chamber. The result of bacteriology test using Total Plate Count (TPC) method showed that the number of bacterial colonies on the sediment substrate was 4.1 × 106 cfu/gr, while the molasses substrate was 7,1 × 104 cfu/gr. The measurement result of electricity showed that 25% sediment and 75% molasses substrate variation resulted in the highest average voltage and power density that are 0.372 V and 813.191 mW/m2. The conclusion of this research is that the mixture of sediment with molasses substrate can increase the production of electricity produced by MFC system.

Colonization of overlaying water by bacteria from dry river sediments.

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Fazi, Stefano; Amalfitano, Stefano; Piccini, Claudia; Zoppini, Annamaria; Puddu, Alberto; Pernthaler, Jakob

2008-10-01

We studied the diversity, community composition and activity of the primary microbial colonizers of the water above freshly re-wetted sediments from a temporary river. Dried sediments, collected from Mulargia River (Sardinia, Italy), were covered with sterile freshwater in triplicate microcosms, and changes of the planktonic microbial assemblage were monitored over a 48 h period. During the first 9 h bacterial abundance was low (1.5 x 10(4) cells ml(-1)); it increased to 3.4 x 10(6) cells ml(-1) after 28 h and did not change thereafter. Approximately 20% of bacteria exhibited DNA de novo synthesis already after 9 h of incubation. Changes of the ratios of (3)H-leucine to (3)H-thymidine incorporation rates indicated a shift of growth patterns during the experiment. Extracellular enzyme activity showed a maximum at 48 h with aminopeptidase activity (430.8 +/- 22.6 nmol MCA l(-1) h(-1)) significantly higher than alkaline phosphatase (98.6 +/- 4.3 nmol MUF l(-1) h(-1)). The primary microbial colonizers of the overlaying water - as determined by 16S rRNA gene sequence analysis - were related to at least six different phylogenetic lineages of Bacilli and to Alphaproteobacteria (Brevundimonas spp. and Caulobacter spp.). Large bacterial cells affiliated to one clade of Bacillus sp. were rare in the dried sediments, but constituted the majority of the planktonic microbial assemblage and of cells with detectable DNA-synthesis until 28 h after re-wetting. Their community contribution decreased in parallel with a rise of flagellated and ciliated protists. Estimates based on cell production rates suggested that the rapidly enriched Bacillus sp. suffered disproportionally high loss rates from selective predation, thus favouring the establishment of a more heterogenic assemblage of microbes (consisting of Proteobacteria, Actinobacteria and Cytophaga-Flavobacteria). Our results suggest that the primary microbial colonizers of the water above dried sediments are passively released

The Canadian approach to microbial studies in nuclear waste management and disposal

International Nuclear Information System (INIS)

Stroes-Gascoyne, S.; Sargent, F.P.

1998-01-01

Many countries considering radioactive waste disposal have, or are considering programs to study and quantify microbial effects in terms of their particular disposal concept. Although there is an abundance of qualitative information, there is a need for quantitative data. Quantitative research should cover topics such as the kinetics of microbial activity in geological media, microbial effects on radionuclide migration in host rock (including effects of biofilms), tolerance to extreme conditions of radiation, heat and desiccation, microbially-influenced corrosion of waste containers and microbial gas production. The research should be performed in relevant disposal environments with the ultimate objective to quantify those effects that need to be included in models for predictive and safety assessment purposes. The Canadian approach to dealing with microbial effects involves a combination of pertinent, quantitative measurements from carefully designed laboratory studies and from large scale engineering experiments in AECL's Underground Research Laboratory (URL). The validity of these quantitative data is measured against observations from natural environments and analogues. An example is the viability of microbes in clay-based scaling materials. Laboratory studies have shown that the clay content of these barriers strongly affects microbial activity and movement. This is supported by natural environment and analogue observations that show clay deposits to contain very old tree segments and dense clay lenses in sediments to contain much smaller, less diverse and less active microbial populations than more porous sediments. This approach has allowed for focused, quantitative research on microbial effects in Canada. (author)

Distributions, abundances and activities of microbes associated with the nitrogen cycle in riparian and stream sediments of a river tributary.

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Kim, Haryun; Bae, Hee-Sung; Reddy, K Ramesh; Ogram, Andrew

2016-12-01

River tributaries are ecologically important environments that function as sinks of inorganic nitrogen. To gain greater insight into the nitrogen cycle (N-cycle) in these environments, the distributions and activities of microbial populations involved in the N-cycle were studied in riparian and stream sediments of the Santa Fe River (SFR) tributaries located in northern Florida, USA. Riparian sediments were characterized by much higher organic matter content, and extracellular enzyme activities, including cellobiohydrolase, β-d-glucosidase, and phenol oxidase than stream sediments. Compared with stream sediments, riparian sediments exhibited significantly higher activities of nitrification, denitrification, dissimilatory nitrate reduction to ammonia (DNRA) and anaerobic ammonia oxidation; correspondingly, with higher copies of amoA (a biomarker for enumerating nitrifiers), nirS and nirK (for denitrifiers), and nrfA (for DNRA bacteria). Among N-cycle processes, denitrification showed the highest activities and the highest concentrations of the corresponding gene (nirK and nirS) copy numbers. In riparian sediments, substantial nitrification activities (6.3 mg-N kg soil -1 d -1 average) and numbers of amoA copies (7.3 × 10 7  copies g soil -1 average) were observed, and nitrification rates correlate with denitrification rates. The guild structures of denitrifiers and nitrifiers in riparian sediments differed significantly from those found in stream sediments, as revealed by analysis of nirS and archaeal amoA sequences. This study shows that riparian sediments serve as sinks for inorganic nitrogen loads from non-point sources of agricultural runoff, with nitrification and denitrification associated with elevated levels of carbon and nitrogen contents and extracellular enzyme activities. Copyright © 2016 Elsevier Ltd. All rights reserved.

A survey of alterations in microbial community diversity in marine sediments in response to oil from the Deepwater Horizon spill: Northern Gulf of Mexico shoreline, Texas to Florida

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Lisle, John T.

2011-01-01

Microbial community genomic DNA was extracted from sediment samples collected from the northern Gulf of Mexico (NGOM) coast. These samples had a high probability of being impacted by Macondo-1 (M-1) well oil from the Deepwater Horizon (DWH) drilling site. The hypothesis for this project was that presence of M-1 oil in coastal sediments would significantly alter the diversity within the microbial communities associated with the impacted sediments. To determine if community-level changes did or did not occur following exposure to M-1 oil, microbial community-diversity fingerprints were generated and compared. Specific sequences within the community's genomic DNA were first amplified using the polymerase chain reaction (PCR) using a primer set that provides possible resolution to the species level. A second nested PCR that was performed on the primary PCR products using a primer set on which a GC-clamp was attached to one of the primers. These nested PCR products were separated using denaturing-gradient gel electrophoresis (DGGE) that resolves the nested PCR products based on sequence dissimilarities (or similarities), forming a genomic fingerprint of the microbial diversity within the respective samples. Sediment samples with similar fingerprints were grouped and compared to oil-fingerprint data from Rosenbauer and others (2010). The microbial community fingerprints grouped closely when identifying those sites that had been impacted by M-1 oil (N=12) and/or some mixture of M-1 and other oil (N=4), based upon the oil fingerprints. This report represents some of the first information on naturally occurring microbial communities in sediment from shorelines along the NGOM coast. These communities contain microbes capable of degrading oil and related hydrocarbons, making this information relevant to response and recovery of the NGOM from the DWH incident.

Microbial Activity and Silica Degradation in Rice Straw

Science.gov (United States)

Kim, Esther Jin-kyung

Abundantly available agricultural residues like rice straw have the potential to be feedstocks for bioethanol production. Developing optimized conditions for rice straw deconstruction is a key step toward utilizing the biomass to its full potential. One challenge associated with conversion of rice straw to bioenergy is its high silica content as high silica erodes machinery. Another obstacle is the availability of enzymes that hydrolyze polymers in rice straw under industrially relevant conditions. Microbial communities that colonize compost may be a source of enzymes for bioconversion of lignocellulose to products because composting systems operate under thermophilic and high solids conditions that have been shown to be commercially relevant. Compost microbial communities enriched on rice straw could provide insight into a more targeted source of enzymes for the breakdown of rice straw polysaccharides and silica. Because rice straw is low in nitrogen it is important to understand the impact of nitrogen concentrations on the production of enzyme activity by the microbial community. This study aims to address this issue by developing a method to measure microbial silica-degrading activity and measure the effect of nitrogen amendment to rice straw on microbial activity and extracted enzyme activity during a high-solids, thermophilic incubation. An assay was developed to measure silica-degrading enzyme or silicase activity. This process included identifying methods of enzyme extraction from rice straw, identifying a model substrate for the assay, and optimizing measurement techniques. Rice straw incubations were conducted with five different levels of nitrogen added to the biomass. Microbial activity was measured by respiration and enzyme activity. A microbial community analysis was performed to understand the shift in community structure with different treatments. With increased levels of nitrogen, respiration and cellulose and hemicellulose degrading activity

A Microbial Community in Sediments Beneath the Western Antarctic Ice Sheet, Ice Stream C (Kamb)

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Skidmore, M.; Han, S.; Foo, W.; Bui, D.; Lanoil, B.

2004-12-01

In 2000, an ice-drilling project focusing on the "sticky spot" of Ice Stream C recovered cores of sub-glacial sediments from beneath the Western Antarctic Ice Sheet. We have characterized several chemical and microbiological parameters of the sole intact sediment core. Pore waters extracted from these sediments were brackish and some were supersaturated with respect to calcite. Ion chromatography demonstrated the presence of several organic acids at low, but detectable, levels in the pore water. DAPI direct cell counts were approximately 107 cells g-1. Aerobic viable plate counts were much lower than direct cell counts; however, they were two orders of magnitude higher on plates incubated at low temperature (4 ° C; 3.63 x 105 CFU ml-1) than at higher temperatures (ca. 22° C; 1.5 x 103 CFU ml-1); no colonies were detected on plates incubated anaerobically at either temperature. 16S rDNA clone library analysis indicates extremely limited bacterial diversity in these samples: six phylogenetic clades were detected. The three dominant bacterial phylogenetic clades in the clone libraries (252 clones total) were most closely related to Thiobacillus thioparus (180 clones), Polaromonas vacuolata (34 clones), and Gallionella ferruginea (35 clones) and their relatives; one clone each represented the other three phylogenetic clades (most closely related to Ralstonia pickettii, Lysobacter antibioticus, and Xylella fastidiosa, respectively). These sequences match closely with sequences previously obtained from other subglacial environments in Alaska, Ellesmere Island, Canada and New Zealand. Implications of this microbial community to subglacial chemistry and microbial biogeography will be discussed.

DESIGN CONSIDERATION INVOLVING ACTIVE SEDIMENT CAPS

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When contaminated sediments pose unacceptable risks to human health and the environment, management activities such as removal, treatment, or isolation of contaminated sediments may be required. Various capping designs are being considered for isolating contaminated sediment are...

Active Microbial Communities Inhabit Sulphate-Methane Interphase in Deep Bedrock Fracture Fluids in Olkiluoto, Finland

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Malin Bomberg

2015-01-01

Full Text Available Active microbial communities of deep crystalline bedrock fracture water were investigated from seven different boreholes in Olkiluoto (Western Finland using bacterial and archaeal 16S rRNA, dsrB, and mcrA gene transcript targeted 454 pyrosequencing. Over a depth range of 296–798 m below ground surface the microbial communities changed according to depth, salinity gradient, and sulphate and methane concentrations. The highest bacterial diversity was observed in the sulphate-methane mixing zone (SMMZ at 250–350 m depth, whereas archaeal diversity was highest in the lowest boundaries of the SMMZ. Sulphide-oxidizing ε-proteobacteria (Sulfurimonas sp. dominated in the SMMZ and γ-proteobacteria (Pseudomonas spp. below the SMMZ. The active archaeal communities consisted mostly of ANME-2D and Thermoplasmatales groups, although Methermicoccaceae, Methanobacteriaceae, and Thermoplasmatales (SAGMEG, TMG were more common at 415–559 m depth. Typical indicator microorganisms for sulphate-methane transition zones in marine sediments, such as ANME-1 archaea, α-, β- and δ-proteobacteria, JS1, Actinomycetes, Planctomycetes, Chloroflexi, and MBGB Crenarchaeota were detected at specific depths. DsrB genes were most numerous and most actively transcribed in the SMMZ while the mcrA gene concentration was highest in the deep methane rich groundwater. Our results demonstrate that active and highly diverse but sparse and stratified microbial communities inhabit the Fennoscandian deep bedrock ecosystems.

Microbial diversity in Cenozoic sediments recovered from the Lomonosov Ridge in the Central Arctic basin.

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Forschner, Stephanie R; Sheffer, Roberta; Rowley, David C; Smith, David C

2009-03-01

The current understanding of microbes inhabiting deeply buried marine sediments is based largely on samples collected from continental shelves in tropical and temperate latitudes. The geographical range of marine subsurface coring was expanded during the Integrated Ocean Drilling Program Arctic Coring Expedition (IODP ACEX). This expedition to the ice-covered central Arctic Ocean successfully cored the entire 428 m sediment stack on the Lomonosov Ridge during August and September 2004. The recovered cores vary from siliciclastic sediment low in organic carbon ( 200 m below sea floor) sulfate reduction zone. The diversity of microbes within each zone was assessed using 16S rRNA phylogenetic markers. Bacterial 16S rRNA genes were successfully amplified from each of the biogeochemical zones, while archaea was only amplified from the deep sulfate reduction zone. The microbial communities at each zone are phylogenetically different and are most closely related to those from other deep subsurface environments.

Microcosms for evaluating microbial indicator persistence and mobilization in fluvial sediments during rainfall events.

Science.gov (United States)

Martín-Díaz, Julia; García-Aljaro, Cristina; Pascual-Benito, Míriam; Galofré, Belén; Blanch, Anicet R; Lucena, Francisco

2017-10-15

Mediterranean rivers, which are subject to long, dry periods and heavy rainfall events, could be particularly useful for understanding future climate scenarios. This study generated microcosms that mimicked riverbank sediment resuspension into the water of a typical Mediterranean river as a consequence of heavy rainfall. The mobilization and inactivation of six fecal pollution indicators and microbial source tracking markers were evaluated. The T 90 values in the sediments were: 4 days for sorbitol-fermenting Bifidobacterium, 11 days for culturable E. coli, 36 days for bacteriophages infecting Bacteroides thetaiotaomicron strain GA17 and more than 42 days for qPCR-detected E. coli, somatic coliphages and sulfite-reducing clostridia spores. Bacteriophages and bacteria showed different resuspension and sedimentation patterns. The data obtained could be used in predictive models to assess the effects of climate change on surface water quality. Pathogen mobilization into the water column poses a risk for humans, animals and the natural environment, and breaches the One Health approach. Copyright © 2017 Elsevier Ltd. All rights reserved.

Bacterial community survey of sediments at Naracoorte Caves, Australia

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Ball Andrew S.

2012-07-01

Full Text Available Bacterial diversity in sediments at UNESCO World Heritage listed Naracoorte Caves was surveyed as part of an investigation carried out in a larger study on assessing microbial communities in caves. Cave selection was based on tourist accessibility; Stick Tomato and Alexandra Cave (> 15000 annual visits and Strawhaven Cave was used as control (no tourist access. Microbial analysis showed that Bacillus was the most commonly detected microbial genus by culture dependent and independent survey of tourist accessible and inaccessible areas of show (tourist accessible and control caves. Other detected sediment bacterial groups were assigned to the Firmicutes, Actinobacteria and Proteobacteria. The survey also showed differences in bacterial diversity in caves with human access compared to the control cave with the control cave having unique microbial sequences (Acinetobacter, Agromyces, Micrococcus and Streptomyces. The show caves had higher bacterial counts, different 16S rDNA based DGGE cluster patterns and principal component groupings compared to Strawhaven. Different factors such as human access, cave use and configurations could have been responsible for the differences observed in the bacterial community cluster patterns (tourist accessible and inaccessible areas of these caves. Cave sediments can therefore act as reservoirs of microorganisms. This might have some implications on cave conservation activities especially if these sediments harbor rock art degrading microorganisms in caves with rock art.

Impact of protists on a hydrocarbon-degrading bacterial community from deep-sea Gulf of Mexico sediments: A microcosm study

Science.gov (United States)

Beaudoin, David J.; Carmichael, Catherine A.; Nelson, Robert K.; Reddy, Christopher M.; Teske, Andreas P.; Edgcomb, Virginia P.

2016-07-01

In spite of significant advancements towards understanding the dynamics of petroleum hydrocarbon degrading microbial consortia, the impacts (direct or indirect via grazing activities) of bacterivorous protists remain largely unknown. Microcosm experiments were used to examine whether protistan grazing affects the petroleum hydrocarbon degradation capacity of a deep-sea sediment microbial community from an active Gulf of Mexico cold seep. Differences in n-alkane content between native sediment microcosms and those treated with inhibitors of eukaryotes were assessed by comprehensive two-dimensional gas chromatography following 30-90 day incubations and analysis of shifts in microbial community composition using small subunit ribosomal RNA gene clone libraries. More biodegradation was observed in microcosms supplemented with eukaryotic inhibitors. SSU rRNA gene clone libraries from oil-amended treatments revealed an increase in the number of proteobacterial clones (particularly γ-proteobacteria) after spiking sediments with diesel oil. Bacterial community composition shifted, and degradation rates increased, in treatments where protists were inhibited, suggesting protists affect the hydrocarbon degrading capacity of microbial communities in sediments collected at this Gulf of Mexico site.

Microbial Mn(IV) and Fe(III) reduction in northern Barents Sea sediments under different conditions of ice cover and organic carbon deposition

DEFF Research Database (Denmark)

Nickel, Maren; Vandieken, Verona; Brüchert, Volker

2008-01-01

station, with seasonally extended ice cover, low organic carbon content and sedimentation rate combined with relatively high concentrations of Mn and Fe(III) oxides favored dissimilatory Fe and Mn reduction (98% of anaerobic carbon oxidation) over sulfate reduction in the top 12 cm of the sediment....... In contrast, in a sediment that had not been ice covered for at least 12 months and with more organic carbon and a higher sedimentation rate, sulfate reduction was the most important anaerobic electron-accepting process (>80% of anaerobic carbon oxidation). In the upper 3 cm, microbial Fe and sulfate...

Soil Microbial Community Contribution to Small Headwater Stream Metabolism.

Science.gov (United States)

Clapcott, J. E.; Gooderham, J. P.; Barmuta, L. A.; Davies, P. E.

2005-05-01

The temporal dynamics of sediment respiration were examined in seven small headwater streams in forested catchments in 2004. A strong seasonal response was observed with higher respiration rates in depositional zones than in gravel runs. The data were also examined in the context of proportional habitat distributions that highlighted the importance of high flow events in shaping whole stream metabolic budgets. This study specifically examines the question of terrestrial soil respiration contribution to whole stream metabolism by the controlled inundation of terrestrial soils. The experiment included six experimentally inundated terrestrial zones, six terrestrial controls, and six in-stream depositional zones. Sediment bacterial respiration was measured using 14C leucine incorporation and cotton strip bioassays were also employed to provide an indicative measure of sediment microbial activity. Despite high variability and exhibiting significantly lower bacterial activity than in-stream sediments, modelling using flow data and habitat mapping illustrated the important contribution of terrestrial soil respiration to the whole stream metabolic budgets of small headwater streams. In addition, microbial community composition examined using phospholipid fatty acid analysis clearly differentiated between terrestrial and aquatic communities. Freshly inundated terrestrial communities remained similar to un-inundated controls after 28 days.

Short-chain alkane cycling in deep Gulf of Mexico cold-seep sediments

Science.gov (United States)

Sibert, R.; Joye, S. B.; Hunter, K.

2015-12-01

Mixtures of light hydrocarbon gases are common in deep Gulf of Mexico cold-seep sediments, and are typically dissolved in pore fluids, adsorbed to sediment particles, trapped in methane ice, or as free gas. The dominant component in these natural gas mixtures is usually methane (>80% C1), but ethane (C2) and propane (C3) are nearly always present in trace amounts (95% of the methane produced at depth never reaches the water column. Production of C1 and C2 in deep-sea sediments has been historically attributed only to thermocatalytic processes, though limited data suggests production of C2/C3 compounds through the activity of archaea at depth. Furthermore, carbon isotopic data on ethane and propane from deep cores of Gulf of Mexico sediments suggest alkanogenesis at >3 m depth in the sediment column and alkane oxidation in uppermost oxidant-rich sediments. Additional studies have also isolated microorganisms capable of oxidizing ethane and propane in the laboratory, but field studies of microbial-driven dynamics of C2/C3 gases in cold-seep sediments are rare. Here, we present the results of a series of incubation experiments using sediment slurries culled from surface sediments from one of the most prolific natural oil and gas seeps in the Gulf of Mexico. Rates of alkane oxidation were measured under a variety of conditions to assess the surface-driven microbial controls on C2/C3 cycling in cold-seep environments. Such microbial processes are important in terms of the possible 'oxidative overprinting' of alkane isotopic signatures produced at depth, possibly obscuring typical microbial isotopic signals.

Uranium geochemistry in estuarine sediments: Controls on removal and release processes

International Nuclear Information System (INIS)

Barnes, C.E.; Cochran, J.K.

1993-01-01

Porewater uranium profiles from Long Island Sound (LIS) and Amazon shelf sediments and LIS sediment incubation experiments indicate that both removal and release processes control U geochemistry in estuarine sediments. Release of U from sediments occurs in association with Fe reduction. A correlation between U and Fe (and Mn) observed in sediment incubation experiments suggests that there is release of U from Fe-Mn-oxides as they are reduced, consistent with data from the Amazon shelf. In both sediment porewater profiles (LIS and Amazon) and sediment incubation experiments (LIS), there is removal of U from porewater under conditions of sulfate reduction. Sediment incubation experiments indicate that the removal rate is first-order with respect to U concentration, and the rate constant is linearly correlated to sulfate reduction rates. The link between U removal and sulfate reduction (a measure of diagenetic microbial activity) is consistent with a microbial mediation of U reduction. The diffusion flux of U into LIS sediments is estimated from porewater profiles. The inclusion of this estuarine removal term in the oceanic U balance increases the importance of the sediment sink. 62 refs., 12 figs., 2 tabs

Abundance and activity of oil-degrading and indigenous bacteria in sediment microcosms

International Nuclear Information System (INIS)

Araujo, R.; Molina, M.; Bachoon, D.

1995-01-01

The responses of bacterial community composition and degradation crude oil to applications of bioremediation products and plant detrital material were investigated in wetlands microcosms. The microcosms were constructed of sieved sediments and operated as tidal marshes. Products included nutrients, organisms, surfactants and combinations thereof; dried ground Spartina was the source of detrital material. Plate count and most probable-number techniques were used to enumerate microbial populations and GC/MS analysis of indicator petroleum hydrocarbons was used to assess oil degradation. Microbial communities were characterized by whole-genome hybridization and specific probes for bacterial groups, including Pseudomonas, Streptomycetes, Vibrio, and sulfate-reducing bacteria. Although the total microbial numbers were similar in all bioremediation treatments, the numbers of oil degraders increased two to three log units in the fertilizer and microbial-degrader-enriched treatments. Oil-degraders comprised the largest fraction of the total population in the treatment amended with microbial degraders, apparently at the expense of indigenous bacteria, as indicated by specific probes. Oil-degraders were also detected in the subsurface in all treatments except the controls. The extent of oil degradation was not consistent with bacterial numbers; only nutrient additions resulted in significantly enhanced degradation of oil. After 1 month of microcosm operation, oil-degraders had increased at least two orders of magnitude in sediment surface layers when oil was added alone or with Spartina detritus, although total bacterial numbers and the number of oil-degraders decreased to near initial levels by 2 months. The peak coincides with bacterial utilization of the alkane fraction of petroleum hydrocarbons

Phosphorus fractions, microbial biomass and enzyme activities in ...

African Journals Online (AJOL)

Potohar, northern Punjab, Pakistan in September, 2008 and analysed for P fractions and microbial parameters including microbial biomass C, microbial biomass N, microbial biomass P, and activities of dehydrogenase and alkaline phosphatase enzymes. The average size of different P fractions (% of total P) in the soils ...

Relationships between waste physicochemical properties, microbial activity and vegetation at coal ash and sludge disposal sites.

Science.gov (United States)

Woch, Marcin W; Radwańska, Magdalena; Stanek, Małgorzata; Łopata, Barbara; Stefanowicz, Anna M

2018-06-11

The aim of the study was to assess the relationships between vegetation, physicochemical and microbial properties of substrate at coal ash and sludge disposal sites. The study was performed on 32 plots classified into 7 categories: dried ash sedimentation ponds, dominated by a grass Calamagrostis epigejos (AH-Ce), with the admixture of Pinus sylvestris (AH-CePs) or Robinia pseudoacacia (AH-CeRp), dry ash landfill dominated by Betula pendula and Pinus sylvestris (AD-BpPs) or Salix viminalis (AD-Sv) and coal sludge pond with drier parts dominated by Tussilago farfara (CS-Tf) and the wetter ones by Cyperus flavescens (CS-Cf). Ash sites were covered with soil layer imported as a part of technical reclamation. Ash had relatively high concentrations of some alkali and alkaline earth metals, Mn and pH, while coal sludge had high water and C, S, P and K contents. Concentrations of heavy metals were lower than allowable limits in all substrate types. Microbial biomass and, particularly, enzymatic activity in ash and sludge were generally low. The only exception were CS-Tf plots characterized by the highest microbial biomass, presumably due to large deposits of organic matter that became available for aerobic microbial biomass when water level fell. The properties of ash and sludge adversely affected microbial biomass and enzymatic activity as indicated by significant negative correlations between the content of alkali/alkaline earth metals, heavy metals, and macronutrients with enzymatic activity and/or microbial biomass, as well as positive correlations of these parameters with metabolic quotient (qCO 2 ). Plant species richness and cover were relatively high, which may be partly associated with alleviating influence of soil covering the ash. The effect of the admixture of R. pseudoacacia or P. sylvestris to stands dominated by C. epigejos was smaller than expected. The former species increased NNH 4 , NNO 3 and arylsulfatase activity, while the latter reduced activity of

Microbial Life of North Pacific Oceanic Crust

Science.gov (United States)

Schumann, G.; Koos, R.; Manz, W.; Reitner, J.

2003-12-01

Information on the microbiology of the deep subsurface is necessary in order to understand the factors controlling the rate and extent of the microbially catalyzed reactions that influence the geophysical properties of these environments. Drilling into 45-Ma oceanic basaltic crust in a deepwater environment during ODP Leg 200 provided a promising opportunity to explore the abundance, diversity and activity of micro-organisms. The combined use of culture-independent molecular phylogenetic analyses and enrichment culture techniques is an advantageous approach in investigating subsurface microbial ecosystems. Enrichment culture methods allow the evaluation of potential activities and functions. Microbiological investigations revealed few aerobic cultivable, in part hitherto unknown, micro-organisms in deep submarine sediments and basaltic lava flows. 16S rDNA sequencing of isolates from sediment revealed the next relatives to be members of the genera Halomonas, Pseudomonas, and Lactobacillus. Within the Pseudomonadaceae the closest relative is Acinetobacter sp., which was isolated from a deep subsurface environment. The next phylogenetical relatives within the Halomonadaceae are bacteria typically isolated from Soda lakes, which are considered as model of early life conditions. Interestingly, not only sediment bacteria could be obtained in pure culture. Aerobic strains could also be successfully isolated from the massive tholeiitic basalt layer at a depth of 76.16 mbsf (46 m below the sediment/basement contact). These particular isolates are gram-positive with low G+C content of DNA, phylogenetically affiliated to the phylum Firmicutes. The closest neighbors are e.g. a marine Bacillus isolated from the Gulf of Mexico and a low G+C gram-positive bacterium, which belongs to the microbial flora in the deepest sea mud of the Mariana Trench, isolated from a depth of 10,897 m. Based on the similarity values, the isolates represent hitherto undescribed species of the deep

Controls of Sediment Nitrogen Dynamics in Tropical Coastal Lagoons

Science.gov (United States)

Enrich-Prast, Alex; Figueiredo, Viviane; Esteves, Francisco de Assis; Nielsen, Lars Peter

2016-01-01

Sediment denitrification rates seem to be lower in tropical environments than in temperate environments. Using the isotope pairing technique, we measured actual denitrification rates in the sediment of tropical coastal lagoons. To explain the low denitrification rates observed at all study sites (<5 μmol N2 m-2 h-1), we also evaluated potential oxygen (O2) consumption, potential nitrification, potential denitrification, potential anammox, and estimated dissimilatory nitrate (NO3-) reduction to ammonium (NH4+; DNRA) in the sediment. 15NO3- and 15NH4+ conversion was measured in oxic and anoxic slurries from the sediment surface. Sediment potential O2 consumption was used as a proxy for overall mineralization activity. Actual denitrification rates and different potential nitrogen (N) oxidation and reduction processes were significantly correlated with potential O2 consumption. The contribution of potential nitrification to total O2 consumption decreased from contributing 9% at sites with the lowest sediment mineralization rates to less than 0.1% at sites with the highest rates. NO3- reduction switched completely from potential denitrification to estimated DNRA. Ammonium oxidation and nitrite (NO2-) reduction by potential anammox contributed up to 3% in sediments with the lowest sediment mineralization rates. The majority of these patterns could be explained by variations in the microbial environments from stable and largely oxic conditions at low sediment mineralization sites to more variable conditions and the prevalences of anaerobic microorganisms at high sediment mineralization sites. Furthermore, the presence of algal and microbial mats on the sediment had a significant effect on all studied processes. We propose a theoretical model based on low and high sediment mineralization rates to explain the growth, activity, and distribution of microorganisms carrying out denitrification and DNRA in sediments that can explain the dominance or coexistence of DNRA and

Final Report Real Time Monitoring of Rates of Subsurface Microbial Activity Associated with Natural Attenuation and Electron Donor Availability

Energy Technology Data Exchange (ETDEWEB)

Lovley, Derek R. [Univ. of Massachusetts, Amherst, MA (United States)

2016-03-22

The project was successful in developing new sensing technologies for monitoring rates of microbial activity in soils and sediments and also developed a novel proof-of-concept for monitoring the presence of bioavailable concentrations of a diversity of metabolites and toxic components in sedimentary environments. These studies led not only to publications in the peer-reviewed literature, but also two patent applications and a start-up company.

In situ hydrogen consumption kinetics as an indicator of subsurface microbial activity

Science.gov (United States)

Harris, S.H.; Smith, R.L.; Suflita, J.M.

2007-01-01

There are few methods available for broadly assessing microbial community metabolism directly within a groundwater environment. In this study, hydrogen consumption rates were estimated from in situ injection/withdrawal tests conducted in two geochemically varying, contaminated aquifers as an approach towards developing such a method. The hydrogen consumption first-order rates varied from 0.002 nM h-1 for an uncontaminated, aerobic site to 2.5 nM h-1 for a contaminated site where sulfate reduction was a predominant process. The method could accommodate the over three orders of magnitude range in rates that existed between subsurface sites. In a denitrifying zone, the hydrogen consumption rate (0.02 nM h-1) was immediately abolished in the presence of air or an antibiotic mixture, suggesting that such measurements may also be sensitive to the effects of environmental perturbations on field microbial activities. Comparable laboratory determinations with sediment slurries exhibited hydrogen consumption kinetics that differed substantially from the field estimates. Because anaerobic degradation of organic matter relies on the rapid consumption of hydrogen and subsequent maintenance at low levels, such in situ measures of hydrogen turnover can serve as a key indicator of the functioning of microbial food webs and may be more reliable than laboratory determinations. ?? 2007 Federation of European Microbiological Societies.

Electricity generation by anaerobic bacteria and anoxic sediments from hypersaline soda lakes

Science.gov (United States)

Miller, L.G.; Oremland, R.S.

2008-01-01

Anaerobic bacteria and anoxic sediments from soda lakes produced electricity in microbial fuel cells (MFCs). No electricity was generated in the absence of bacterial metabolism. Arsenate respiring bacteria isolated from moderately hypersaline Mono Lake (Bacillus selenitireducens), and salt-saturated Searles Lake, CA (strain SLAS-1) oxidized lactate using arsenate as the electron acceptor. However, these cultures grew equally well without added arsenate using the MFC anode as their electron acceptor, and in the process oxidized lactate more efficiently. The decrease in electricity generation by consumption of added alternative electron acceptors (i.e. arsenate) which competed with the anode for available electrons proved to be a useful indicator of microbial activity and hence life in the fuel cells. Shaken sediment slurries from these two lakes also generated electricity, with or without added lactate. Hydrogen added to sediment slurries was consumed but did not stimulate electricity production. Finally, electricity was generated in statically incubated "intact" sediment cores from these lakes. More power was produced in sediment from Mono Lake than from Searles Lake, however microbial fuel cells could detect low levels of metabolism operating under moderate and extreme conditions of salt stress. ?? 2008 US Government.

Methymercury Formation in Marine and Freshwater Systems: Sediment Characteristics, Microbial Activity and SRB Phylogeny Control Formation Rates and Food-Chain Exposure

Science.gov (United States)

King, J. K.; Saunders, F. M.

2004-05-01

Mercury research in freshwater and marine systems suggests that sediment characteristics such as organic substrate, mercury speciation, and sulfate/sulfide concentrations influence availability of inorganic mercury for methylation. Similarly, sediment characteristics also influence sulfate-reducing bacterial (SRB) respiration as well as the presence/distribution of phylogenetic groups responsible for mercury methylation. Our work illustrates that the process of methylmercury formation in freshwater and marine systems are not dissimilar. Rather, the same geochemical parameters and SRB phylogenetic groups determine the propensity for methylmercury formation and are applicable in both fresh- and marine-water systems. The presentation will include our integration of sediment geochemical and microbial parameters affecting mercury methylation in specific freshwater and marine systems. Constructed wetlands planted with Schoenoplectus californicus and amended with gypsum (CaSO4) have demonstrated a capacity to remove inorganic mercury from industrial outfalls. However, bioaccumulation studies of periphyton, eastern mosquitofish (Gambusia holbrooki) and lake chubsucker (Erimyzon sucetta) were conducted in order to ascertain the availability of wetland-generated methylmercury to biota. Total mercury concentrations in mosquitofish from non-sulfate treated controls and the reference location were significantly lower than those from the low and high sulfate treatments while mean total mercury concentrations in lake chubsuckers were also significantly elevated in the high sulfate treatment compared to the low sulfate, control and reference populations. Methylmercury concentrations in periphyton also corresponded with mercury levels found in the tissue of the lake chubsuckers, and these findings fit well given the trophic levels identified for both species of fish. Overall, data from this study suggest that the initial use of gypsum to accelerate the maturity of a constructed

Patterns of microbial activity in the shallow bottom sediments of Lake ...

African Journals Online (AJOL)

FDA), was investigated in two sediment cores collected from Manzala Lake during November 2011. FDA hydrolysis positively correlated with total bacterial counts, bacterial biomass and chlorophyll a in both cores. The 10–20 cm subsurface layer ...

Milankovitch-scale correlations between deeply buried microbial populations and biogenic ooze lithology

Science.gov (United States)

Aiello, I.W.; Bekins, B.A.

2010-01-01

The recent discoveries of large, active populations of microbes in the subseafloor of the world's oceans supports the impact of the deep biosphere biota on global biogeochemical cycles and raises important questions concerning the functioning of these extreme environments for life. These investigations demonstrated that subseafloor microbes are unevenly distributed and that cell abundances and metabolic activities are often independent from sediment depths, with increased prokaryotic activity at geochemical and/or sedimentary interfaces. In this study we demonstrate that microbial populations vary at the scale of individual beds in the biogenic oozes of a drill site in the eastern equatorial Pacific (Ocean Drilling Program Leg 201, Site 1226). We relate bedding-scale changes in biogenic ooze sediment composition to organic carbon (OC) and microbial cell concentrations using high-resolution color reflectance data as proxy for lithology. Our analyses demonstrate that microbial concentrations are an order of magnitude higher in the more organic-rich diatom oozes than in the nannofossil oozes. The variations mimic small-scale variations in diatom abundance and OC, indicating that the modern distribution of microbial biomass is ultimately controlled by Milankovitch-frequency variations in past oceanographic conditions. ?? 2010 Geological Society of America.

Distribution of dehalogenation activity in subseafloor sediments of the Nankai Trough subduction zone.

Science.gov (United States)

Futagami, Taiki; Morono, Yuki; Terada, Takeshi; Kaksonen, Anna H; Inagaki, Fumio

2013-04-19

Halogenated organic matter buried in marine subsurface sediment may serve as a source of electron acceptors for anaerobic respiration of subseafloor microbes. Detection of a diverse array of reductive dehalogenase-homologous (rdhA) genes suggests that subseafloor organohalide-respiring microbial communities may play significant ecological roles in the biogeochemical carbon and halogen cycle in the subseafloor biosphere. We report here the spatial distribution of dehalogenation activity in the Nankai Trough plate-subduction zone of the northwest Pacific off the Kii Peninsula of Japan. Incubation experiments with slurries of sediment collected at various depths and locations showed that degradation of several organohalides tested only occurred in the shallow sedimentary basin, down to 4.7 metres below the seafloor, despite detection of rdhA in the deeper sediments. We studied the phylogenetic diversity of the metabolically active microbes in positive enrichment cultures by extracting RNA, and found that Desulfuromonadales bacteria predominate. In addition, for the isolation of genes involved in the dehalogenation reaction, we performed a substrate-induced gene expression screening on DNA extracted from the enrichment cultures. Diverse DNA fragments were obtained and some of them showed best BLAST hit to known organohalide respirers such as Dehalococcoides, whereas no functionally known dehalogenation-related genes such as rdhA were found, indicating the need to improve the molecular approach to assess functional genes for organohalide respiration.

Microbial diversity in sediment ecosystems (evaporites domes, microbial mats and crusts of hypersaline Laguna Tebenquiche, Salar de Atacama, Chile

Directory of Open Access Journals (Sweden)

Ana Beatriz Fernandez

2016-08-01

Full Text Available We combined nucleic acid-based molecular methods, biogeochemical measurements and physicochemical characteristics to investigate microbial sedimentary ecosystems of Laguna Tebenquiche, Atacama Desert, Chile. Molecular diversity and biogeochemistry of hypersaline microbial mats, rhizome-associated concretions and an endoevaporite were compared with: The V4 hypervariable region of the 16S rRNA gene was amplified by pyrosequencing to analyze the total microbial diversity (i.e., bacteria and archaea in bulk samples and, in addition, in detail on a millimeter scale in one microbial mat and in one evaporite. Archaea were more abundant than bacteria. Euryarchaeota was one of the most abundant phyla in all samples, and particularly dominant (97% of total diversity in the most lithified ecosystem, the evaporite. Most of the euryarchaeal OTUs could be assigned to the class Halobacteria or anaerobic and methanogenic archaea. Planctomycetes potentially also play a key role in mats and rhizome-associated concretions, notably the aerobic organoheterotroph members of the class Phycisphaerae. In addition to cyanobacteria, members of Chromatiales and possibly the candidate family Chlorotrichaceae contributed to photosynthetic carbon fixation. Other abundant uncultured taxa such as the candidate division MSBL1, the uncultured MBGB and the phylum Acetothermia potentially play an important metabolic role in these ecosystems. Lithifying microbial mats contained calcium carbonate precipitates, whereas endoevoporites consisted of gypsum and halite. Biogeochemical measurements revealed that based on depth profiles of O2 and sulfide, metabolic activities were much higher in the non-lithifying mat (peaking in the least lithified systems than in lithifying mats with the lowest activity in endoevaporites. This trend in decreasing microbial activity reflects the increase in salinity, which may play an important role in the biodiversity.

Development of a novel multi-functional active membrane capping barrier for the remediation of nitrobenzene-contaminated sediment.

Science.gov (United States)

Wang, Qing; Li, Yi; Wang, Chao; Wu, Yue; Wang, Peifang

2014-07-15

A novel bio-reactive capping barrier composed of polysulfone/granular activated carbon (PS/GAC) hybrid membranes immobilized with microorganism was developed for the remediation of nitrobenzene in sediments. The SEM observation demonstrated that all the membranes had a dense top layer and a porous sublayer, this structure can block the transfer of nitrobenzene from sediment to the water and enhance nitrobenzene degradation. Adsorption behaviors of nitrobenzene on membranes showed that the membrane impregnated with GAC had better performance than the pure PS membrane. The values of Kads increased from 4.64 (without GAC) to 6.19 (1:2 GAC). 20mg/L nitrobenzene can be completely degraded by Pseudomonas putida immobilized on membranes. The biodegradation rate of activated carbon-filled membrane system was little higher than that of pure PS membrane system. For remediation experiments, only about 21.7, 28.3 and 43.9% of nitrobenzene in the sediment was removed by the end of the experiments for PS/GAC membrane, sand-alone and sand amended with activated carbon capping systems, respectively. While for PS/GAC+microorganisms capping system, more than 70% of nitrobenzene loss was observed. This demonstrated that nitrobenzene can be effectively removed from contaminated sediments by microbial degradation in the bio-reactive capping system. Copyright © 2014 Elsevier B.V. All rights reserved.

Profiling of Sediment Microbial Community in Dongting Lake before and after Impoundment of the Three Gorges Dam

Directory of Open Access Journals (Sweden)

Wei Huang

2016-06-01

Full Text Available The sediment microbial community in downstream-linked lakes can be affected by the operation of large-scale water conservancy projects. The present study determined Illumina reads (16S rRNA gene amplicons to analyze and compare the bacterial communities from sediments in Dongting Lake (China before and after impoundment of the Three Gorges Dam (TGD, the largest hydroelectric project in the world. Bacterial communities in sediment samples in Dongting Lake before impoundment of the TGD (the high water period had a higher diversity than after impoundment of the TGD (the low water period. The most abundant phylum in the sediment samples was Proteobacteria (36.4%–51.5%, and this result was due to the significant abundance of Betaproteobacteria and Deltaproteobacteria in the sediment samples before impoundment of the TGD and the abundance of Gammaproteobacteria in the sediment samples after impoundment of the TGD. In addition, bacterial sequences of the sediment samples are also affiliated with Acidobacteria (11.0% on average, Chloroflexi (10.9% on average, Bacteroidetes (6.7% on average, and Nitrospirae (5.1% on average. Variations in the composition of the bacterial community within some sediment samples from the river estuary into Dongting Lake were related to the pH values. The bacterial community in the samples from the three lake districts of Dongting Lake before and after impoundment of the TGD was linked to the nutrient concentration.

Culture-dependent and independent studies of microbial diversity in highly copper-contaminated Chilean marine sediments.

Science.gov (United States)

Besaury, Ludovic; Marty, Florence; Buquet, Sylvaine; Mesnage, Valérie; Muyzer, Gerard; Quillet, Laurent

2013-02-01

Cultivation and molecular-based approaches were used to study microbial diversity in two Chilean marine sediments contaminated with high (835 ppm) and very high concentrations of copper (1,533 ppm). The diversity of cultivable bacteria resistant to copper was studied at oxic and anoxic conditions, focusing on sulfate-, thiosulfate-, and iron-reducing bacteria. For both sediments, the cultivable bacteria isolated at oxic conditions were mostly affiliated to the genus Bacillus, while at anoxic conditions the majority of the cultivable bacteria found were closely related to members of the genera Desulfovibrio, Sphingomonas, and Virgibacillus. Copper resistance was between 100 and 400 ppm, with the exception of a strain affiliated to members of the genus Desulfuromonas, which was resistant up to 1,000 ppm of copper. In parallel, cloning and sequencing of 16S rRNA was performed to study the total bacterial diversity in the sediments. A weak correlation was observed between the isolated strains and the 16S rRNA operational taxonomic units detected. The presence of copper resistance genes (copA, cusA, and pcoA) was tested for all the strains isolated; only copA was detected in a few isolates, suggesting that other copper resistance mechanisms could be used by the bacteria in those highly copper-contaminated sediments.

Microbial and viral-like rhodopsins present in coastal marine sediments from four polar and subpolar regions

Energy Technology Data Exchange (ETDEWEB)

López, José L.; Golemba, Marcelo; Hernández, Edgardo; Lozada, Mariana; Dionisi, Hebe; Jansson, Janet K.; Carroll, Jolynn; Lundgren, Leif; Sjöling, Sara; Mac Cormack, Walter P.; Sobecky, Patricia

2016-11-03

Rhodopsins are broadly distributed. In this work, we analyzed 23 metagenomes corresponding to marine sediment samples from four regions that share cold climate conditions (Norway; Sweden; Argentina and Antarctica). In order to investigate the genes evolution of viral rhodopsins, an initial set of 6224 bacterial rhodopsin sequences according to COG5524 were retrieved from the 23 metagenomes. After selection by the presence of transmembrane domains and alignment, 123 viral (51) and non-viral (72) sequences (>50 amino acids) were finally included in further analysis. Viral rhodopsin genes were homologs of Phaeocystis globosa virus and Organic lake Phycodnavirus. Non-viral microbial rhodopsin genes were ascribed to Bacteroidetes, Planctomycetes, Firmicutes, Actinobacteria, Cyanobacteria, Proteobacteria, Deinococcus-Thermus and Cryptophyta and Fungi. A rescreening using Blastp, using as queries the viral sequences previously described, retrieved 30 sequences (>100 amino acids). Phylogeographic analysis revealed a geographical clustering of the sequences affiliated to the viral group. This clustering was not observed for the microbial non-viral sequences. The phylogenetic reconstruction allowed us to propose the existence of a putative ancestor of viral rhodopsin genes related to Actinobacteria and Chloroflexi. This is the first report about the existence of a phylogeographic association of the viral rhodopsin sequences from marine sediments.

Discovery of enzymes for toluene synthesis from anoxic microbial communities

DEFF Research Database (Denmark)

Beller, Harry R.; Rodrigues, Andria V.; Zargar, Kamrun

2018-01-01

Microbial toluene biosynthesis was reported in anoxic lake sediments more than three decades ago, but the enzyme catalyzing this biochemically challenging reaction has never been identified. Here we report the toluene-producing enzyme PhdB, a glycyl radical enzyme of bacterial origin that catalyzes...... phenylacetate decarboxylation, and its cognate activating enzyme PhdA, a radical S-adenosylmethionine enzyme, discovered in two distinct anoxic microbial communities that produce toluene. The unconventional process of enzyme discovery from a complex microbial community (>300,000 genes), rather than from...... a microbial isolate, involved metagenomics- and metaproteomics-enabled biochemistry, as well as in vitro confirmation of activity with recombinant enzymes. This work expands the known catalytic range of glycyl radical enzymes (only seven reaction types had been characterized previously) and aromatic...

Biogeochemical and microbial variation across 5500 km of Antarctic surface sediment implicates organic matter as a driver of benthic community structure

Directory of Open Access Journals (Sweden)

Deric R Learman

2016-03-01

Full Text Available Western Antarctica, one of the fastest warming locations on Earth, is a unique environment that is underexplored with regards to biodiversity. Although pelagic microbial communities in the Southern Ocean and coastal Antarctic waters have been well studied, there are fewer investigations of benthic communities and most have a focused geographic range. We sampled surface sediment from 24 sites across a 5,500 km region of Western Antarctica (covering the Ross Sea to the Weddell Sea to examine relationships between microbial communities and sediment geochemistry. Sequencing of the 16S and 18S rRNA genes showed microbial communities in sediments from the Antarctic Peninsula (AP and Western Antarctica (WA, including the Ross, Amundsen, and Bellingshausen Seas, could be distinguished by correlations with organic matter concentrations and stable isotope fractionation (total organic carbon; TOC, nitrogen, and δ13C. Overall, samples from the AP were higher in nutrient content (TOC, nitrogen, and NH4+ and communities in these samples had higher relative abundances of operational taxonomic units (OTUs classified as the diatom, Chaetoceros, a marine cercozoan and four OTUs classified as Cytophaga or Flavobacteria. As these OTUs were strongly correlated with TOC, the data suggests the diatoms could be a source of organic matter and the Bacteroidetes and cercozoan are grazers that consume the organic matter. Additionally, samples from WA have lower nutrients and were dominated by Thaumarchaeota, which could be related to their known ability to thrive as lithotrophs. This study documents the largest analysis of benthic microbial communities to date in the Southern Ocean, representing almost half the continental shoreline of Antarctica, and documents trophic interactions and coupling of pelagic and benthic communities. Our results indicate potential modifications in carbon sequestration processes related to change in community composition, identifying a

DESIGN CONSIDERATION INVOLVING ACTIVE SEDIMENT CAPS (PRESENTATION)

Science.gov (United States)

When contaminated sediments pose unacceptable risks to human health and the environment, management activities such as removal, treatment, or isolation of contaminated sediments may be required. Various capping designs are being considered for isolating contaminated sediment are...

Gravitational sedimentation of flocculated waste activated sludge.

Science.gov (United States)

Chu, C P; Lee, D J; Tay, J H

2003-01-01

The sedimentation characteristics of flocculated wastewater sludge have not been satisfactorily explored using the non-destructive techniques, partially owing to the rather low solid content (ca. 1-2%) commonly noted in the biological sediments. This paper investigated, for the first time, the spatial-temporal gravitational settling characteristics of original and polyelectrolyte flocculated waste activated sludge using Computerized Axial Tomography Scanner. The waste activated sludge possessed a distinct settling characteristic from the kaolin slurries. The waste activated sludges settled more slowly and reached a lower solid fraction in the final sediment than the latter. Flocculation markedly enhanced the settleability of both sludges. Although the maximum achievable solid contents for the kaolin slurries were reduced, flocculation had little effects on the activated sludge. The purely plastic rheological model by Buscall and White (J Chem Soc Faraday Trans 1(83) (1987) 873) interpreted the consolidating sediment data, while the purely elastic model by Tiller and Leu (J. Chin. Inst. Chem. Eng. 11 (1980) 61) described the final equilibrated sediment. Flocculation produced lower yield stress during transient settling, thereby resulting in the more easily consolidated sludge than the original sample. Meanwhile, the flocculated activated sludge was stiffer in the final sediment than in the original sample. The data reported herein are valuable to the theories development for clarifier design and operation.

Polycyclic aromatic hydrocarbons (PAHs) biodegradation potential and diversity of microbial consortia enriched from tsunami sediments in Miyagi, Japan

Energy Technology Data Exchange (ETDEWEB)

Bacosa, Hernando Pactao, E-mail: hernando.bacosa@utexas.edu [Graduate School of Environmental Studies, Tohoku University, Aoba 6-6-20, Aramaki, Aoba-ku, Sendai 980-8579 (Japan); Marine Science Institute, The University of Texas at Austin, 750 Channel View Drive, Port Aransas, TX 78373 (United States); Inoue, Chihiro [Graduate School of Environmental Studies, Tohoku University, Aoba 6-6-20, Aramaki, Aoba-ku, Sendai 980-8579 (Japan)

2015-02-11

Highlights: • Most bacterial consortia from tsunami sediment degraded PAH mixture and pyrene. • The consortia were dominated by known and unknown PAHs-degrading bacteria. • Dokdonella clone is a potential new species and PAH degrader from tsunami sediment. • PAH-RHDα is better than nidA gene for estimating pyrene-degraders in the consortia. • First report on the PAH degradation and PAH-degrading bacteria from tsunami sediment. - Abstract: The Great East Japan Earthquake caused tsunamis and resulted in widespread damage to human life and infrastructure. The disaster also resulted in contamination of the environment by chemicals such as polycyclic aromatic hydrocarbons (PAHs). This study was conducted to investigate the degradation potential and describe the PAH-degrading microbial communities from tsunami sediments in Miyagi, Japan. PAH-degrading bacteria were cultured by enrichment using PAH mixture or pyrene alone as carbon and energy sources. Among the ten consortia tested for PAH mixture, seven completely degraded fluorene and more than 95% of phenanthrene in 10 days, while only four consortia partially degraded pyrene. Six consortia partially degraded pyrene as a single substrate. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) revealed that each sample was dominated by unique microbial populations, regardless of sampling location. The consortia were dominated by known PAHs degraders including Sphingomonas, Pseudomonas, and Sphingobium; and previously unknown degraders such as Dokdonella and Luteimonas. A potentially novel and PAH-degrading Dokdonella was detected for the first time. PAH-ring hydroxylating dioxygenase (PAH-RHDα) gene was shown to be more effective than nidA in estimating pyrene-degrading bacteria in the enriched consortia. The consortia obtained in this study are potential candidates for remediation of PAHs contaminated soils.

Polycyclic aromatic hydrocarbons (PAHs) biodegradation potential and diversity of microbial consortia enriched from tsunami sediments in Miyagi, Japan

International Nuclear Information System (INIS)

Bacosa, Hernando Pactao; Inoue, Chihiro

2015-01-01

Highlights: • Most bacterial consortia from tsunami sediment degraded PAH mixture and pyrene. • The consortia were dominated by known and unknown PAHs-degrading bacteria. • Dokdonella clone is a potential new species and PAH degrader from tsunami sediment. • PAH-RHDα is better than nidA gene for estimating pyrene-degraders in the consortia. • First report on the PAH degradation and PAH-degrading bacteria from tsunami sediment. - Abstract: The Great East Japan Earthquake caused tsunamis and resulted in widespread damage to human life and infrastructure. The disaster also resulted in contamination of the environment by chemicals such as polycyclic aromatic hydrocarbons (PAHs). This study was conducted to investigate the degradation potential and describe the PAH-degrading microbial communities from tsunami sediments in Miyagi, Japan. PAH-degrading bacteria were cultured by enrichment using PAH mixture or pyrene alone as carbon and energy sources. Among the ten consortia tested for PAH mixture, seven completely degraded fluorene and more than 95% of phenanthrene in 10 days, while only four consortia partially degraded pyrene. Six consortia partially degraded pyrene as a single substrate. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) revealed that each sample was dominated by unique microbial populations, regardless of sampling location. The consortia were dominated by known PAHs degraders including Sphingomonas, Pseudomonas, and Sphingobium; and previously unknown degraders such as Dokdonella and Luteimonas. A potentially novel and PAH-degrading Dokdonella was detected for the first time. PAH-ring hydroxylating dioxygenase (PAH-RHDα) gene was shown to be more effective than nidA in estimating pyrene-degrading bacteria in the enriched consortia. The consortia obtained in this study are potential candidates for remediation of PAHs contaminated soils

Impacts of Activated Carbon Amendment on Hg Methylation, Demethylation and Microbial Activity in Marsh Soils

Science.gov (United States)

Gilmour, C. C.; Ghosh, U.; Santillan, E. F. U.; Soren, A.; Bell, J. T.; Butera, D.; McBurney, A. W.; Brown, S.; Henry, E.; Vlassopoulos, D.

2015-12-01

In-situ sorbent amendments are a low-impact approach for remediation of contaminants in sediments, particular in habitats like wetlands that provide important ecosystem services. Laboratory microcosm trials (Gilmour et al. 2013) and early field trials show that activated carbon (AC) can effectively increase partitioning of both inorganic Hg and methylmercury to the solid phase. Sediment-water partitioning can serve as a proxy for Hg and MeHg bioavailability in soils. One consideration in using AC in remediation is its potential impact on organisms. For mercury, a critical consideration is the potential impact on net MeHg accumulation and bioavailability. In this study, we specifically evaluated the impact of AC on rates of methylmercury production and degradation, and on overall microbial activity, in 4 different Hg-contaminated salt marsh soils. The study was done over 28 days in anaerobic, sulfate-reducing slurries. A double label of enriched mercury isotopes (Me199Hg and inorganic 201Hg) was used to separately follow de novo Me201Hg production and Me199Hg degradation. AC amendments decreased both methylation and demethylation rate constants relative to un-amended controls, but the impact on demethylation was stronger. The addition of 5% (dry weight) regenerated AC to soil slurries drove demethylation rate constants to nearly zero; i.e. MeHg sorption to AC almost totally blocked its degradation. The net impact was increased solid phase MeHg concentrations in some of the soil slurries with the highest methylation rate constants. However, the net impact of AC amendments was to increase MeHg (and inorganic Hg) partitioning to the soil phase and decrease concentrations in the aqueous phase. AC significantly decreased aqueous phase inorganic Hg and MeHg concentrations after 28 days. Overall, the efficacy of AC in reducing aqueous MeHg was highest in the soils with the highest MeHg concentrations. The AC addition did not significantly impact microbial activity, as

Effects of organic carbon supply rates on uranium mobility in a previously bioreduced contaminated sediment.

Science.gov (United States)

Wan, Jiamin; Tokunaga, Tetsu K; Kim, Yongman; Brodie, Eoin; Daly, Rebecca; Hazen, Terry C; Firestone, Mary K

2008-10-15

Bioreduction-based strategies for remediating uranium (U)-contaminated sediments face the challenge of maintaining the reduced status of U for long times. Because groundwater influxes continuously bring in oxidizing terminal electron acceptors (O2, NO3(-)), it is necessary to continue supplying organic carbon (OC) to maintain the reducing environment after U bioreduction is achieved. We tested the influence of OC supply rates on mobility of previously microbial reduced uranium U(IV) in contaminated sediments. We found that high degrees of U mobilization occurred when OC supply rates were high, and when the sediment still contained abundant Fe(III). Although 900 days with low levels of OC supply minimized U mobilization, the sediment redox potential increased with time as did extractable U(VI) fractions. Molecular analyses of total microbial activity demonstrated a positive correlation with OC supply and analyses of Geobacteraceae activity (RT-qPCR of 16S rRNA) indicated continued activity even when the effluent Fe(II) became undetectable. These data support our hypothesis on the mechanisms responsible for remobilization of U under reducing conditions; that microbial respiration caused increased (bi)carbonate concentration and formation of stable uranyl carbonate complexes, thereby shifted U(IV)/U(VI) equilibrium to more reducing potentials. The data also suggested that low OC concentrations could not sustain the reducing condition of the sediment for much longer time. Bioreduced U(IV) is not sustainable in an oxidizing environment for a very long time.

Virus Dynamics Are Influenced by Season, Tides and Advective Transport in Intertidal, Permeable Sediments.

Science.gov (United States)

Vandieken, Verona; Sabelhaus, Lara; Engelhardt, Tim

2017-01-01

Sandy surface sediments of tidal flats exhibit high microbial activity due to the fast and deep-reaching transport of oxygen and nutrients by porewater advection. On the other hand during low tide, limited transport results in nutrient and oxygen depletion concomitant to the accumulation of microbial metabolites. This study represents the first attempt to use flow-through reactors to investigate virus production, virus transport and the impact of tides and season in permeable sediments. The reactors were filled with intertidal sands of two sites (North beach site and backbarrier sand flat of Spiekeroog island in the German Wadden Sea) to best simulate advective porewater transport through the sediments. Virus and cell release along with oxygen consumption were measured in the effluents of reactors during continuous flow of water through the sediments as well as in tidal simulation experiments where alternating cycles with and without water flow (each for 6 h) were operated. The results showed net rates of virus production (0.3-13.2 × 10 6 viruses cm -3 h -1 ) and prokaryotic cell production (0.3-10.0 × 10 5 cells cm -3 h -1 ) as well as oxygen consumption rates (56-737 μmol l -1 h -1 ) to be linearly correlated reflecting differences in activity, season and location of the sediments. Calculations show that total virus turnover was fast with 2 to 4 days, whereas virus-mediated cell turnover was calculated to range between 5-13 or 33-91 days depending on the assumed burst sizes (number of viruses released upon cell lysis) of 14 or 100 viruses, respectively. During the experiments, the homogenized sediments in the reactors became vertically structured with decreasing microbial activities and increasing impact of viruses on prokaryotic mortality with depth. Tidal simulation clearly showed a strong accumulation of viruses and cells in the top sections of the reactors when the flow was halted indicating a consistently high virus production during low tide. In

Microbial Remobilisation on Riverbed Sediment Disturbance in Experimental Flumes and a Human-Impacted River: Implication for Water Resource Management and Public Health in Developing Sub-Saharan African Countries.

Science.gov (United States)

Abia, Akebe Luther King; James, Chris; Ubomba-Jaswa, Eunice; Benteke Momba, Maggy Ndombo

2017-03-15

Resuspension of sediment-borne microorganisms (including pathogens) into the water column could increase the health risk for those using river water for different purposes. In the present work, we (1) investigated the effect of sediment disturbance on microbial resuspension from riverbed sediments in laboratory flow-chambers and in the Apies River, Gauteng, South Africa; and (2) estimated flow conditions for sediment-borne microorganism entrainment/resuspension in the river. For mechanical disturbance, the top 2 cm of the sediment in flow-chambers was manually stirred. Simulating sudden discharge into the river, water (3 L) was poured within 30 s into the chambers at a 45° angle to the chamber width. In the field, sediment was disturbed by raking the riverbed and by cows crossing in the river. Water samples before and after sediment disturbance were analysed for Escherichia coli. Sediment disturbance caused an increase in water E. coli counts by up to 7.9-35.8 times original values. Using Shields criterion, river-flow of 0.15-0.69 m³/s could cause bed particle entrainment; while ~1.57-7.23 m³/s would cause resuspension. Thus, sediment disturbance in the Apies River would resuspend E. coli (and pathogens), with possible negative health implications for communities using such water. Therefore, monitoring surface water bodies should include microbial sediment quality.

Microbial Remobilisation on Riverbed Sediment Disturbance in Experimental Flumes and a Human-Impacted River: Implication for Water Resource Management and Public Health in Developing Sub-Saharan African Countries

Science.gov (United States)

Abia, Akebe Luther King; James, Chris; Ubomba-Jaswa, Eunice; Benteke Momba, Maggy Ndombo

2017-01-01

Resuspension of sediment-borne microorganisms (including pathogens) into the water column could increase the health risk for those using river water for different purposes. In the present work, we (1) investigated the effect of sediment disturbance on microbial resuspension from riverbed sediments in laboratory flow-chambers and in the Apies River, Gauteng, South Africa; and (2) estimated flow conditions for sediment-borne microorganism entrainment/resuspension in the river. For mechanical disturbance, the top 2 cm of the sediment in flow-chambers was manually stirred. Simulating sudden discharge into the river, water (3 L) was poured within 30 s into the chambers at a 45° angle to the chamber width. In the field, sediment was disturbed by raking the riverbed and by cows crossing in the river. Water samples before and after sediment disturbance were analysed for Escherichia coli. Sediment disturbance caused an increase in water E. coli counts by up to 7.9–35.8 times original values. Using Shields criterion, river-flow of 0.15–0.69 m3/s could cause bed particle entrainment; while ~1.57–7.23 m3/s would cause resuspension. Thus, sediment disturbance in the Apies River would resuspend E. coli (and pathogens), with possible negative health implications for communities using such water. Therefore, monitoring surface water bodies should include microbial sediment quality. PMID:28295001

Microbial Remobilisation on Riverbed Sediment Disturbance in Experimental Flumes and a Human-Impacted River: Implication for Water Resource Management and Public Health in Developing Sub-Saharan African Countries

Directory of Open Access Journals (Sweden)

Akebe Luther King Abia

2017-03-01

Full Text Available Resuspension of sediment-borne microorganisms (including pathogens into the water column could increase the health risk for those using river water for different purposes. In the present work, we (1 investigated the effect of sediment disturbance on microbial resuspension from riverbed sediments in laboratory flow-chambers and in the Apies River, Gauteng, South Africa; and (2 estimated flow conditions for sediment-borne microorganism entrainment/resuspension in the river. For mechanical disturbance, the top 2 cm of the sediment in flow-chambers was manually stirred. Simulating sudden discharge into the river, water (3 L was poured within 30 s into the chambers at a 45° angle to the chamber width. In the field, sediment was disturbed by raking the riverbed and by cows crossing in the river. Water samples before and after sediment disturbance were analysed for Escherichia coli. Sediment disturbance caused an increase in water E. coli counts by up to 7.9–35.8 times original values. Using Shields criterion, river-flow of 0.15–0.69 m3/s could cause bed particle entrainment; while ~1.57–7.23 m3/s would cause resuspension. Thus, sediment disturbance in the Apies River would resuspend E. coli (and pathogens, with possible negative health implications for communities using such water. Therefore, monitoring surface water bodies should include microbial sediment quality.

Bacterial Production and Enzymatic Activities in Deep-Sea Sediments of the Pacific Ocean: Biogeochemical Implications of Different Temperature Constraints

Science.gov (United States)

Danovaro, R.; Corinaldesi, C.; dell'Anno, A.

2002-12-01

The deep-sea bed, acting as the ultimate sink for organic material derived from the upper oceans primary production, is now assumed to play a key role in biogeochemical cycling of organic matter on global scale. Early diagenesis of organic matter in marine sediments is dependent upon biological processes (largely mediated by bacterial activity) and by molecular diffusion. Organic matter reaching the sea floor by sedimentation is subjected to complex biogeochemical transformations that make organic matter largely unsuitable for direct utilization by benthic heterotrophs. Extracellular enzymatic activities in the sediment is generally recognized as the key step in the degradation and utilization of organic polymers by bacteria and a key role in biopolymeric carbon mobilization is played by aminopeptidase, alkaline phosphatase and glucosidase activities. In the present study we investigated bacterial density, bacterial C production and exo-enzymatic activities (aminopeptidase, glucosidase and phosphatase activity) in deep-sea sediments of the Pacific Ocean in relation with the biochemical composition of sediment organic matter (proteins, carbohydrates and lipids), in order to gather information on organic matter cycling and diagenesis. Benthic viral abundance was also measured to investigate the potential role of viruses on microbial loop functioning. Sediment samples were collected at eight stations (depth ranging from 2070-3100 m) along two transects located at the opposite side (north and south) of ocean seismic ridge Juan Fernandez (along latitudes 33° 20' - 33° 40'), constituted by the submerged vulcanoes, which connects the Chilean coasts to Rapa Nui Island. Since the northern and southern sides of this ridge apparently displayed small but significant differences in deep-sea temperature (related to the general ocean circulation), this sampling strategy allowed also investigating the role of different temperature constraints on bacterial activity and

Microbial Interactions With Dissolved Organic Matter Drive Carbon Dynamics and Community Succession

Directory of Open Access Journals (Sweden)

Xiaoqin Wu

2018-06-01

Full Text Available Knowledge of dynamic interactions between natural organic matter (NOM and microbial communities is critical not only to delineate the routes of NOM degradation/transformation and carbon (C fluxes, but also to understand microbial community evolution and succession in ecosystems. Yet, these processes in subsurface environments are usually studied independently, and a comprehensive view has been elusive thus far. In this study, we fed sediment-derived dissolved organic matter (DOM to groundwater microbes and continually analyzed microbial transformation of DOM over a 50-day incubation. To document fine-scale changes in DOM chemistry, we applied high-resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS and soft X-ray absorption spectroscopy (sXAS. We also monitored the trajectory of microbial biomass, community structure and activity over this time period. Together, these analyses provided an unprecedented comprehensive view of interactions between sediment-derived DOM and indigenous subsurface groundwater microbes. Microbial decomposition of labile C in DOM was immediately evident from biomass increase and total organic carbon (TOC decrease. The change of microbial composition was closely related to DOM turnover: microbial community in early stages of incubation was influenced by relatively labile tannin- and protein-like compounds; while in later stages the community composition evolved to be most correlated with less labile lipid- and lignin-like compounds. These changes in microbial community structure and function, coupled with the contribution of microbial products to DOM pool affected the further transformation of DOM, culminating in stark changes to DOM composition over time. Our study demonstrates a distinct response of microbial communities to biotransformation of DOM, which improves our understanding of coupled interactions between sediment-derived DOM, microbial processes, and community structure in

The flux and recovery of bioactive substances in the surface sediments of deep basins off southern California

Energy Technology Data Exchange (ETDEWEB)

Jahnke, R.A.

1990-06-11

Sediment microbial community biomass and activity in Santa Monica Basin, a nearshore basin in the California Continental Borderland, were examined in October 1985, 1986 and 1987, May 1986, April 1987 and January 1990. Millimeter-scale ATP profiles and incubation of intact cores with {sup 3}H-adenine indicated a high-biomass interface microbial population in the low-oxygen central basin, which was absent in samples from the basin slope sediments. A majority of microbial activity and organic matter mineralization occurred in the top cm of sediment. Comparison of measured ATP and total organic carbon profiles suggest that the C:ATP ratio (wt:wt) ranges between 47:1 and 77:1 in central basin interfacial populations, substantially lower than reported for other aquatic environments. Carbon production estimated from DNA synthesis measurements via {sup 3}H-adenine incorporation was compared with TCO{sub 2} fluxes measured by in situ benthic chamber experiments. Within the uncertainty of the C:ATP ratio, an overall microbial carbon assimilation efficiency of 75--90% was indicated. The low C:ATP ratios and high carbon assimilation efficiencies significantly affect estimates of microbial growth and respiration and are substantially different than those often assumed in the literature. These results suggest that without independent knowledge of these ratios, the uncertainty in tracer-derived microbial growth and respiration rates may be larger than previously reported. 66 refs., 8 figs., 3 tabs.

The flux and recovery of bioactive substances in the surface sediments of deep basins off southern California

International Nuclear Information System (INIS)

Jahnke, R.A.

1990-01-01

Sediment microbial community biomass and activity in Santa Monica Basin, a nearshore basin in the California Continental Borderland, were examined in October 1985, 1986 and 1987, May 1986, April 1987 and January 1990. Millimeter-scale ATP profiles and incubation of intact cores with 3 H-adenine indicated a high-biomass interface microbial population in the low-oxygen central basin, which was absent in samples from the basin slope sediments. A majority of microbial activity and organic matter mineralization occurred in the top cm of sediment. Comparison of measured ATP and total organic carbon profiles suggest that the C:ATP ratio (wt:wt) ranges between 47:1 and 77:1 in central basin interfacial populations, substantially lower than reported for other aquatic environments. Carbon production estimated from DNA synthesis measurements via 3 H-adenine incorporation was compared with TCO 2 fluxes measured by in situ benthic chamber experiments. Within the uncertainty of the C:ATP ratio, an overall microbial carbon assimilation efficiency of 75--90% was indicated. The low C:ATP ratios and high carbon assimilation efficiencies significantly affect estimates of microbial growth and respiration and are substantially different than those often assumed in the literature. These results suggest that without independent knowledge of these ratios, the uncertainty in tracer-derived microbial growth and respiration rates may be larger than previously reported. 66 refs., 8 figs., 3 tabs

Long-term effects of aided phytostabilisation of trace elements on microbial biomass and activity, enzyme activities, and composition of microbial community in the Jales contaminated mine spoils

Energy Technology Data Exchange (ETDEWEB)

Renella, Giancarlo [Department of Soil Science and Plant Nutrition, University of Florence, Piazzale delle Cascine 28, I-50144 Florence (Italy)], E-mail: giancarlo.renella@unifi.it; Landi, Loretta; Ascher, Judith; Ceccherini, Maria Teresa; Pietramellara, Giacomo; Mench, Michel; Nannipieri, Paolo [Department of Soil Science and Plant Nutrition, University of Florence, Piazzale delle Cascine 28, I-50144 Florence (Italy)

2008-04-15

We studied the effectiveness of remediation on microbial endpoints, namely microbial biomass and activity, microbial and plant species richness, of an As-contaminated mine spoil, amended with compost (C) alone and in combination with beringite (B) or zerovalent iron grit (Z), to increase organic matter content and reduce trace elements mobility, and to allow Holcus lanatus and Pinus pinaster growth. Untreated spoil showed the lowest microbial biomass and activity and hydrolase activities, and H. lanatus as sole plant species, whereas the presented aided phytostabilisation option, especially CBZ treatment, significantly increased microbial biomass and activity and allowed colonisation by several plant species, comparable to those of an uncontaminated sandy soil. Microbial species richness was only increased in spoils amended with C alone. No clear correlation occurred between trace element mobility and microbial parameters and plant species richness. Our results indicate that the choice of indicators of soil remediation practices is a bottleneck. - Organo-mineral amendment and revegetation of a gold mine spoil increased microbial activity but did not increase microbial species richness.

Long-term effects of aided phytostabilisation of trace elements on microbial biomass and activity, enzyme activities, and composition of microbial community in the Jales contaminated mine spoils

International Nuclear Information System (INIS)

Renella, Giancarlo; Landi, Loretta; Ascher, Judith; Ceccherini, Maria Teresa; Pietramellara, Giacomo; Mench, Michel; Nannipieri, Paolo

2008-01-01

We studied the effectiveness of remediation on microbial endpoints, namely microbial biomass and activity, microbial and plant species richness, of an As-contaminated mine spoil, amended with compost (C) alone and in combination with beringite (B) or zerovalent iron grit (Z), to increase organic matter content and reduce trace elements mobility, and to allow Holcus lanatus and Pinus pinaster growth. Untreated spoil showed the lowest microbial biomass and activity and hydrolase activities, and H. lanatus as sole plant species, whereas the presented aided phytostabilisation option, especially CBZ treatment, significantly increased microbial biomass and activity and allowed colonisation by several plant species, comparable to those of an uncontaminated sandy soil. Microbial species richness was only increased in spoils amended with C alone. No clear correlation occurred between trace element mobility and microbial parameters and plant species richness. Our results indicate that the choice of indicators of soil remediation practices is a bottleneck. - Organo-mineral amendment and revegetation of a gold mine spoil increased microbial activity but did not increase microbial species richness

Effects of Conservation Agriculture and Fertilization on Soil Microbial Diversity and Activity

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Johan Habig

2015-07-01

Full Text Available Soil microbial communities perform critical functions in ecosystem processes. These functions can be used to assess the impact of agricultural practices on sustainable crop production. In this five-year study, the effect of various agricultural practices on soil microbial diversity and activity was investigated in a summer rainfall area under South African dryland conditions. Microbial diversity and activity were measured in the 0–15 cm layer of a field trial consisting of two fertilizer levels, three cropping systems, and two tillage systems. Using the Shannon–Weaver and Evenness diversity indices, soil microbial species richness and abundance were measured. Microbial enzymatic activities: β-glucosidase, phosphatase and urease, were used to evaluate ecosystem functioning. Cluster analysis revealed a shift in soil microbial community diversity and activity over time. Microbial diversity and activity were higher under no-till than conventional tillage. Fertilizer levels seemed to play a minor role in determining microbial diversity and activity, whereas the cropping systems played a more important role in determining the activity of soil microbial communities. Conservation agriculture yielded the highest soil microbial diversity and activity in diversified cropping systems under no-till.

Biodegradation of organic compounds in vadose zone and aquifer sediments

International Nuclear Information System (INIS)

Konopka, A.; Turco, R.

1991-01-01

The microbial processes that occur in the subsurface under a typical Midwest agricultural soil were studied. A 26-m bore was installed in November of 1988 at a site of the Purdue University Agronomy Research Center. Aseptic collections of soil materials were made at 17 different depths. Physical analysis indicated that the site contained up to 14 different strata. The site materials were primarily glacial tills with a high carbonate content. The N,P, and organic C contents of sediments tended to decrease with depth. Ambient water content was generally less than the water content, which corresponds to a -0.3-bar equivalent. No pesticides were detected in slurry incubations of up to 128 days. The sorption of atrazine and metolachlor was correlated with the clay content of the sediments. Microbial biomass (determined by direct microscopic count, viable count, and phospholipid assay) in the tills was lower than in either the surface materials or the aquifer located at 25 m. The biodegradation of glucose and phenol occurred rapidly and without a lag in samples from the aquifer capillary fringe, saturated zone, and surface soils. In contrast, lag periods and smaller biodegradation rates were found in the till samples. Subsurface sediments are rich in microbial numbers and activity. The most active strata appear to be transmissive layers in the saturated zone. This implies that the availability of water may limit activity in the profile

Response of soil microbial activities and microbial community structure to vanadium stress.

Science.gov (United States)

Xiao, Xi-Yuan; Wang, Ming-Wei; Zhu, Hui-Wen; Guo, Zhao-Hui; Han, Xiao-Qing; Zeng, Peng

2017-08-01

High levels of vanadium (V) have long-term, hazardous impacts on soil ecosystems and biological processes. In the present study, the effects of V on soil enzymatic activities, basal respiration (BR), microbial biomass carbon (MBC), and the microbial community structure were investigated through 12-week greenhouse incubation experiments. The results showed that V content affected soil dehydrogenase activity (DHA), BR, and MBC, while urease activity (UA) was less sensitive to V stress. The average median effective concentration (EC 50 ) thresholds of V were predicted using a log-logistic dose-response model, and they were 362mgV/kg soil for BR and 417mgV/kg soil for DHA. BR and DHA were more sensitive to V addition and could be used as biological indicators for soil V pollution. According to a polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis, the structural diversity of the microbial community decreased for soil V contents ranged between 254 and 1104mg/kg after 1 week of incubation. As the incubation time increased, the diversity of the soil microbial community structure increased for V contents ranged between 354 and 1104mg/kg, indicating that some new V-tolerant bacterial species might have replicated under these conditions. Copyright © 2017 Elsevier Inc. All rights reserved.

Diffuse flow environments within basalt- and sediment-based hydrothermal vent ecosystems harbor specialized microbial communities.

Science.gov (United States)

Campbell, Barbara J; Polson, Shawn W; Zeigler Allen, Lisa; Williamson, Shannon J; Lee, Charles K; Wommack, K Eric; Cary, S Craig

2013-01-01

Hydrothermal vents differ both in surface input and subsurface geochemistry. The effects of these differences on their microbial communities are not clear. Here, we investigated both alpha and beta diversity of diffuse flow-associated microbial communities emanating from vents at a basalt-based hydrothermal system along the East Pacific Rise (EPR) and a sediment-based hydrothermal system, Guaymas Basin. Both Bacteria and Archaea were targeted using high throughput 16S rRNA gene pyrosequencing analyses. A unique aspect of this study was the use of a universal set of 16S rRNA gene primers to characterize total and diffuse flow-specific microbial communities from varied deep-sea hydrothermal environments. Both surrounding seawater and diffuse flow water samples contained large numbers of Marine Group I (MGI) Thaumarchaea and Gammaproteobacteria taxa previously observed in deep-sea systems. However, these taxa were geographically distinct and segregated according to type of spreading center. Diffuse flow microbial community profiles were highly differentiated. In particular, EPR dominant diffuse flow taxa were most closely associated with chemolithoautotrophs, and off axis water was dominated by heterotrophic-related taxa, whereas the opposite was true for Guaymas Basin. The diversity and richness of diffuse flow-specific microbial communities were strongly correlated to the relative abundance of Epsilonproteobacteria, proximity to macrofauna, and hydrothermal system type. Archaeal diversity was higher than or equivalent to bacterial diversity in about one third of the samples. Most diffuse flow-specific communities were dominated by OTUs associated with Epsilonproteobacteria, but many of the Guaymas Basin diffuse flow samples were dominated by either OTUs within the Planctomycetes or hyperthermophilic Archaea. This study emphasizes the unique microbial communities associated with geochemically and geographically distinct hydrothermal diffuse flow environments.

Penanganan limbah industri dengan cara immobilisasi microbial cell

Directory of Open Access Journals (Sweden)

Prayitno Prayitno

1997-12-01

Full Text Available An immobilized microbial cell is a physical confinement or localization of intact cell to a certain defined region of space with the preservation of some desired catalytic activity. The immobilization cell process has been increasingly used, one of those is for waste water treatment industry. Microbial entrapping process one of the method for the microbial cell immobilization by using some carrier such as collagen, gelatin, alginate, carragena and cellulose tri acetat at the time being is commonly used. Immobilization cell is effective enough for waste water treatment containing toxic substance such as phenol and by using immobilization cell, secondary sedimentation tanks is no longer used.

Microbial processes at the beds of glaciers and ice sheets: a look at life below the Whillans Ice Stream

Science.gov (United States)

Mikucki, J.; Campen, R.; Vancleave, S.; Scherer, R. P.; Coenen, J. J.; Powell, R. D.; Tulaczyk, S. M.

2017-12-01

Groundwater, saturated sediments and hundreds of subglacial lakes exist below the ice sheets of Antarctica. The few Antarctic subglacial environments sampled to date all contain viable microorganisms. This is a significant finding because microbes are known to be key in mediating biogeochemical cycles. In sediments, microbial metabolic activity can also result in byproducts or direct interactions with sediment particles that influence the physical and geochemical characteristics of the matrix they inhabit. Subglacial Lake Whillans (SLW), a fresh water lake under the Whillans Ice Stream that drains into the Ross Sea at its grounding zone, was recently sampled as part of the NSF-funded Whillans Ice Stream Subglacial Access Research Drilling (WISSARD) project. Sediments from both SLW and its grounding zone contain microbial taxa related to iron, sulfur, nitrogen and methane oxidizers. In addition to molecular data, biogeochemical measurements and culture based experiments on Whillans sediments support the notion that the system is chemosynthetic with energy derived in part by cycling inorganic compounds. Etch pitting and mineral precipitates on fossil sponge spicules suggest that spicules may also provide microbial nutrients in these environments. Perhaps the most widespread microbial process that affects sediment structure and mineral weathering is the production of extra polymeric substances (EPS). Several phylogenetic groups detected in Whillans sediments are known to produce EPS and we have observed its production in pure cultures enriched directly from these sediments. Our data sheds light on how microbial life persists below the Antarctic Ice Sheet despite extended isolation in icy darkness, and how these microbes may be shaping their environment.

Quantitative microbial risk assessment (QMRA) shows increased public health risk associated with exposure to river water under conditions of riverbed sediment resuspension

CSIR Research Space (South Africa)

Abia

2016-10-01

Full Text Available of The Total Environment, 556-557, pp 1143-1151 Quantitative microbial risk assessment (QMRA) shows increased public health risk associated with exposure to river water under conditions of riverbed sediment resuspension Akebe Luther King Abia a...

Application of microbial biomass and activity measures to assess in situ bioremediation of chlorinated solvents

International Nuclear Information System (INIS)

Phelps, T.J.; Herbes, S.E.; Palumbo, A.V.; Pfiffner, S.M.; Mackowski, R.; Ringelberg, D.; White, D.C.; Tennessee Univ., Knoxville, TN

1993-01-01

Evaluating the effectiveness of chlorinated solvent remediation in the subsurface can be a significant problem given uncertainties in estimating the total mass of contaminants present. If the remediation technique is a biological activity, information on the progress and success of the remediation may be gained by monitoring changes in the mass and activities of microbial populations. The in situ bioremediation demonstration at the US Department of Energy (DOE) Savannah River Site (SRS) is designed to test the effectiveness of methane injection for the stimulation of in sediments. Past studies have shown the potential for degradation by native microbial populations. The design and implementation of the SRS Integrated Demonstration is described in this volume. A control phase without treatment was followed by a phase withdrawing air. The next phase included vacuum extraction plus air injection into the lower horizontal well located below the water table. The next period included the injection of 1% methane in air followed by injection of 4% methane in air. Based on the literature, it was hypothesized that the injection of methane would stimulate methanotrophic populations and thus accelerate biological degradation of TCE. Measuring the success of bioremediation is a complex effort that includes monitoring of changes in microbial populations associated with TCE degradation. These monitoring efforts are described in this paper and in related papers in this volume

Microbial activity in bentonite buffers. Literature study

Energy Technology Data Exchange (ETDEWEB)

Ratto, M.; Itavaara, M.

2012-07-01

The proposed disposal concept for high-level radioactive wastes involves storing the wastes underground in copper-iron containers embedded in buffer material of compacted bentonite. Hydrogen sulphide production by sulphate-reducing prokaryotes is a potential mechanism that could cause corrosion of waste containers in repository conditions. The prevailing conditions in compacted bentonite buffer will be harsh. The swelling pressure is 7-8 MPa, the amount of free water is low and the average pore and pore throat diameters are small. This literature study aims to assess the potential of microbial activity in bentonite buffers. Literature on the environmental limits of microbial life in extreme conditions and the occurrence of sulphatereducing prokaryotes in extreme environments is reviewed briefly and the results of published studies characterizing microbes and microbial processes in repository conditions or in relevant subsurface environments are presented. The presence of bacteria, including SRBs, has been confirmed in deep groundwater and bentonite-based materials. Sulphate reducers have been detected in various high-pressure environments, and sulphate-reduction based on hydrogen as an energy source is considered a major microbial process in deep subsurface environments. In bentonite, microbial activity is strongly suppressed, mainly due to the low amount of free water and small pores, which limit the transport of microbes and nutrients. Spore-forming bacteria have been shown to survive in compacted bentonite as dormant spores, and they are able to resume a metabolically active state after decompaction. Thus, microbial sulphide production may increase in repository conditions if the dry density of the bentonite buffer is locally reduced. (orig.)

MATHEMATICAL MODELING OF THE ELECTRIC CURRENT GENERATION IN A MICROBIAL FUEL CELL INOCULATED WITH MARINE SEDIMENT

Directory of Open Access Journals (Sweden)

J. T. Teleken

Full Text Available Abstract Microbial fuel cells (MFC are electrochemical devices that utilize the ability of some microorganisms to oxidize organic matter and transfer electrons resulting from their metabolism to an insoluble acceptor. The goal of the present study was to model the kinetics of electrical current generation from an MFC inoculated with marine sediment. For this purpose, a differential equation system was used, including the Nernst-Monod relationship and Ohm's Law, to describe the microbial metabolism and the mechanism of extracellular electron transfer (EET, respectively. The experimental data obtained by cyclic voltammetry analysis were properly described by the model. It was concluded that marine microorganisms preferably use a direct mechanism of EET by means of nanowires to establish the electrochemical contact with the anode. The mathematical modeling could help understand MFC operation and, consequently, contribute to improving power generation from this source.

Microbial activities and dissolved organic matter dynamics in oil-contaminated surface seawater from the Deepwater Horizon oil spill site.

Science.gov (United States)

Ziervogel, Kai; McKay, Luke; Rhodes, Benjamin; Osburn, Christopher L; Dickson-Brown, Jennifer; Arnosti, Carol; Teske, Andreas

2012-01-01

The Deepwater Horizon oil spill triggered a complex cascade of microbial responses that reshaped the dynamics of heterotrophic carbon degradation and the turnover of dissolved organic carbon (DOC) in oil contaminated waters. Our results from 21-day laboratory incubations in rotating glass bottles (roller bottles) demonstrate that microbial dynamics and carbon flux in oil-contaminated surface water sampled near the spill site two weeks after the onset of the blowout were greatly affected by activities of microbes associated with macroscopic oil aggregates. Roller bottles with oil-amended water showed rapid formation of oil aggregates that were similar in size and appearance compared to oil aggregates observed in surface waters near the spill site. Oil aggregates that formed in roller bottles were densely colonized by heterotrophic bacteria, exhibiting high rates of enzymatic activity (lipase hydrolysis) indicative of oil degradation. Ambient waters surrounding aggregates also showed enhanced microbial activities not directly associated with primary oil-degradation (β-glucosidase; peptidase), as well as a twofold increase in DOC. Concurrent changes in fluorescence properties of colored dissolved organic matter (CDOM) suggest an increase in oil-derived, aromatic hydrocarbons in the DOC pool. Thus our data indicate that oil aggregates mediate, by two distinct mechanisms, the transfer of hydrocarbons to the deep sea: a microbially-derived flux of oil-derived DOC from sinking oil aggregates into the ambient water column, and rapid sedimentation of the oil aggregates themselves, serving as vehicles for oily particulate matter as well as oil aggregate-associated microbial communities.

Microbial activities and dissolved organic matter dynamics in oil-contaminated surface seawater from the Deepwater Horizon oil spill site.

Directory of Open Access Journals (Sweden)

Kai Ziervogel

Full Text Available The Deepwater Horizon oil spill triggered a complex cascade of microbial responses that reshaped the dynamics of heterotrophic carbon degradation and the turnover of dissolved organic carbon (DOC in oil contaminated waters. Our results from 21-day laboratory incubations in rotating glass bottles (roller bottles demonstrate that microbial dynamics and carbon flux in oil-contaminated surface water sampled near the spill site two weeks after the onset of the blowout were greatly affected by activities of microbes associated with macroscopic oil aggregates. Roller bottles with oil-amended water showed rapid formation of oil aggregates that were similar in size and appearance compared to oil aggregates observed in surface waters near the spill site. Oil aggregates that formed in roller bottles were densely colonized by heterotrophic bacteria, exhibiting high rates of enzymatic activity (lipase hydrolysis indicative of oil degradation. Ambient waters surrounding aggregates also showed enhanced microbial activities not directly associated with primary oil-degradation (β-glucosidase; peptidase, as well as a twofold increase in DOC. Concurrent changes in fluorescence properties of colored dissolved organic matter (CDOM suggest an increase in oil-derived, aromatic hydrocarbons in the DOC pool. Thus our data indicate that oil aggregates mediate, by two distinct mechanisms, the transfer of hydrocarbons to the deep sea: a microbially-derived flux of oil-derived DOC from sinking oil aggregates into the ambient water column, and rapid sedimentation of the oil aggregates themselves, serving as vehicles for oily particulate matter as well as oil aggregate-associated microbial communities.

Response of microbial community and catabolic genes to simulated petroleum hydrocarbon spills in soils/sediments from different geographic locations.

Science.gov (United States)

Liu, Q; Tang, J; Liu, X; Song, B; Zhen, M; Ashbolt, N J

2017-10-01

Study the response of microbial communities and selected petroleum hydrocarbon (PH)-degrading genes on simulated PH spills in soils/sediments from different geographic locations. A microcosm experiment was conducted by spiking mixtures of petroleum hydrocarbons (PHs) to soils/sediments collected from four different regions of China, including the Dagang Oilfield (DG), Sand of Bohai Sea (SS), Northeast China (NE) and Xiamen (XM). Changes in bacterial community and the abundance of PH-degrading genes (alkB, nah and phe) were analysed by denaturing gradient electrophoresis (DGGE) and qPCR, respectively. Degradation of alkanes and PAHs in SS and NE materials were greater (P < 0·05) than those in DG and XM. Clay content was negatively correlated with the degradation of total alkanes by 112 days and PAHs by 56 days, while total organic carbon content was negatively correlated with initial degradation of total alkanes as well as PAHs. Abundances of alkB, nah and phe genes increased 10- to 100-fold and varied by soil type over the incubation period. DGGE fingerprints identified the dominance of α-, β- and γ-Proteobacteria (Gram -ve) and Actinobacteria (Gram +ve) bacteria associated with degradation of PHs in the materials studied. The geographic divergence resulting from the heterogeneity of physicochemical properties of soils/sediments appeared to influence the abundance of metabolic genes and community structure of microbes capable of degrading PHs. When developing practical in-situ bioremediation approaches for PHs contamination of soils/sediment, appropriate microbial community structures and the abundance of PH-degrading genes appear to be influenced by geographic location. © 2017 The Society for Applied Microbiology.

Reductive dehalogenation activity of indigenous microorganism in sediments of the Hackensack River, New Jersey.

Science.gov (United States)

Sohn, Seo Yean; Häggblom, Max M

2016-07-01

Organohalogen pollutants are of concern in many river and estuarine environments, such as the New York-New Jersey Harbor estuary and its tributaries. The Hackensack River is contaminated with various metals, hydrocarbons and halogenated organics, including polychlorinated biphenyls (PCBs) and polychlorinated dibenzo-p-dioxins. In order to examine the potential for microbial reductive dechlorination by indigenous microorganisms, sediment samples were collected from five different estuarine locations along the Hackensack River. Hexachlorobenzene (HCB), hexabromobenzene (HBB), and pentachloroaniline (PCA) were selected as model organohalogen pollutants to assess anaerobic dehalogenating potential. Dechlorinating activity of HCB and PCA was observed in sediment microcosms for all sampling sites. HCB was dechlorinated via pentachlorobenzene (PeCB) and trichlorobenzene (TriCB) to dichlorobenzene (DCB). PCA was dechlorinated via tetrachloroaniline (TeCA), trichloroanilines (TriCA), and dichloroanilines (DCA) to monochloroaniline (MCA). No HBB debromination was observed over 12 months of incubation. However, with HCB as a co-substrate slow HBB debromination was observed with production of tetrabromobenzene (TeBB) and tribromobenzene (TriBB). Chloroflexi specific 16S rRNA gene PCR-DGGE followed by sequence analysis detected Dehalococcoides species in sediments of the freshwater location, but not in the estuarine site. Analysis targeting 12 putative reductive dehalogenase (rdh) genes showed that these were enriched concomitant with HCB or PCA dechlorination in freshwater sediment microcosms. Copyright © 2016 Elsevier Ltd. All rights reserved.

[Impacts of Asian clams (Corbicula fluminea) on lake sediment properties and phosphorus movement].

Science.gov (United States)

Zhang, Lei; Gu, Xiao-Zhi; Shao, Shi-Guang; Hu, Hai-Yan; Zhong, Ji-Cheng; Fan, Cheng-Xin

2011-01-01

To examine the impact of Corbicula fluminea on sediment properties and phosphorus dynamics across sediment-water interface in lake, the microcosm experiment was carried out with sediment and lake water from the estuary of Dapu River, a eutrophic area in Taihu Lake. Rhizon samplers were used to acquire pore water, and soluble reactive phosphorus (SRP) flux across sediment-water interface and sediment properties were determined. The activity of C. fluminea destroyed the initial sediment structure, mixed sediment in different depths, increased oxygen penetration depth, sediment water content, and total microbial activity in sediment. The downward movement of overlying water was enhanced by the activity of C. fluminea, which decreased Fe2+ in pore water by oxidation. The production of ferric iron oxyhydroxide adsorbed SRP from pore water and decreased SRP concentration in pore water, and this increased iron bound phosphorus in corresponding sediment. The emergence of C. fluminea accelerated SRP release from sediment to overlying water, and enhanced SRP flux increased with the rise of introduced C. fluminea density. Metabolization of C. fluminea might play an important role in accelerating SRP release.

Continuous exposure of pesticides in an aquifer changes microbial biomass, diversity and degradation potential

DEFF Research Database (Denmark)

de Lipthay, J. R.; Johnsen, K.; Aamand, J.

2000-01-01

We studied in situ effects of pesticide exposure on microbial degradation potential and community structure of aquifer sediments. Sediment samples pre-exposed to pesticides were significantly different to non-exposed control samples. Pre-exposed sediment showed an increased degradation potential ...... towards phenoxyalcanoic acid herbicides as well as impact on microbial diversity was observed. Furthermore, bacterial biomass was changed, e.g. increased numbers of phenoxyalcanoic acid degraders in pesticide exposed sediment.......We studied in situ effects of pesticide exposure on microbial degradation potential and community structure of aquifer sediments. Sediment samples pre-exposed to pesticides were significantly different to non-exposed control samples. Pre-exposed sediment showed an increased degradation potential...

Effects of microbial inhibitors on anaerobic degradation of DDT

Energy Technology Data Exchange (ETDEWEB)

Wang, Y.S.; Chiu, T.C.; Yen, J.H. [National Taiwan Univ., Taipei (Taiwan)

2004-09-15

Chlorinated insecticide DDT [1,1,1-trichloro-2,2-bis(p-chlorophenyl)ethane] was extensively used for controlling pests in the agricultural field and human-being living environments in the past several decades. Due to the chemical stability, DDT was extremely persistent and recalcitrant in soils and sediments and it was banned by nations. Microorganisms usually play important roles in reducing organochlorine compounds in the environments. Under low-oxygen conditions, microbial dechlorination is thought as the onset of highly chlorinated compounds. Methanogenic and sulfate-reducing bacteria participate in microbial dechlorination under anaerobic condition has been reported. In this study, a mixed anaerobic culture enabling to dechlorinate DDT was obtained from river sediment in Taiwan. In order to understand the effect of these microorganisms on DDT dechlorination, microbial inhibitors BESA (2-bromoethanesulfonate) and molybdate, for inhibiting methanogenic and sulfate-reducing bacteria, respectively, were chosen to investigate the interaction between specific microbial communities and their degradation activities. Besides, a molecular technique, denaturing gradient gel electrophoresis (DGGE), based on analyzing the 16S rDNA of bacteria, was used for monitoring the bacterial community structure in this study.

Quantification of Microbial Communities in Subsurface Marine Sediments of the Black Sea and off Namibia.

Science.gov (United States)

Schippers, Axel; Kock, Dagmar; Höft, Carmen; Köweker, Gerrit; Siegert, Michael

2012-01-01

Organic-rich subsurface marine sediments were taken by gravity coring up to a depth of 10 m below seafloor at six stations from the anoxic Black Sea and the Benguela upwelling system off Namibia during the research cruises Meteor 72-5 and 76-1, respectively. The quantitative microbial community composition at various sediment depths was analyzed using total cell counting, catalyzed reporter deposition - fluorescence in situ hybridization (CARD-FISH) and quantitative real-time PCR (Q-PCR). Total cell counts decreased with depths from 10(9) to 10(10) cells/mL at the sediment surface to 10(7)-10(9) cells/mL below one meter depth. Based on CARD-FISH and Q-PCR analyses overall similar proportions of Bacteria and Archaea were found. The down-core distribution of prokaryotic and eukaryotic small subunit ribosomal RNA genes (16S and 18S rRNA) as well as functional genes involved in different biogeochemical processes was quantified using Q-PCR. Crenarchaeota and the bacterial candidate division JS-1 as well as the classes Anaerolineae and Caldilineae of the phylum Chloroflexi were highly abundant. Less abundant but detectable in most of the samples were Eukarya as well as the metal and sulfate-reducing Geobacteraceae (only in the Benguela upwelling influenced sediments). The functional genes cbbL, encoding for the large subunit of RuBisCO, the genes dsrA and aprA, indicative of sulfate-reducers as well as the mcrA gene of methanogens were detected in the Benguela upwelling and Black Sea sediments. Overall, the high organic carbon content of the sediments goes along with high cell counts and high gene copy numbers, as well as an equal abundance of Bacteria and Archaea.

Effect of ion exchange on the rate of aerobic microbial oxidation of ammonium in hyporheic zone sediments.

Science.gov (United States)

Yan, Ailan; Liu, Chongxuan; Liu, Yuanyuan; Xu, Fen

2018-03-01

Microbially mediated ammonium oxidation is a major process affecting nitrogen transformation and cycling in natural environments. This study investigated whether ion exchange process can affect microbially mediated aerobic oxidation of ammonium in a hyporheic zone (HZ) sediments from the Columbia River at US Department of Energy's Hanford site, Washington State. Experiments were conducted using synthetic groundwater and river water to investigate their effect on ammonium oxidation. Results indicated that ammonium sorption through ion exchange reactions decreased the rate of ammonium oxidation, apparently resulting from the influence of the ion exchange on dissolved ammonium concentration, thus decreasing the bioavailability of ammonium for microbial oxidation. However, with the decrease in dissolved ammonium concentration, the sorbed ammonium released back to aqueous phase, and became bioavailable so that all the ammonium in the suspensions were oxidized. Our results implied a dynamic change in ammonium oxidation rates in an environment such as at HZ where river water and groundwater with different chemical compositions exchange frequently that can affect ammonium sorption and desorption through ion exchange reactions.

The impact of major earthquakes and subsequent sewage discharges on the microbial quality of water and sediments in an urban river.

Science.gov (United States)

Devane, Megan L; Moriarty, Elaine M; Wood, David; Webster-Brown, Jenny; Gilpin, Brent J

2014-07-01

A series of large earthquakes struck the city of Christchurch, New Zealand in 2010-2011. Major damage sustained by the sewerage infrastructure required direct discharge of up to 38,000 m(3)/day of raw sewage into the Avon River of Christchurch for approximately six months. This allowed evaluation of the relationship between concentrations of indicator microorganisms (Escherichia coli, Clostridium perfringens and F-RNA phage) and pathogens (Campylobacter, Giardia and Cryptosporidium) in recreational water and sediment both during and post-cessation of sewage discharges. Giardia was the pathogen found most frequently in river water and sediment, although Campylobacter was found at higher levels in water samples. E. coli levels in water above 550 CFU/100 mL were associated with increased likelihood of detection of Campylobacter, Giardia and Cryptosporidium, supporting the use of E. coli as a reliable indicator for public health risk. The strength of the correlation of microbial indicators with pathogen detection in water decreased in the following order: E. coli>F-RNA phage>C. perfringens. All the microorganisms assayed in this study could be recovered from sediments. C. perfringens was observed to accumulate in sediments, which may have confounded its usefulness as an indicator of fresh sewage discharge. F-RNA phage, however, did not appear to accumulate in sediment and in conjunction with E. coli, may have potential as an indicator of recent human sewage discharge in freshwater. There is evidence to support the low-level persistence of Cryptosporidium and Giardia, but not Campylobacter, in river sediments after cessation of sewage discharges. In the event of disturbances of the sediment, it is highly probable that there could be re-mobilisation of microorganisms beyond the sediment-water exchange processes occurring under base flow conditions. Re-suspension events do, therefore, increase the potential risk to human health for those who participate in recreational

INTERACTIONS AMONG PHOSPHATE AMENDMENTS, MICROBES AND URANIUM MOBILITY IN CONTAMINATED SEDIMENTS

Energy Technology Data Exchange (ETDEWEB)

Knox, A

2007-08-30

The use of sequestering agents for the transformation of radionuclides in low concentrations in contaminated soils/sediments offers considerable potential for long-term environmental cleanup. This study evaluated the influence of four phosphate amendments and two microbial amendments on U availability. The synchrotron X-ray fluorescence mapping of the untreated U-contaminated sediment showed that U was closely associated with Mn. All tested phosphate amendments reduced aqueous U concentration more than 90%, likely due to formation of insoluble phosphate precipitates. The addition of A. piechaudii and P. putida alone were found to reduce U concentrations 63% and 31% respectively. Uranium sorption in phosphate treatments was significantly reduced in the presence of microbes. However, increased microbial activity in the treated sediment led to reduction of phosphate effectiveness. The average U concentration in 1 M MgCl{sub 2} extract from U amended sediment was 437 {micro}g/kg, but in the same sediment without microbes (autoclaved sediment), the extractable U concentration was only 103 {micro}g/kg. When the autoclaved amended sediment was treated with autoclaved biological apatite, U concentration in the 1 M MgCl{sub 2} extract was {approx}0 {micro}g/kg. Together these tests suggest that microbes may enhance U leaching and reduce phosphate amendment remedial effectiveness.

The influence of permanently submerged macrophytes on sediment mercury distribution, mobility and methylation potential in a brackish Norwegian fjord.

Science.gov (United States)

Olsen, Marianne; Schaanning, Morten Thorne; Braaten, Hans Fredrik Veiteberg; Eek, Espen; Moy, Frithjof E; Lydersen, Espen

2018-01-01

Macrophytes are shown to affect the microbial activity in different aqueous environments, with an altering of the sediment cycling of mercury (Hg) as a potential effect. Here, we investigated how a meadow with permanently submerged macrophytes in a contaminated brackish fjord in southern Norway influenced the conditions for sulfate reducing microbial activity, the methyl-Hg (MeHg) production and the availability of MeHg. Historically discharged Hg from a chlor-alkali plant (60-80tons, 1947-1987) was evident through high Hg concentrations (491mgTot-Hgkg -1 , 268μgMeHgkg -1 ) in intermediate sediment depths (10-20cm) outside of the meadow, with reduced concentrations within the meadow. Natural recovery of the fjord was revealed by lower sediment surface concentrations (1.9-15.5mgTot-Hgkg -1 , 1.3-3.2μgMeHgkg -1 ). Within the meadow, vertical gradients of sediment hydrogen sulfide (H 2 S) E h and pH suggested microbial sulfate reduction in 2-5cm depths, coinciding with peak values of relative MeHg levels (0.5% MeHg). We assume that MeHg production rates was stimulated by the supply and availability of organic carbon, microbial activity and a sulfide oxidizing agent (e.g. O 2 ) within the rhizosphere. Following this, % MeHg in sediment (0-5cm) within the meadow was approximately 10× higher compared to outside the meadow. Further, enhanced availability of MeHg within the meadow was demonstrated by significantly higher fluxes (p<0.01) from sediment to overlying water (0.1-0.6ngm -2 d -1 ) compared to sediment without macrophytes (0.02-0.2ngm -2 d -1 ). Considering the productivity and species richness typical for such habitats, submerged macrophyte meadows located within legacy Hg contaminated sediment sites may constitute important entry points for MeHg into food webs. Copyright © 2017 Elsevier B.V. All rights reserved.

Enhanced particle fluxes and heterotrophic bacterial activities in Gulf of Mexico bottom waters following storm-induced sediment resuspension

Science.gov (United States)

Ziervogel, K.; Dike, C.; Asper, V.; Montoya, J.; Battles, J.; D`souza, N.; Passow, U.; Diercks, A.; Esch, M.; Joye, S.; Dewald, C.; Arnosti, C.

2016-07-01

Bottom nepheloid layers (BNLs) in the deep sea transport and remobilize considerable amounts of particulate matter, enhancing microbial cycling of organic matter in cold, deep water environments. We measured bacterial abundance, bacterial protein production, and activities of hydrolytic enzymes within and above a BNL that formed in the deep Mississippi Canyon, northern Gulf of Mexico, shortly after Hurricane Isaac had passed over the study area in late August 2012. The BNL was detected via beam attenuation in CTD casts over an area of at least 3.5 km2, extending up to 200 m above the seafloor at a water depth of 1500 m. A large fraction of the suspended matter in the BNL consisted of resuspended sediments, as indicated by high levels of lithogenic material collected in near-bottom sediment traps shortly before the start of our sampling campaign. Observations of suspended particle abundance and sizes throughout the water column, using a combined camera-CTD system (marine snow camera, MSC), revealed the presence of macroaggregates (>1 mm in diameter) within the BNL, indicating resuspension of canyon sediments. A distinct bacterial response to enhanced particle concentrations within the BNL was evident from the observation that the highest enzymatic activities (peptidase, β-glucosidase) and protein production (3H-leucine incorporation) were found within the most particle rich sections of the BNL. To investigate the effects of enhanced particle concentrations on bacterial activities in deep BNLs more directly, we conducted laboratory experiments with roller bottles filled with bottom water and amended with experimentally resuspended sediments from the study area. Macroaggregates formed within 1 day from resuspended sediments; by day 4 of the incubation bacterial cell numbers in treatments with resuspended sediments were more than twice as high as in those lacking sediment suspensions. Cell-specific enzymatic activities were also generally higher in the sediment

Porosity and Organic Carbon Controls on Naturally Reduced Zone (NRZ) Formation Creating Microbial ';Hotspots' for Fe, S, and U Cycling in Subsurface Sediments

Science.gov (United States)

Jones, M. E.; Janot, N.; Bargar, J.; Fendorf, S. E.

2013-12-01

Previous studies have illustrated the importance of Naturally Reduced Zones (NRZs) within saturated sediments for the cycling of metals and redox sensitive contaminants. NRZs can provide a source of reducing equivalents such as reduced organic compounds or hydrogen to stimulate subsurface microbial communities. These NRZ's are typically characterized by low permeability and elevated concentrations of organic carbon and trace metals. However, both the formation of NRZs and their importance to the overall aquifer carbon remineralization is not fully understood. Within NRZs the hydrolysis of particulate organic carbon (POC) and subsequent fermentation of dissolved organic carbon (DOC) to form low molecular weight dissolved organic carbon (LMW-DOC) provides electron donors necessary for the respiration of Fe, S, and in the case of the Rifle aquifer, U. Rates of POC hydrolysis and subsequent fermentation have been poorly constrained and rates in excess and deficit to the rates of subsurface anaerobic respiratory processes have been suggested. In this study, we simulate the development of NRZ sediments in diffusion-limited aggregates to investigate the physical and chemical conditions required for NRZ formation. Effects of sediment porosity and POC loading on Fe, S, and U cycling on molecular and nanoscale are investigated with synchrotron-based Near Edge X-ray Absorption Fine Structure Spectroscopy (NEXAFS). Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR-MS) and Fourier Transform Infrared spectroscopy (FTIR) are used to characterize the transformations in POC and DOC. Sediment aggregates are inoculated with the natural microbial biota from the Rifle aquifer and population dynamics are monitored by 16S RNA analysis. Overall, establishment of low permeability NRZs within the aquifer stimulate microbial respiration beyond the diffusion-limited zones and can limit the transport of U through a contaminated aquifer. However, the long-term stability of

Microbial colonization and degradation of polyethylene and biodegradable plastic bags in temperate fine-grained organic-rich marine sediments.

Science.gov (United States)

Nauendorf, Alice; Krause, Stefan; Bigalke, Nikolaus K; Gorb, Elena V; Gorb, Stanislav N; Haeckel, Matthias; Wahl, Martin; Treude, Tina

2016-02-15

To date, the longevity of plastic litter at the sea floor is poorly constrained. The present study compares colonization and biodegradation of plastic bags by aerobic and anaerobic benthic microbes in temperate fine-grained organic-rich marine sediments. Samples of polyethylene and biodegradable plastic carrier bags were incubated in natural oxic and anoxic sediments from Eckernförde Bay (Western Baltic Sea) for 98 days. Analyses included (1) microbial colonization rates on the bags, (2) examination of the surface structure, wettability, and chemistry, and (3) mass loss of the samples during incubation. On average, biodegradable plastic bags were colonized five times higher by aerobic and eight times higher by anaerobic microbes than polyethylene bags. Both types of bags showed no sign of biodegradation during this study. Therefore, marine sediment in temperate coastal zones may represent a long-term sink for plastic litter and also supposedly compostable material. Copyright © 2016 Elsevier Ltd. All rights reserved.

Strong linkage between active microbial communities and microbial carbon usage in a deglaciated terrain of the High Arctic

Science.gov (United States)

Kim, M.; Gyeong, H. R.; Lee, Y. K.

2017-12-01

Soil microorganisms play pivotal roles in ecosystem development and carbon cycling in newly exposed glacier forelands. However, little is known about carbon utilization pattern by metabolically active microbes over the course of ecosystem succession in these nutrient-poor environments. We investigated RNA-based microbial community dynamics and its relation to microbial carbon usage along the chronosequence of a High Arctic glacier foreland. Among microbial taxa surveyed (bacteria, archaea and fungi), bacteria are among the most metabolically active taxa with a dominance of Cyanobacteria and Actinobacteria. There was a strong association between microbial carbon usage and active Actinobacterial communities, suggesting that member of Actinobacteria are actively involved in organic carbon degradation in glacier forelands. Both bacterial community and microbial carbon usage are converged towards later stage of succession, indicating that the composition of soil organic carbon plays important roles in structuring bacterial decomposer communities during ecosystem development.

Soil Microbial Activity in Conventional and Organic Agricultural Systems

Directory of Open Access Journals (Sweden)

Romero F.V. Carneiro

2009-06-01

Full Text Available The aim of this study was to evaluate microbial activity in soils under conventional and organic agricultural system management regimes. Soil samples were collected from plots under conventional management (CNV, organic management (ORG and native vegetation (AVN. Soil microbial activity and biomass was significantly greater in ORG compared with CNV. Soil bulk density decreased three years after adoption of organic system. Soil organic carbon (SOC was higher in the ORG than in the CNV. The soil under organic agricultural system presents higher microbial activity and biomass and lower bulk density than the conventional agricultural system.

The pH and pCO2 dependence of sulfate reduction in shallow-sea hydrothermal CO2 - venting sediments (Milos Island, Greece).

Science.gov (United States)

Bayraktarov, Elisa; Price, Roy E; Ferdelman, Timothy G; Finster, Kai

2013-01-01

Microbial sulfate reduction (SR) is a dominant process of organic matter mineralization in sulfate-rich anoxic environments at neutral pH. Recent studies have demonstrated SR in low pH environments, but investigations on the microbial activity at variable pH and CO2 partial pressure are still lacking. In this study, the effect of pH and pCO2 on microbial activity was investigated by incubation experiments with radioactive (35)S targeting SR in sediments from the shallow-sea hydrothermal vent system of Milos, Greece, where pH is naturally decreased by CO2 release. Sediments differed in their physicochemical characteristics with distance from the main site of fluid discharge. Adjacent to the vent site (T ~40-75°C, pH ~5), maximal sulfate reduction rates (SRR) were observed between pH 5 and 6. SR in hydrothermally influenced sediments decreased at neutral pH. Sediments unaffected by hydrothermal venting (T ~26°C, pH ~8) expressed the highest SRR between pH 6 and 7. Further experiments investigating the effect of pCO2 on SR revealed a steep decrease in activity when the partial pressure increased from 2 to 3 bar. Findings suggest that sulfate reducing microbial communities associated with hydrothermal vent system are adapted to low pH and high CO2, while communities at control sites required a higher pH for optimal activity.

Assessment of the performance of SMFCs in the bioremediation of PAHs in contaminated marine sediments under different redox conditions and analysis of the associated microbial communities

KAUST Repository

Hamdan, Hamdan Z.; Salam, Darine A.; Rao, Hari Ananda; Semerjian, Lucy; Saikaly, Pascal

2016-01-01

The biodegradation of naphthalene, 2-methylnaphthalene and phenanthrene was evaluated in marine sediment microbial fuel cells (SMFCs) under different biodegradation conditions, including sulfate reduction as a major biodegradation pathway

Methanotrophy in surface sediments of streams

Science.gov (United States)

Bagnoud, Alexandre; Pramateftaki, Paraskevi; Peter, Hannes; Battin, Tom

2017-04-01

Because streams are often found to be supersaturated in methane (CH4), they are considered as atmospheric sources of this greenhouse gas. However, little is known about the processes driving CH4 cycling in these environments, i.e. production, consumption and fluxes. CH4 is thought to be produced in deeper anoxic sediments, before it migrates up to reach the oxic stream water, where it can be oxidized by methanotrophs. In order to gain insights into this process, we investigated 14 different streams across Switzerland. We characterized the chemistry of surface and sediment waters by measuring dissolved chemical profiles. We also sampled surface sediments and determined methanotrophic rates with laboratory incubations and Michaelis-Menten modeling. Interestingly, rates were strongly correlated with the CH4 concentrations in stream waters, rather than in sediment waters. This indicates that methantrophic populations feed on CH4 from the surface streamwater, even though CH4 concentrations are higher in the sediment waters. Methanotrophy rates were also correlated with Crenothrix counts (based on 16S rRNA sequencing), a strict methanotroph, while this latter was correlated with pmoA counts (based on quantitative PCR), a gene involved in methanotrophy. These results show that Crenothrix genera are the most active methanotrophs in surface sediments of streams, and can represent more than 2% of microbial communities. Remarkably, the dominating Crenothrix species was detected in all 14 samples. This work allows the assessment of in situ methanotrophic rates, of the environmental parameters driving this process, and of the microbial populations carrying it out, and thus brings useful insights about carbon cycling in streams.

Succession of Hydrocarbon Degradation and Microbial Diversity during a Simulated Petroleum Seepage in Caspian Sea Sediments

Science.gov (United States)

Mishra, S.; Stagars, M.; Wefers, P.; Schmidt, M.; Knittel, K.; Krueger, M.; Leifer, I.; Treude, T.

2016-02-01

Microbial degradation of petroleum was investigated in intact sediment cores of Caspian Sea during a simulated petroleum seepage using a sediment-oil-flow-through (SOFT) system. Over the course of the SOFT experiment (190 days), distinct redox zones established and evolved in the sediment core. Methanogenesis and sulfate reduction were identified to be important processes in the anaerobic degradation of hydrocarbons. C1 to C6 n-alkanes were completely exhausted in the sulfate-reducing zone and some higher alkanes decreased during the upward migration of petroleum. A diversity of sulfate-reducing bacteria was identified by 16s rRNA phylogenetic studies, some of which are associated with marine seeps and petroleum degradation. The δ13C signal of produced methane decreased from -33.7‰ to -49.5‰ indicating crude oil degradation by methanogenesis, which was supported by enrichment culturing of methanogens with petroleum hydrocarbons and presence of methanogenic archaea. The SOFT system is, to the best of our knowledge, the first system that simulates an oil-seep like condition and enables live monitoring of biogeochemical changes within a sediment core during petroleum seepage. During our presentation we will compare the Caspian Sea data with other sediments we studied using the SOFT system from sites such as Santa Barbara (Pacific Ocean), the North Alex Mud Volcano (Mediterranean Sea) and the Eckernfoerde Bay (Baltic Sea). This research was funded by the Deutsche Forschungsgemeinschaft (SPP 1319) and DEA Deutsche Erdoel AG. Further support came from the Helmholtz and Max Planck Gesellschaft.

Sediment transport in an active erodible channel bend

Indian Academy of Sciences (India)

Local variation of sediment transport is primarily controlled by active bank erosion, land spur and sand bar formation. Vertical distribution of suspended sediment concentration follows a power function with normalized depth. Average bed-material concentration at the reach level is computed from observed sediment profiles, ...

The pH and pCO2 dependence of sulfate reduction in shallow-sea hydrothermal CO2 – venting sediments (Milos Island, Greece)

Science.gov (United States)

Bayraktarov, Elisa; Price, Roy E.; Ferdelman, Timothy G.; Finster, Kai

2013-01-01

Microbial sulfate reduction (SR) is a dominant process of organic matter mineralization in sulfate-rich anoxic environments at neutral pH. Recent studies have demonstrated SR in low pH environments, but investigations on the microbial activity at variable pH and CO2 partial pressure are still lacking. In this study, the effect of pH and pCO2 on microbial activity was investigated by incubation experiments with radioactive 35S targeting SR in sediments from the shallow-sea hydrothermal vent system of Milos, Greece, where pH is naturally decreased by CO2 release. Sediments differed in their physicochemical characteristics with distance from the main site of fluid discharge. Adjacent to the vent site (T ~40–75°C, pH ~5), maximal sulfate reduction rates (SRR) were observed between pH 5 and 6. SR in hydrothermally influenced sediments decreased at neutral pH. Sediments unaffected by hydrothermal venting (T ~26°C, pH ~8) expressed the highest SRR between pH 6 and 7. Further experiments investigating the effect of pCO2 on SR revealed a steep decrease in activity when the partial pressure increased from 2 to 3 bar. Findings suggest that sulfate reducing microbial communities associated with hydrothermal vent system are adapted to low pH and high CO2, while communities at control sites required a higher pH for optimal activity. PMID:23658555

Increase the Visibility of Microbial Growth in a Winogradsky Column by Substituting Diatomaceous Earth for Sediment

Directory of Open Access Journals (Sweden)

Thomas G. Benoit

2015-02-01

Full Text Available The difficulty students have seeing the color associated with microbial growth in a traditional Winogradsky column can be overcome by substituting diatomaceous earth (DE for sediment. Microbial growth in a DE column is visible from the early stages of ecological succession and the colors produced appear more vibrant. A flat-sided tissue culture flask can be used as a column container to provide a large surface area for observation. The enhanced visual experience provided by a DE column increases student engagement and learning. Editor's Note:The ASM advocates that students must successfully demonstrate the ability to explain and practice safe laboratory techniques. For more information, read the laboratory safety section of the ASM Curriculum Recommendations: Introductory Course in Microbiology and the Guidelines for Biosafety in Teaching Laboratories, available at www.asm.org. The Editors of JMBE recommend that adopters of the protocols included in this article follow a minimum of Biosafety Level 1 practices.

Microbial biomass carbon and enzyme activities of urban soils in Beijing.

Science.gov (United States)

Wang, Meie; Markert, Bernd; Shen, Wenming; Chen, Weiping; Peng, Chi; Ouyang, Zhiyun

2011-07-01

To promote rational and sustainable use of soil resources and to maintain the urban soil quality, it is essential to assess urban ecosystem health. In this study, the microbiological properties of urban soils in Beijing and their spatial distribution patterns across the city were evaluated based on measurements of microbial biomass carbon and urease and invertase activities of the soils for the purpose of assessing the urban ecosystem health of Beijing. Grid sampling design, normal Kriging technique, and the multiple comparisons among different land use types were used in soil sampling and data treatment. The inherent chemical characteristics of urban soils in Beijing, e.g., soil pH, electronic conductivity, heavy metal contents, total N, P and K contents, and soil organic matter contents were detected. The size and diversity of microbial community and the extent of microbial activity in Beijing urban soils were measured as the microbial biomass carbon content and the ratio of microbial biomass carbon content to total soil organic carbon. The microbial community health measured in terms of microbial biomass carbon, urease, and invertase activities varied with the organic substrate and nutrient contents of the soils and were not adversely affected by the presence of heavy metals at p urban soils influenced the nature and activities of the microbial communities.

Microbial ecology of terrestrial Antarctica: Are microbial systems at risk from human activities?

Energy Technology Data Exchange (ETDEWEB)

White, G.J.

1996-08-01

Many of the ecological systems found in continental Antarctica are comprised entirely of microbial species. Concerns have arisen that these microbial systems might be at risk either directly through the actions of humans or indirectly through increased competition from introduced species. Although protection of native biota is covered by the Protocol on Environmental Protection to the Antarctic Treaty, strict measures for preventing the introduction on non-native species or for protecting microbial habitats may be impractical. This report summarizes the research conducted to date on microbial ecosystems in continental Antarctica and discusses the need for protecting these ecosystems. The focus is on communities inhabiting soil and rock surfaces in non-coastal areas of continental Antarctica. Although current polices regarding waste management and other operations in Antarctic research stations serve to reduce the introduction on non- native microbial species, importation cannot be eliminated entirely. Increased awareness of microbial habitats by field personnel and protection of certain unique habitats from physical destruction by humans may be necessary. At present, small-scale impacts from human activities are occurring in certain areas both in terms of introduced species and destruction of habitat. On a large scale, however, it is questionable whether the introduction of non-native microbial species to terrestrial Antarctica merits concern.

Toward Understanding the Dynamics of Microbial Communities in an Estuarine System

KAUST Repository

Zhang, Weipeng; Bougouffa, Salim; Wang, Yong; Lee, On On; Yang, Jiangke; Chan, Colin; Song, Xingyu; Qian, Pei-Yuan

2014-01-01

Community assembly theories such as species sorting theory provide a framework for understanding the structures and dynamics of local communities. The effect of theoretical mechanisms can vary with the scales of observation and effects of specific environmental factors. Based on 16S rRNA gene tag pyrosequencing, different structures and temporal succession patterns were discovered between the surface sediments and bottom water microbial communities in the Pearl River Estuary (PRE). The microbial communities in the surface sediment samples were more diverse than those in the bottom water samples, and several genera were specific for the water or sediment communities. Moreover, water temperature was identified as the main variable driving community dynamics and the microbial communities in the sediment showed a greater temporal change. We speculate that nutrient-based species sorting and bacterial plasticity to the temperature contribute to the variations observed between sediment and water communities in the PRE. This study provides a more comprehensive understanding of the microbial community structures in a highly dynamic estuarine system and sheds light on the applicability of ecological theoretical mechanisms.

Toward understanding the dynamics of microbial communities in an estuarine system.

Directory of Open Access Journals (Sweden)

Weipeng Zhang

Full Text Available Community assembly theories such as species sorting theory provide a framework for understanding the structures and dynamics of local communities. The effect of theoretical mechanisms can vary with the scales of observation and effects of specific environmental factors. Based on 16S rRNA gene tag pyrosequencing, different structures and temporal succession patterns were discovered between the surface sediments and bottom water microbial communities in the Pearl River Estuary (PRE. The microbial communities in the surface sediment samples were more diverse than those in the bottom water samples, and several genera were specific for the water or sediment communities. Moreover, water temperature was identified as the main variable driving community dynamics and the microbial communities in the sediment showed a greater temporal change. We speculate that nutrient-based species sorting and bacterial plasticity to the temperature contribute to the variations observed between sediment and water communities in the PRE. This study provides a more comprehensive understanding of the microbial community structures in a highly dynamic estuarine system and sheds light on the applicability of ecological theoretical mechanisms.

Toward Understanding the Dynamics of Microbial Communities in an Estuarine System

KAUST Repository

Zhang, Weipeng

2014-04-14

Community assembly theories such as species sorting theory provide a framework for understanding the structures and dynamics of local communities. The effect of theoretical mechanisms can vary with the scales of observation and effects of specific environmental factors. Based on 16S rRNA gene tag pyrosequencing, different structures and temporal succession patterns were discovered between the surface sediments and bottom water microbial communities in the Pearl River Estuary (PRE). The microbial communities in the surface sediment samples were more diverse than those in the bottom water samples, and several genera were specific for the water or sediment communities. Moreover, water temperature was identified as the main variable driving community dynamics and the microbial communities in the sediment showed a greater temporal change. We speculate that nutrient-based species sorting and bacterial plasticity to the temperature contribute to the variations observed between sediment and water communities in the PRE. This study provides a more comprehensive understanding of the microbial community structures in a highly dynamic estuarine system and sheds light on the applicability of ecological theoretical mechanisms.

Internal nitrogen removal from sediments by the hybrid system of microbial fuel cells and submerged aquatic plants.

Directory of Open Access Journals (Sweden)

Peng Xu

Full Text Available Sediment internal nitrogen release is a significant pollution source in the overlying water of aquatic ecosystems. This study aims to remove internal nitrogen in sediment-water microcosms by coupling sediment microbial fuel cells (SMFCs with submerged aquatic plants. Twelve tanks including four treatments in triplicates were designed: open-circuit (SMFC-o, closed-circuit (SMFC-c, aquatic plants with open-circuit (P-SMFC-o and aquatic plants with closed-circuit (P-SMFC-c. The changes in the bio-electrochemical characteristics of the nitrogen levels in overlying water, pore water, sediments, and aquatic plants were documented to explain the migration and transformation pathways of internal nitrogen. The results showed that both electrogenesis and aquatic plants could facilitate the mineralization of organic nitrogen in sediments. In SMFC, electrogenesis promoted the release of ammonium from the pore water, followed by the accumulation of ammonium and nitrate in the overlying water. The increased redox potential of sediments due to electrogenesis also contributed to higher levels of nitrate in overlying water when nitrification in pore water was facilitated and denitrification at the sediment-water interface was inhibited. When the aquatic plants were introduced into the closed-circuit SMFC, the internal ammonium assimilation by aquatic plants was advanced by electrogenesis; nitrification in pore water and denitrification in sediments were also promoted. These processes might result in the maximum decrease of internal nitrogen with low nitrogen levels in the overlying water despite the lower power production. The P-SMFC-c reduced 8.1%, 16.2%, 24.7%, and 25.3% of internal total nitrogen compared to SMFC-o on the 55th, 82th, 136th, and 190th days, respectively. The smaller number of Nitrospira and the larger number of Bacillus and Pseudomonas on the anodes via high throughput sequencing may account for strong mineralization and denitrification in the

Microbial mat structures in profile: The Neoproterozoic Sonia Sandstone, Rajasthan, India

Science.gov (United States)

Samanta, Pradip; Mukhopadhyay, Soumik; Mondal, Anudeb; Sarkar, Subir

2011-01-01

Ubiquitous microorganisms, especially cyanobacteria preferably grow on the sediment surface thereby producing microbial mats. In the absence of grazers and bioturbators, microbial mat is a unique feature of the Proterozoic. Most of the papers so far published described a wide variety of bed surface microbial mat structures with rare illustrations from sections perpendicular to bedding. Nonetheless, bed surface exposures are relatively rare in rock records. This limitation of bed surface exposures in rock records suggest that a study of microbial mats in bed-across sections is needed. The 60 m thick coastal marine interval of the Sonia Sandstone Formation is bounded between two terrestrial intervals, a transgressive lag at the base and an unconformity at the top, and has been chosen for exploration of microbial mat structures in bed-across sections. A wide variety of microbial mat-induced structures in bed-across sections are preserved within the coastal interval of the Sonia Sandstone. Though many of these structures are similar in some aspects with bed surface structures, some of those presented here are new. The palaeogeographic range of these microbial structures extends from supralittoral to neritic. Diagenetic alterations of microbial mats produce pyrite and those zones are suitable for the preservation of microbial remains. SEM and EDAX analyses show fossil preservation of filamentous microbial remains that confirm the presence of microbial mats within the coastal interval of the Sonia Sandstone. Effects of proliferation of microbial mats in the siliciclastic depositional setting are numerous. The mat-cover on sediment surfaces hinders reworking and/or erosion of the sediments thereby increases the net sedimentation rate. Successive deposition and preservation of thick microbial mat layer under reducing environments should have a great potential for hydrocarbon production and preservation and therefore these Proterozoic formations could be a target for

Assessment of the performance of SMFCs in the bioremediation of PAHs in contaminated marine sediments under different redox conditions and analysis of the associated microbial communities

KAUST Repository

Hamdan, Hamdan Z.

2016-10-09

The biodegradation of naphthalene, 2-methylnaphthalene and phenanthrene was evaluated in marine sediment microbial fuel cells (SMFCs) under different biodegradation conditions, including sulfate reduction as a major biodegradation pathway, employment of anode as terminal electron acceptor (TEA) under inhibited sulfate reducing bacteria activity, and combined sulfate and anode usage as electron acceptors. A significant removal of naphthalene and 2-methylnaphthalene was observed at early stages of incubation in all treatments and was attributed to their high volatility. In the case of phenanthrene, a significant removal (93.83 ± 1.68%) was measured in the closed circuit SMFCs with the anode acting as the main TEA and under combined anode and sulfate reduction conditions (88.51 ± 1.3%). A much lower removal (40.37 ± 3.24%) was achieved in the open circuit SMFCs operating with sulfate reduction as a major biodegradation pathway. Analysis of the anodic bacterial community using 16S rRNA gene pyrosequencing revealed the enrichment of genera with potential exoelectrogenic capability, namely Geoalkalibacter and Desulfuromonas, on the anode of the closed circuit SMFCs under inhibited SRB activity, while they were not detected on the anode of open circuit SMFCs. These results demonstrate the role of the anode in enhancing PAHs biodegradation in contaminated marine sediments and suggest a higher system efficiency in the absence of competition between microbial redox processes (under SRB inhibition), namely due to the anode enrichment with exoelectrogenic bacteria, which is a more energetically favorable mechanism for PAHs oxidation than sulfate.

Viruses-to-mobile genetic elements skew in the deep Atlantis II brine pool sediments

KAUST Repository

Adel, Mustafa

2016-09-06

The central rift of the Red Sea has 25 brine pools with different physical and geochemical characteristics. Atlantis II (ATIID), Discovery Deeps (DD) and Chain Deep (CD) are characterized by high salinity, temperature and metal content. Several studies reported microbial communities in these brine pools, but few studies addressed the brine pool sediments. Therefore, sediment cores were collected from ATIID, DD, CD brine pools and an adjacent brine-influenced site. Sixteen different lithologic sediment sections were subjected to shotgun DNA pyrosequencing to generate 1.47 billion base pairs (1.47 × 109 bp). We generated sediment-specific reads and attempted to annotate all reads. We report the phylogenetic and biochemical uniqueness of the deepest ATIID sulfur-rich brine pool sediments. In contrary to all other sediment sections, bacteria dominate the deepest ATIID sulfur-rich brine pool sediments. This decrease in virus-to-bacteria ratio in selected sections and depth coincided with an overrepresentation of mobile genetic elements. Skewing in the composition of viruses-to-mobile genetic elements may uniquely contribute to the distinct microbial consortium in sediments in proximity to hydrothermally active vents of the Red Sea and possibly in their surroundings, through differential horizontal gene transfer.

Monitoring Soil Microbial Activities in Different Cropping Systems Using Combined Methods

Institute of Scientific and Technical Information of China (English)

YUAN Zhimin; LIU Haijun; HAN Jun; SUN Jingjing; WU Xiaoying; YAO Jun

2017-01-01

Cropping activities may affect soil microbial activities and biomass,which would affect C and N cycling in soil and thus the crop yields and quality.In the present study,a combination of microcalorimetric,enzyme activity (sucrase,urease,catalase,and fluorescein diacetate hydrolysis),and real-time polymerase chain reaction (RT-PCR) analyses was used to investigate microbial status of farmland soils,collected from 5 different sites in Huazhong Agriculture University,China.Our results showed that among the 5 sites,both positive and negative impacts of cropping activities on soil microbial activity were observed.Enzyme activity analysis showed that cropping activities reduced soil sucrase and urease activities,which would influence the C and N cycles in soil.Much more attentions should be given to microbial status affected by cropping activities in future.According to the correlation analysis,fluorescein diacetate hydrolysis showed a significantly (P ＜ 0.05) negative correlation with the time to reach the maximum power output (R =--0.898),but a significantly (P ＜ 0.05) positive correlation with bacterial gene copy number (R =0.817).Soil catalase activity also showed a significantly (P ＜ 0.05) positive correlation with bacterial gene copy number (R =0.965).Using combined methods would provide virtual information of soil microbial status.

Copper effects on bacterial activity of estuarine silty sediments

Science.gov (United States)

Almeida, Adelaide; Cunha, Ângela; Fernandes, Sandra; Sobral, Paula; Alcântara, Fernanda

2007-07-01

Bacteria of silty estuarine sediments were spiked with copper to 200 μg Cu g -1 dry weight sediment in order to assess the impact of copper on bacterial degradation of organic matter and on bacterial biomass production. Bacterial density was determined by direct counting under epifluorescence microscopy and bacterial production by the incorporation of 3H-Leucine. Leucine turnover rate was evaluated by 14C-leucine incorporation and ectoenzymatic activities were estimated as the hydrolysis rate of model substrates for β-glucosidase and leucine-aminopeptidase. The presence of added copper in the microcosms elicited, after 21 days of incubation, generalised anoxia and a decrease in organic matter content. The non-eroded surface of the copper-spiked sediment showed, when compared to the control, a decrease in bacterial abundance and significant lower levels of bacterial production and of leucine turnover rate. Bacterial production and leucine turnover rate decreased to 1.4% and 13% of the control values, respectively. Ectoenzymatic activities were also negatively affected but by smaller factors. After erosion by the water current in laboratory flume conditions, the eroded surface of the control sediment showed a generalised decline in all bacterial activities. The erosion of the copper-spiked sediment showed, however, two types of responses with respect to bacterial activities at the exposed surface: positive responses of bacterial production and leucine turnover rate contrasting with slight negative responses of ectoenzymatic activities. The effects of experimental erosion in the suspended cells were also different in the control and in the copper-spiked sediment. Bacterial cells in the control microcosm exhibited, when compared to the non-eroded sediment cells, decreases in all activities after the 6-h suspension. The response of the average suspended copper-spiked sediment cell differed from the control by a less sharp decrease in ectoenzymatic activities and

The shift of microbial communities and their roles in sulfur and iron cycling in a copper ore bioleaching system

Science.gov (United States)

Niu, Jiaojiao; Deng, Jie; Xiao, Yunhua; He, Zhili; Zhang, Xian; van Nostrand, J. D.; Liang, Yili; Deng, Ye; Liu, Xueduan; Yin, Huaqun

2016-10-01

Bioleaching has been employed commercially to recover metals from low grade ores, but the production efficiency remains to be improved due to limited understanding of the system. This study examined the shift of microbial communities and S&Fe cycling in three subsystems within a copper ore bioleaching system: leaching heap (LH), leaching solution (LS) and sediment under LS. Results showed that both LH and LS had higher relative abundance of S and Fe oxidizing bacteria, while S and Fe reducing bacteria were more abundant in the Sediment. GeoChip analysis showed a stronger functional potential for S0 oxidation in LH microbial communities. These findings were consistent with measured oxidation activities to S0 and Fe2+, which were highest by microbial communities from LH, lower by those from LS and lowest form Sediment. Moreover, phylogenetic molecular ecological network analysis indicated that these differences might be related to interactions among microbial taxa. Last but not the least, a conceptual model was proposed, linking the S&Fe cycling with responsible microbial populations in the bioleaching systems. Collectively, this study revealed the microbial community and functional structures in all three subsystems of the copper ore, and advanced a holistic understanding of the whole bioleaching system.

Impact of silver nanoparticles on benthic prokaryotes in heavy metal-contaminated estuarine sediments in a tropical environment.

Science.gov (United States)

Antizar-Ladislao, B; Bhattacharya, B D; Ray Chaudhuri, S; Sarkar, S K

2015-10-15

Little knowledge is available about the potential impact of commercial silver nanoparticles (Ag-NPs) on estuarine microbial communities. The Hugli river estuary, India, is susceptible to heavy metals pollution through boat traffic, and there is the potential for Ag-NP exposure via effluent discharged from ongoing municipal and industrial activities located in close proximity. This study investigated the effects of commercial Ag-NPs on native microbial communities in estuarine sediments collected from five stations, using terminal restriction fragment length polymorphism (T-RFLP) technique. An increase in the number of bacteria in consortium in sediments was observed following exposure to Ag-NPs. In general microbial communities may be resistant in estuarine systems to the antimicrobial effects of commercial Ag-NPs, but key microorganisms, such as Pelobacter propionicus, disappeared following exposure to Ag-NPs. In conclusion, the T-RFLP analysis indicated that Ag-NPs have the potential to shape estuarine sediment bacterial community structure. Copyright © 2015 Elsevier Ltd. All rights reserved.

Organic nitrogen rearranges both structure and activity of the soil-borne microbial seedbank.

Science.gov (United States)

Leite, Márcio F A; Pan, Yao; Bloem, Jaap; Berge, Hein Ten; Kuramae, Eiko E

2017-02-15

Use of organic amendments is a valuable strategy for crop production. However, it remains unclear how organic amendments shape both soil microbial community structure and activity, and how these changes impact nutrient mineralization rates. We evaluated the effect of various organic amendments, which range in Carbon/Nitrogen (C/N) ratio and degradability, on the soil microbiome in a mesocosm study at 32, 69 and 132 days. Soil samples were collected to determine community structure (assessed by 16S and 18S rRNA gene sequences), microbial biomass (fungi and bacteria), microbial activity (leucine incorporation and active hyphal length), and carbon and nitrogen mineralization rates. We considered the microbial soil DNA as the microbial seedbank. High C/N ratio favored fungal presence, while low C/N favored dominance of bacterial populations. Our results suggest that organic amendments shape the soil microbial community structure through a feedback mechanism by which microbial activity responds to changing organic inputs and rearranges composition of the microbial seedbank. We hypothesize that the microbial seedbank composition responds to changing organic inputs according to the resistance and resilience of individual species, while changes in microbial activity may result in increases or decreases in availability of various soil nutrients that affect plant nutrient uptake.

Volatilization of selenium from agricultural evaporation pond sediments.

Science.gov (United States)

Karlson, U; Frankenberger, W T

1990-03-01

Microbial volatilization of Se was evaluated as a means of detoxifying Se-contaminated sediments. Sediment samples containing 60.7 (Kesterson Reservoir) and 9.0 mg Se kg-1 (Peck ponds) were incubated for 273 days in closed systems located in the greenhouse. Volatile Se was collected from a continuous air-exchange stream using activated carbon. Various economical and readily available organic and inorganic amendments were tested for their capacity to enhance the microbial process, including Citrus (orange) peel, Vitis (grape) pomace, feedlot manure, barley straw, chitin, pectin, ZnSO4, (NH4)2SO4, and an inoculum of Acremonium falciforme (an active Se methylating fungus). With the Kesterson sediment, the highest Se removal (44.0%) resulted from the combined application of citrus peel and ZnSO4, followed by citrus peal alone (39.6%), and citrus peel combined with ZnSO4, (NH4)2SO4 and A. falciforme (30.1%). Manure (19.5%), pectin (16.4%), chitin (9.8%) and straw plus N (8.8%) had less pronounced effects. Without the amendments, cumulative Se volatilization was 6.1% of the initial inventory. Grape pomace (3.0%) inhibited the process. With the Peck sediment, the highest amount of Se removed was observed with chitin (28.6%), manure (28.5%), and citrus peel alone (27.3%). Without amendments, 14.0% of the native Se was volatilized in 273 days. Cumulative Se volatilization was 24.7% with citrus plus Zn and N, 17.2% with citrus plus Zn, and 18.8% with citrus plus Zn, N and A. falciforme. Pectin (15.2%), straw plus N (16.4%), and grape pomace (7.3%) were among the less effective amendments for the Peck sediment. The differences in the effectiveness of each treatment between the two seleniferous soils may be a result of the residual N content of the sediments. With the Kesterson sediment, which was high in organic C and N, added N inhibited volatilization of Se, while with Peck sediments (low in organic C and N) N-rich materials tended to accelerate Se volatilization

Microbial activities and communities in oil sands tailings ponds

Energy Technology Data Exchange (ETDEWEB)

Gieg, Lisa; Ramos, Esther; Clothier, Lindsay; Bordenave, Sylvain; Lin, Shiping; Voordouw, Gerrit; Dong, Xiaoli; Sensen, Christoph [University of Calgary (Canada)

2011-07-01

This paper discusses how the microbial communities and their activity play a vital role in tailings ponds. The ponds contain microorganisms along with metals, hydrocarbon diluent, naphthenic acid and others. The ponds play an important role in mining operations because they store bitumen extraction waste and also allow water to be re-used in the bitumen extraction process. Pond management presents a few challenges that include, among others, gas emissions and the presence of toxic and corrosive acids. Microbial activities and communities help in managing these ponds. Microbial activity measurement in active and inactive ponds is described and analyzed and the results are presented. The conditions for reducing sulfate, nitrate and iron are also presented. From the results it can be concluded that naphthenic acids can potentially serve as substrates for anaerobic populations in tailings ponds.

Quantification of microbial communities in subsurface marine sediments of the Black Sea and off Namibia

Directory of Open Access Journals (Sweden)

Axel eSchippers

2012-01-01

Full Text Available Organic-rich subsurface marine sediments were taken by gravity coring up to a depth of 10 meters below seafloor at six stations from the anoxic Black Sea and the Benguela upwelling system off Namibia during the research cruises R/V Meteor 72/5 and 76/1, respectively. The quantitative microbial community composition at various sediment depths was analyzed using total cell counting, CARD-FISH and quantitative real-time PCR (Q-PCR. Total cell counts decreased with depths from 109 – 1010 cells /mL at the sediment surface to 107 – 109 cells /mL below one meter depth. Based on CARD-FISH and Q-PCR analysis overall similar proportions of Bacteria and Archaea were determined. The down core quantitative distribution of prokaryotic and eukaryotic small subunit ribosomal RNA genes as well as functional genes involved in different biogeochemical processes was successfully revealed by Q-PCR. Crenarchaeota and the bacterial candidate division JS-1 and the classes Anaerolineae and Caldilineae of the phylum Chloroflexi were as highly abundant as Archaea and Bacteria, respectively. Less abundant but detectable in most of the samples in high gene copy numbers were Eukarya and the Fe(III- and Mn(IV-reducing bacterial group Geobacteriaceae (off Namibia as well as the functional genes cbbL encoding for the large subunit of Rubisco, the functional genes dsrA and aprA of sulfate-reducers and the gene mcrA of methanogens. Overall the high organic carbon content of the sediments goes along with high cell counts and high gene copy numbers, as well as an equal abundance of Bacteria and Archaea.

Microbial Communities of the Okinawa Backarc Basin Subvent Biosphere

Science.gov (United States)

Brandt, L. D.; House, C. H.

2014-12-01

IODP Expedition 331 to the Okinawa backarc basin provided an opportunity to study the microbial stratigraphy within the sediments surrounding a hydrothermal vent. The Okinawa backarc basin is a sedimented region of the seafloor located on a continental margin, and also hosts a hydrothermal network within the subsurface. Site C0014 within the Iheya North hydrothermal field is located 450 m east of the active vent and has a surface temperature of 5°C with no evidence of hydrothermal alteration within the top 10 m. Temperature increases with depth at an estimated rate of 3°C/m and transitions from non-hydrothermal margin sediments to a hydrothermally altered regime below 10 m. Site C0014 is a unique location to study changes in microbial communities with depth, as the hydrothermal system generates a thermally and geochemically restrictive subvent biosphere. In this study, we utilized deep 16S rRNA sequencing of DNA from IODP Expedition 331 Site C0014 sediment horizons in order to assess diversity throughout the sediment column as well as determine the potential limits of the biosphere. Analysis of the amplicon data suggests that Archaea represent a significant proportion of the indigenous community throughout the top 15 m of sediment, where Archaea then abruptly disappear. Furthermore, a deeper classification of Archaeal sequences suggests a transition from a mesophilic community to a potentially thermophilic one, where there is an increasingly stronger signal of Miscellaneous Crenarchaeotic Group (MCG) followed by Terrestrial Hot Spring Crenarchaeotic Group (THSCG). Additionally, there are several horizons in which methanotrophy is likely supported, indicated by peaks in anaerobic methanotrophic Archaea. The cessation of Archaea as well as Chloroflexi, a common marine subsurface bacterial phylum, at approximately 15 meters below seafloor (mbsf) is suggestive of a potential boundary within Site C0014 in which the environmental conditions have become too restrictive

Effects of Sediment Chemical Properties on Phosphorus Release Rates in the Sediment-Water Interface of the Steppe Wetlands.

Science.gov (United States)

He, Jing; Su, Derong; Lv, Shihai; Diao, Zhaoyan; Xie, Jingjie; Luo, Yan

2017-11-22

Rising temperature causes a process of phosphorus release, which can be characterized well using phosphorus release rates (V P ). The objective of the present study was to investigate the major factors affecting sediment phosphorus release rates through a wetland habitat simulation experiment. The results showed that the V P of different wetland sediments were different and changed with the order of W-R (river wetland) > W-L (lake wetland) > W-M (grassy marsh wetland) > W-A (reservoir wetland). The main driving factors which influenced sediment phosphorus flux velocity in the sediment-water interface were sediment B-SO₄ 2- , B-MBN and A-MBP content. Path analysis and determination coefficient analysis indicated the standard multiple regression equation for sediment phosphorus release rates in the sediment-water interface, and each main factor was Y = -0.105 + 0.096X₁ + 0.275X₂ - 0.010X₃ ( r = 0.416, p phosphorus release rates; X₁ is sediment B-SO₄ 2- content; X₂ is sediment B-MBN; and X₃ is sediment A-MBP content. Sediment B-SO₄ 2- , B-MBN and A-MBP content and the interaction between them were the main factors affecting sediment phosphorus release rates in the sediment-water interface. Therefore, these results suggest that soil chemical properties and microbial activities likely play an important role in phosphorus release rates in the sediment-water interface. We hope to provide effective scientific management and control methods for relevant environmental protection departments.

Biodegradation of crude oil in different types of marine sediment

International Nuclear Information System (INIS)

Hii, Y.S.; Law, A.T.

1999-01-01

An active oil-oxidizing bacterium, named Nap C was isolated from the sediment sample of Port Dickson coastal area for this study. Nap C is a gram negative, rod shape marine bacterium. It forms spore when the condition is not favorable. Three different types of treated marine sediment; sand, silt and clay were used in this study. The degradation of Malaysian Tapis A crude oil in the different types of marine sediment were assessed. Silt type of marine sediment was found to sustain highest biodegradation compared to clay type and sand type. 8.6.67% of the Malaysian Tapis A crude oil was degraded in silt type of marine sediment within 10 days of incubation. Where as there were only 60% and 73% of the Malaysian Tapis A crude oil was degraded in sand and clay type of marine sediment respectively. Microbial biomass estimation in the sediment was estimated by indirect phospholipid enumeration technique. (author)

Methanogenesis in the sediment of the acidic Lake Caviahue in Argentina

Science.gov (United States)

Koschorreck, Matthias; Wendt-Potthoff, Katrin; Scharf, Burkhard; Richnow, Hans H.

2008-12-01

The biogeochemistry of methane in the sediments of Lake Caviahue was examined by geochemical analysis, microbial activity assays and isotopic analysis. The pH in the water column was 2.6 and increased up to a pH of 6 in the deeper sediment pore waters. The carbon isotope composition of CH 4 was between - 65 and - 70‰ which is indicative for the biological origin of the methane. The enrichment factor ɛ increased from - 46‰ in the upper sediment column to more than - 80 in the deeper sediment section suggesting a transition from acetoclastic methanogenesis to CO 2 reduction with depth. In the most acidic surface layer of the sediment (pH Copahue Volcano, supported high rates of sulfate reduction which probably raised the pH and created favorable conditions for methanogens in deeper sediment layers.

Anaerobic 4-hydroxyproline utilization: Discovery of a new glycyl radical enzyme in the human gut microbiome uncovers a widespread microbial metabolic activity.

Science.gov (United States)

Huang, Yolanda Y; Martínez-Del Campo, Ana; Balskus, Emily P

2018-02-06

The discovery of enzymes responsible for previously unappreciated microbial metabolic pathways furthers our understanding of host-microbe and microbe-microbe interactions. We recently identified and characterized a new gut microbial glycyl radical enzyme (GRE) responsible for anaerobic metabolism of trans-4-hydroxy-l-proline (Hyp). Hyp dehydratase (HypD) catalyzes the removal of water from Hyp to generate Δ 1 -pyrroline-5-carboxylate (P5C). This enzyme is encoded in the genomes of a diverse set of gut anaerobes and is prevalent and abundant in healthy human stool metagenomes. Here, we discuss the roles HypD may play in different microbial metabolic pathways as well as the potential implications of this activity for colonization resistance and pathogenesis within the human gut. Finally, we present evidence of anaerobic Hyp metabolism in sediments through enrichment culturing of Hyp-degrading bacteria, highlighting the wide distribution of this pathway in anoxic environments beyond the human gut.

Feedbacks Between Soil Structure and Microbial Activities in Soil

Science.gov (United States)

Bailey, V. L.; Smith, A. P.; Fansler, S.; Varga, T.; Kemner, K. M.; McCue, L. A.

2017-12-01

Soil structure provides the physical framework for soil microbial habitats. The connectivity and size distribution of soil pores controls the microbial access to nutrient resources for growth and metabolism. Thus, a crucial component of soil research is how a soil's three-dimensional structure and organization influences its biological potential on a multitude of spatial and temporal scales. In an effort to understand microbial processes at scale more consistent with a microbial community, we have used soil aggregates as discrete units of soil microbial habitats. Our research has shown that mean pore diameter (x-ray computed tomography) of soil aggregates varies with the aggregate diameter itself. Analyzing both the bacterial composition (16S) and enzyme activities of individual aggregates showed significant differences in the relative abundances of key members the microbial communities associated with high enzyme activities compared to those with low activities, even though we observed no differences in the size of the biomass, nor in the overall richness or diversity of these communities. We hypothesize that resources and substrates have stimulated key populations in the aggregates identified as highly active, and as such, we conducted further research that explored how such key populations (i.e. fungal or bacterial dominated populations) alter pathways of C accumulation in aggregate size domains and microbial C utilization. Fungi support and stabilize soil structure through both physical and chemical effects of their hyphal networks. In contrast, bacterial-dominated communities are purported to facilitate micro- and fine aggregate stabilization. Here we quantify the direct effects fungal versus bacterial dominated communities on aggregate formation (both the rate of aggregation and the quality, quantity and distribution of SOC contained within aggregates). A quantitative understanding of the different mechanisms through which fungi or bacteria shape aggregate

Metagenomic analysis and metabolite profiling of deep-sea sediments from the Gulf of Mexico following the Deepwater Horizon oil spill

Directory of Open Access Journals (Sweden)

Nikole Elizabeth Kimes

2013-03-01

Full Text Available Marine subsurface environments, such as deep-sea sediments, house abundant and diverse microbial communities that are believed to influence large-scale geochemical processes. These processes include the biotransformation and mineralization of numerous petroleum constituents. Thus, microbial communities in the Gulf of Mexico are thought to be responsible for the intrinsic bioremediation of crude oil released by the Deepwater Horizon (DWH oil spill. While hydrocarbon contamination is known to enrich for aerobic, oil-degrading bacteria in deep-seawater habitats, relatively little is known about the response of communities in deep-sea sediments, where low oxygen levels may hinder such a response. Here, we examined the hypothesis that increased hydrocarbon exposure results in an altered sediment microbial community structure that reflects the prospects for oil biodegradation under the prevailing conditions. We explore this hypothesis using metagenomic analysis and metabolite profiling of deep-sea sediment samples following the DWH oil spill. The presence of aerobic microbial communities and associated functional genes was consistent among all samples, whereas, a greater number of Deltaproteobacteria and anaerobic functional genes were found in sediments closest to the DWH blowout site. Metabolite profiling also revealed a greater number of putative metabolites in sediments surrounding the blowout zone relative to a background site located 127 km away. The mass spectral analysis of the putative metabolites revealed that alkylsuccinates remained below detection levels, but a homologous series of benzylsuccinates (with carbon chain lengths from 5 to 10 could be detected. Our findings suggest that increased exposure to hydrocarbons enriches for Deltaproteobacteria, which are known to be capable of anaerobic hydrocarbon metabolism. We also provide evidence for an active microbial community metabolizing aromatic hydrocarbons in deep-sea sediments of the

Interactions between phototrophic bacteria in marine sediments

NARCIS (Netherlands)

de Wit, Rutger

1989-01-01

Phototrophic bacteria are the most consicious organisms occuring in laminated microbial sediment ecosystems (microbial mats). In the Waddensea area ecosystems consisting of a toplayer of the cyanobacterium Microleus chthonoplastes overlying a red layer of the purple sulfur bacterium Thiocapsa

Effect of sediment size on bioleaching of heavy metals from contaminated sediments of Izmir Inner Bay.

Science.gov (United States)

Guven, Duyusen E; Akinci, Gorkem

2013-09-01

The effect of sediment size on metals bioleaching from bay sediments was investigated by using fine (bioleaching. Microbial activity was provided with mixed cultures of Acidithiobacillus thiooxidans and Acidithiobacillus ferrooxidans. The bioleaching process was carried out in flask experiments for 48 days, by using 5% (W/V) of solid concentration in suspension. Bioleaching was found to be efficient for the removal of selected heavy metals from every size fraction of sediments, where the experiments with the smaller particles resulted in the highest solubilization ratios. At the end of the experimental period, Cr, Cu, Pb and Zn were solubilized to the ratios of 68%, 88%, 72%, and 91% from the fine sediment, respectively. Higher removal efficiencies can be explained by the larger surface area provided by the smaller particles. The changes in the chemical forms of metals were determined and most of the metal releases were observed from the reducible and organic fractions independent from grain size. Higher concentrations were monitored in the residual fraction after bioleaching period, suggesting they are trapped in this fraction, and cannot be solubilized under natural conditions.

PAH effects on meio- and microbial benthic communities strongly depend on bioavailability.

Science.gov (United States)

Lindgren, J Fredrik; Hassellöv, Ida-Maja; Dahllöf, Ingela

2014-01-01

The effects of anthropogenic pollutants in dissimilar habitats can vary depending on differences in bioavailability. The factors determining bioavailability are not yet fully understood. This study was performed to evaluate whether analysis of total PAH concentrations in sediments is a satisfactory measurement to indicate environmental effects or if bioavailability is needed to be taken into account. We have here performed a 60-day experiment, where nominal PAH concentrations of 1,300 μg/kg sediment were added to three different marine sediments. Meiofaunal and microbial communities were analyzed for alterations in community response at 30 and 60 days. Results showed that bioavailability of PAHs varied between the three different sediments. Nonetheless, the petroleum addition gave rise to significant negative effects on all three sediments at both time points. The two direct measurements of toxicity on the microbial community, potential nitrification and denitrification, displayed a lower effect of the PAH addition in the muddy sediment at both time points, compared to the other two sediment types. No effects were seen in the analysis of meiofaunal community structure. Measurements of PAH bioavailability in the three sediment types concurred with the results from the microbial community, revealing a lower bioavailability in the muddy sediment compared to the other two sediment types, 34% compared to sandy and 18% compared to organic at day 0. At day 60 it was 61% lower compared to sandy and 20% lower compared to organic. The negative effects of the PAH addition on the microbial nitrogen cycle were in six out of eight cases best correlated to the amount of alkylated bioavailable PAH in the sediments, and thus microbial nitrogen cycle is a possible good indicator for assessing PAH-induced stress. The results presented here have implications for risk analysis studies of petroleum-contaminated marine sediments; consequently, sediment characteristics and its effects on

Characterizing relationships among fecal indicator bacteria, microbial source tracking markers, and associated waterborne pathogen occurrence in stream water and sediments in a mixed land use watershed

Science.gov (United States)

Bed sediments of streams and rivers may store high concentrations of fecal indicator bacteria (FIB) and pathogens. Due to resuspension events, these contaminants can be mobilized into the water column and affect overall water quality. Other bacterial indicators such as microbial ...

Comparison of the active and resident community of a coastal microbial mat

OpenAIRE

Cardoso, Daniela Clara; Sandionigi, Anna; Cretoiu, Mariana Silvia; Casiraghi, Maurizio; Stal, Lucas; Bolhuis, Henk

2017-01-01

Coastal microbial mats form a nearly closed micro-scale ecosystem harboring a complex microbial community. Previous DNA based analysis did not necessarily provide information about the active fraction of the microbial community because it includes dormant, inactive cells as well as a potential stable pool of extracellular DNA. Here we focused on the active microbial community by comparing 16S rRNA sequences obtained from the ribosomal RNA pool with gene sequences obtained from the DNA fractio...

Antimicrobial activity of filamentous fungi isolated from highly antibiotic-contaminated river sediment

Science.gov (United States)

Svahn, K. Stefan; Göransson, Ulf; El-Seedi, Hesham; Bohlin, Lars; Larsson, D.G. Joakim; Olsen, Björn; Chryssanthou, Erja

2012-01-01

Background Filamentous fungi are well known for their production of substances with antimicrobial activities, several of which have formed the basis for the development of new clinically important antimicrobial agents. Recently, environments polluted with extraordinarily high levels of antibiotics have been documented, leading to strong selection pressure on local sentinel bacterial communities. In such microbial ecosystems, where multidrug-resistant bacteria are likely to thrive, it is possible that certain fungal antibiotics have become less efficient, thus encouraging alternative strategies for fungi to compete with bacteria. Methods In this study, sediment of a highly antibiotic-contaminated Indian river was sampled in order to investigate the presence of cultivable filamentous fungi and their ability to produce substances with antimicrobial activity. Results Sixty one strains of filamentous fungi, predominantly various Aspergillus spp. were identified. The majority of the Aspergillus strains displayed antimicrobial activity against methicillin-resistant Staphylococcus aureus, extended-spectrum beta-lactamase-producing Escherichia coli, vancomycin-resistant Enterococcus faecalis and Candida albicans. Bioassay-guided isolation of the secondary metabolites of A. fumigatus led to the identification of gliotoxin. Conclusion This study demonstrated proof of principle of using bioassay-guided isolation for finding bioactive molecules. PMID:22957125

Antimicrobial activity of filamentous fungi isolated from highly antibiotic-contaminated river sediment

Directory of Open Access Journals (Sweden)

K. Stefan Svahn

2012-05-01

Full Text Available Background: Filamentous fungi are well known for their production of substances with antimicrobial activities, several of which have formed the basis for the development of new clinically important antimicrobial agents. Recently, environments polluted with extraordinarily high levels of antibiotics have been documented, leading to strong selection pressure on local sentinel bacterial communities. In such microbial ecosystems, where multidrug-resistant bacteria are likely to thrive, it is possible that certain fungal antibiotics have become less efficient, thus encouraging alternative strategies for fungi to compete with bacteria. Methods: In this study, sediment of a highly antibiotic-contaminated Indian river was sampled in order to investigate the presence of cultivable filamentous fungi and their ability to produce substances with antimicrobial activity. Results: Sixty one strains of filamentous fungi, predominantly various Aspergillus spp. were identified. The majority of the Aspergillus strains displayed antimicrobial activity against methicillin-resistant Staphylococcus aureus, extended-spectrum beta-lactamase-producing Escherichia coli, vancomycin-resistant Enterococcus faecalis and Candida albicans. Bioassay-guided isolation of the secondary metabolites of A. fumigatus led to the identification of gliotoxin. Conclusion: This study demonstrated proof of principle of using bioassay-guided isolation for finding bioactive molecules.

Microbial activity in the terrestrial subsurface

International Nuclear Information System (INIS)

Kaiser, J.P.; Bollag, J.M.

1990-01-01

Little is known about the layers under the earth's crust. Only in recent years have techniques for sampling the deeper subsurface been developed to permit investigation of the subsurface environment. Prevailing conditions in the subsurface habitat such as nutrient availability, soil composition, redox potential, permeability and a variety of other factors can influence the microflora that flourish in a given environment. Microbial diversity varies between geological formations, but in general sandy soils support growth better than soils rich in clay. Bacteria predominate in subsurface sediments, while eukaryotes constitute only 1-2% of the microorganisms. Recent investigations revealed that most uncontaminated subsurface soils support the growth of aerobic heteroorganotrophic bacteria, but obviously anaerobic microorganisms also exist in the deeper subsurface habitat. The microorganisms residing below the surface of the earth are capable of degrading both natural and xenobiotic contaminants and can thereby adapt to growth under polluted conditions. (author) 4 tabs, 77 refs

Surface sediment quality relative to port activities: A contaminant-spectrum assessment.

Science.gov (United States)

Yu, Shen; Hong, Bing; Ma, Jun; Chen, Yongshan; Xi, Xiuping; Gao, Jingbo; Hu, Xiuqin; Xu, Xiangrong; Sun, Yuxin

2017-10-15

Ports are facing increasing environmental concerns with their importance to the global economy. Numerous studies indicated sediment quality deterioration in ports; however, the deterioration is not discriminated for each port activity. This study investigated a spectrum of contaminants (metals and organic pollutants) in surface sediments at 20 sampling points in Port Ningbo, China, one of the top five world ports by volume. The spectrum of contaminants (metals and organic pollutants) was quantified following marine sediment quality guidelines of China and USA and surface sediment quality was assessed according to thresholds of the two guidelines. Coupling a categorical matrix of port activities with the matrix of sedimentary contaminants revealed that contaminants were highly associated with the port operations. Ship repair posed a severe chemical risk to sediment. Operations of crude oil and coal loadings were two top activities related to organic pollutants in sediments while port operations of ore and container loadings discharged metals. Among the 20 sampling points, Cu, Zn, Pb, and DDT and its metabolites were the priority contaminants influencing sediment quality. Overall, surface sediments in Port Ningbo had relatively low environmental risks but ship repair is an environmental concern that must be addressed. This study provides a practical approach for port activity-related quality assessment of surface sediments in ports that could be applicable in many world sites. Copyright © 2017 Elsevier B.V. All rights reserved.

Physical Factors Correlate to Microbial Community Structure and Nitrogen Cycling Gene Abundance in a Nitrate Fed Eutrophic Lagoon.

Science.gov (United States)

Highton, Matthew P; Roosa, Stéphanie; Crawshaw, Josie; Schallenberg, Marc; Morales, Sergio E

2016-01-01

Nitrogenous run-off from farmed pastures contributes to the eutrophication of Lake Ellesmere, a large shallow lagoon/lake on the east coast of New Zealand. Tributaries periodically deliver high loads of nitrate to the lake which likely affect microbial communities therein. We hypothesized that a nutrient gradient would form from the potential sources (tributaries) creating a disturbance resulting in changes in microbial community structure. To test this we first determined the existence of such a gradient but found only a weak nitrogen (TN) and phosphorous gradient (DRP). Changes in microbial communities were determined by measuring functional potential (quantification of nitrogen cycling genes via nifH , nirS , nosZI , and nosZII using qPCR), potential activity (via denitrification enzyme activity), as well as using changes in total community (via 16S rRNA gene amplicon sequencing). Our results demonstrated that changes in microbial communities at a phylogenetic (relative abundance) and functional level (proportion of the microbial community carrying nifH and nosZI genes) were most strongly associated with physical gradients (e.g., lake depth, sediment grain size, sediment porosity) and not nutrient concentrations. Low nitrate influx at the time of sampling is proposed as a factor contributing to the observed patterns.

Physical factors correlate to microbial community structure and nitrogen cycling gene abundance in a nitrate fed eutrophic lagoon

Directory of Open Access Journals (Sweden)

Matthew Paul Highton

2016-10-01

Full Text Available Nitrogenous run-off from farmed pastures contributes to the eutrophication of Lake Ellesmere, a large shallow lagoon/lake on the east coast of New Zealand. Tributaries periodically deliver high loads of nitrate to the lake which likely affect microbial communities therein. We hypothesized that a nutrient gradient would form from the potential sources (tributaries creating a disturbance resulting in changes in microbial community structure. To test this we first determined the existence of such a gradient but found only a weak nitrogen (TN and phosphorous gradient (DRP. Changes in microbial communities were determined by measuring functional potential (quantification of nitrogen cycling genes via nifH, nirS, nosZI and nosZII using qPCR, potential activity (via denitrification enzyme activity, as well as using changes in total community (via 16S rRNA gene amplicon sequencing. Our results demonstrated that changes in microbial communities at a phylogenetic (relative abundance and functional level (proportion of the microbial community carrying nifH and nosZI genes were most strongly associated with physical gradients (e.g. lake depth, sediment grain size, sediment porosity and not nutrient concentrations. Low nitrate influx at the time of sampling is proposed as a factor contributing to the observed patterns.

Environment-Dependent Distribution of the Sediment nifH-Harboring Microbiota in the Northern South China Sea

Science.gov (United States)

Yang, Jinying; Li, Jing; Luan, Xiwu; Zhang, Yunbo; Gu, Guizhou; Xue, Rongrong; Zong, Mingyue; Klotz, Martin G.

2013-01-01

The South China Sea (SCS), the largest marginal sea in the Western Pacific Ocean, is a huge oligotrophic water body with very limited influx of nitrogenous nutrients. This suggests that sediment microbial N2 fixation plays an important role in the production of bioavailable nitrogen. To test the molecular underpinning of this hypothesis, the diversity, abundance, biogeographical distribution, and community structure of the sediment diazotrophic microbiota were investigated at 12 sampling sites, including estuarine, coastal, offshore, deep-sea, and methane hydrate reservoirs or their prospective areas by targeting nifH and some other functional biomarker genes. Diverse and novel nifH sequences were obtained, significantly extending the evolutionary complexity of extant nifH genes. Statistical analyses indicate that sediment in situ temperature is the most significant environmental factor influencing the abundance, community structure, and spatial distribution of the sediment nifH-harboring microbial assemblages in the northern SCS (nSCS). The significantly positive correlation of the sediment pore water NH4+ concentration with the nifH gene abundance suggests that the nSCS sediment nifH-harboring microbiota is active in N2 fixation and NH4+ production. Several other environmental factors, including sediment pore water PO43− concentration, sediment organic carbon, nitrogen and phosphorus levels, etc., are also important in influencing the community structure, spatial distribution, or abundance of the nifH-harboring microbial assemblages. We also confirmed that the nifH genes encoded by archaeal diazotrophs in the ANME-2c subgroup occur exclusively in the deep-sea methane seep areas, providing for the possibility to develop ANME-2c nifH genes as a diagnostic tool for deep-sea methane hydrate reservoir discovery. PMID:23064334

Vadose zone microbial community structure and activity in metal/radionuclide contaminated sediments. Final technical report

Energy Technology Data Exchange (ETDEWEB)

Balkwill, David L.

2002-08-17

This final technical report describes the research carried out during the final two months of the no-cost extension ending 11/14/01. The primary goals of the project were (1) to determine the potential for transformation of Cr(VI) (oxidized, mobile) to Cr(III) (reduced, immobile) under unsaturated conditions as a function of different levels and combinations of (a) chromium, (b) nitrate (co-disposed with Cr), and (c) molasses (inexpensive bioremediation substrate), and (2) to determine population structure and activity in experimental treatments by characterization of the microbial community by signature biomarker analysis and by RT-PCR and terminal restriction fragment length polymorphism (T-RFLP) and 16S ribosomal RNA genes. It was determined early in the one-year no-cost extension period that the T-RFLP approach was problematic in regard to providing information on the identities of microorganisms in the samples examined. As a result, it could not provide the detailed information on microbial community structure that was needed to assess the effects of treatments with chromium, nitrate, and/or molasses. Therefore, we decided to obtain the desired information by amplifying (using TR-PCR, with the same primers used for T-RFLP) and cloning 16S rRNA gene sequences from the same RNA extracts that were used for T-RFLP analysis. We also decided to use a restriction enzyme digest procedure (fingerprinting procedure) to place the clones into types. The primary focus of the research carried out during this report period was twofold: (a) to complete the sequencing of the clones, and (b) to analyze the clone sequences phylogenetically in order to determine the relatedness of the bacteria detected in the samples to each other and to previously described genera and species.

Microbial Reduction of Fe(III) in Acidic Sediments: Isolation of Acidiphilium cryptum JF-5 Capable of Coupling the Reduction of Fe(III) to the Oxidation of Glucose

OpenAIRE

Küsel, Kirsten; Dorsch, Tanja; Acker, Georg; Stackebrandt, Erko

1999-01-01

To evaluate the microbial populations involved in the reduction of Fe(III) in an acidic, iron-rich sediment, the anaerobic flow of supplemental carbon and reductant was evaluated in sediment microcosms at the in situ temperature of 12°C. Supplemental glucose and cellobiose stimulated the formation of Fe(II); 42 and 21% of the reducing equivalents that were theoretically obtained from glucose and cellobiose, respectively, were recovered in Fe(II). Likewise, supplemental H2 was consumed by acid...

Estimating Population Turnover Rates by Relative Quantification Methods Reveals Microbial Dynamics in Marine Sediment.

Science.gov (United States)

Kevorkian, Richard; Bird, Jordan T; Shumaker, Alexander; Lloyd, Karen G

2018-01-01

growth only in a few clades directly involved in methanogenesis, rather than in the whole microbial community. IMPORTANCE Many microbes cannot be isolated in pure culture to determine their preferential growth conditions and predict their response to changing environmental conditions. We created a microcosm of marine sediments that allowed us to simulate a diagenetic profile using a temporal analog for depth. This allowed for the observation of the microbial community population dynamics caused by the natural shift from sulfate reduction to methanogenesis. Our research provides evidence for the population dynamics of uncultured microbes as well as the application of a novel method of turnover rate analysis for individual taxa within a mixed incubation, FRAxC, which stands for "fraction of read abundance times cells," which was verified by quantitative PCR. This allows for the calculation of population turnover times for microbes in a natural setting and the identification of uncultured clades involved in geochemical processes. Copyright © 2017 American Society for Microbiology.

Cultivation-dependent analysis of the microbial diversity associated with the seagrass meadows in Xincun Bay, South China Sea.

Science.gov (United States)

Jiang, Yu-Feng; Ling, Juan; Wang, You-Shao; Chen, Biao; Zhang, Yan-Ying; Dong, Jun-De

2015-10-01

Microbial communities have largely existed in the seagrass meadows. A total of 496 strains of the bacteria in the seagrass meadows, which belonged to 50 genera, were obtained by the plate cultivation method from three sites of Xincun Bay, South China Sea. The results showed that Bacillales and Vibrionales accounted for the highest proportions of organisms in all communities. The diversity of the bacteria in the sediment was higher than that associated with seagrass. Thalassia hemperichii possessed the highest abundance of bacteria, followed by Enhalus acoroides and Cymodocea rotundata. Robust seasonal dynamics in microbial community composition were also observed. It was found that microbial activities were closely tied to the growth stage of the seagrass. The microbial distribution was the lowest in site 3. The abundance of the bacteria was linked to the interactions between bacteria and plants, the condition of plant and even the coastal water quality and the nutrition level in the sediment.

Arsenic release from shallow aquifers of the Hetao basin, Inner Mongolia: evidence from bacterial community in aquifer sediments and groundwater.

Science.gov (United States)

Li, Yuan; Guo, Huaming; Hao, Chunbo

2014-12-01

Indigenous microbes play crucial roles in arsenic mobilization in high arsenic groundwater systems. Databases concerning the presence and the activity of microbial communities are very useful in evaluating the potential of microbe-mediated arsenic mobilization in shallow aquifers hosting high arsenic groundwater. This study characterized microbial communities in groundwaters at different depths with different arsenic concentrations by DGGE and one sediment by 16S rRNA gene clone library, and evaluated arsenic mobilization in microcosm batches with the presence of indigenous bacteria. DGGE fingerprints revealed that the community structure changed substantially with depth at the same location. It indicated that a relatively higher bacterial diversity was present in the groundwater sample with lower arsenic concentration. Sequence analysis of 16S rRNA gene demonstrated that the sediment bacteria mainly belonged to Pseudomonas, Dietzia and Rhodococcus, which have been widely found in aquifer systems. Additionally, NO3(-)-reducing bacteria Pseudomonas sp. was the largest group, followed by Fe(III)-reducing, SO4(2-)-reducing and As(V)-reducing bacteria in the sediment sample. These anaerobic bacteria used the specific oxyanions as electron acceptor and played a significant role in reductive dissolution of Fe oxide minerals, reduction of As(V), and release of arsenic from sediments into groundwater. Microcosm experiments, using intact aquifer sediments, showed that arsenic release and Fe(III) reduction were microbially mediated in the presence of indigenous bacteria. High arsenic concentration was also observed in the batch without amendment of organic carbon, demonstrating that the natural organic matter in sediments was the potential electron donor for microbially mediated arsenic release from these aquifer sediments.

Phylogenetic & Physiological Profiling of Microbial Communities of Contaminated Soils/Sediments: Identifying Microbial consortia...

Energy Technology Data Exchange (ETDEWEB)

Terence L. Marsh

2004-05-26

The goals of this study were: (1) survey the microbial community in soil samples from a site contaminated with heavy metals using new rapid molecular techniques that are culture-independent; (2) identify phylogenetic signatures of microbial populations that correlate with metal ion contamination; and (3) cultivate these diagnostic strains using traditional as well as novel cultivation techniques in order to identify organisms that may be of value in site evaluation/management or bioremediation.

Microbial community dynamics and transformation of vascular plant detritus in two wetland ecosystems

International Nuclear Information System (INIS)

Moran, M.A.

1987-01-01

The microbial ecology of two wetland ecosystems in southeastern Georgia, USA, was studied with respect to microbial community dynamics and microbially-mediated transformations of vascular plant detritus. In the Okefenokee Swamp, biomass of microorganisms in the water column and sediments was generally lower in winter months and higher during spring and summer. Biomass and activity (measured as 14 C-lignocellulose mineralization) differed significantly among five habitats within the Okefenokee, and also among locations within each habitat. Significant heterogeneity in the structure of Okefenokee microbial communities was found at scales from 30 cm to 150 m. In field and laboratory studies of vascular plant decomposition in the Okefenokee and a salt marsh on Sapelo Island, the mathematical model which best describes decomposition kinetics is the decaying coefficient model

Analyses of outcrop and sediment grains observed and collected from the Sirena Deep and Middle Pond of the Mariana Trench

Science.gov (United States)

Hand, K. P.; Bartlett, D. H.; Fryer, P.

2012-12-01

During a March 2012 expedition we recovered sediments from two locales within the Marina Trench - Middle Pond and Sirena Deep. Samples were recovered from a Niskin bottle deployed on a passive lander platform that released an arm after touching down on the seafloor. The impact of the arm holding the Niskin bottle caused sediments to enter the bottle; this process was seen in images and on video captured by the lander. The combination of imagery and preliminary analyses of the sediments indicates that the Sirena Deep locale is a region of serpentinization and active microbial communities. Images show several outcrops consistent with serpentinization, some of which are coated with filamentous microbial mats. Results and analyses of these samples will be presented.

The effect of hysteresis on microbial activity in computer simulation models

NARCIS (Netherlands)

Whitmore, A.P.; Heinen, M.

1999-01-01

Microbial activity in soils depends on the status or the soil water, which is expressed by pressure head (h) or water content (θ). There is no unique relationship between θ and h because moisture relations exhibit hysteresis. For convenience microbial activity has usually been related to the main

Microbial dehalogenation of organohalides in marine and estuarine environments.

Science.gov (United States)

Zanaroli, Giulio; Negroni, Andrea; Häggblom, Max M; Fava, Fabio

2015-06-01

Marine sediments are the ultimate sink and a major entry way into the food chain for many highly halogenated and strongly hydrophobic organic pollutants, such as polychlorinated biphenyls (PCBs), polychlorinated dibenzo-p-dioxins (PCDDs), polybrominated diphenylethers (PBDEs) and 1,1,1-trichloro-2,2-bis(p-chlorophenyl)ethane (DDT). Microbial reductive dehalogenation in anaerobic sediments can transform these contaminants into less toxic and more easily biodegradable products. Although little is still known about the diversity of respiratory dehalogenating bacteria and their catabolic genes in marine habitats, the occurrence of dehalogenation under actual site conditions has been reported. This suggests that the activity of dehalogenating microbes may contribute, if properly stimulated, to the in situ bioremediation of marine and estuarine contaminated sediments. Copyright © 2015 Elsevier Ltd. All rights reserved.

Seasonal Development of Microbial Activity in Soils of Northern Norway

Institute of Scientific and Technical Information of China (English)

M. B(O)LTER; N. SOETHE; R. HORN; C. UHLIG

2005-01-01

Seasonal development of soil microbial activity and bacterial biomass in sub-polar regions was investigated to determine the impacts of biotic and abiotic factors, such as organic matter content, temperature and moisture. The study was performed during spring thaw from three cultivated meadows and two non-cultivated forest sites near Alta, in northern Norway. Samples from all five sites showed increasing respiration rates directly after the spring thaw with soil respiration activity best related to soil organic matter content. However, distributions of bacterial biomass showed fewer similarities to these two parameters. This could be explained by variations of litter exploitation through the biomass. Microbial activity started immediately after the thaw while root growth had a longer time lag. An influence of root development on soil microbes was proposed for sites where microorganisms and roots had a tight relationship caused by a more intensive root structure. Also a reduction of microbial activity due to soil compaction in the samples from a wheel track could not be observed under laboratory conditions. New methodological approaches of differential staining for live and dead organisms were applied in order to follow changes within the microbial community. Under laboratory conditions freeze and thaw cycles showed a damaging influence on parts of the soil bacteria. Additionally, different patterns for active vs.non-active bacteria were noticeable after freeze-thaw cycles.

Characterization of microbial degradation of oxytetracycline in river ...

African Journals Online (AJOL)

Characterization of microbial degradation of oxytetracycline in river water and sediment using reversed phase high performance liquid chromatography. ... African Journal of Biotechnology ... The present results have shown that microbial degradation plays a major role in the removal of OTC in natural environments.

Linking specific heterotrophic bacterial populations to bioreduction of uranium and nitrate using stable isotope probing in contaminated subsurface sediments

International Nuclear Information System (INIS)

Akob, Denise M.; Kerkhof, Lee; Kusel, Kirsten; Watson, David B.; Palumbo, Anthony Vito; Kostka, Joel

2011-01-01

Shifts in terminal electron-accepting processes during biostimulation of uranium-contaminated sediments were linked to the composition of stimulated microbial populations using DNA-based stable isotope probing. Nitrate reduction preceded U(VI) and Fe(III) reduction in [ 13 C]ethanol-amended microcosms. The predominant, active denitrifying microbial groups were identified as members of the Betaproteobacteria, whereas Actinobacteria dominated under metal-reducing conditions.

Extracellular enzyme activity assay as indicator of soil microbial functional diversity and activity

DEFF Research Database (Denmark)

Hendriksen, Niels Bohse; Winding, Anne

2012-01-01

Extracellular enzyme activity assay as indicator of soil microbial functional diversity and activity Niels Bohse Hendriksen, Anne Winding. Department of Environmental Science, Aarhus University, 4000 Roskilde, Denmark Soils provide numerous essential ecosystem services such as carbon cycling...... of soil microbial functions is still needed. In soil, enzymes originate from a variety of organisms, notably fungi and bacteria and especially hydrolytic extracellular enzymes are of pivotal importance for decomposition of organic substrates and biogeochemical cycling. Their activity will reflect...... the functional diversity and activity of the microorganisms involved in decomposition processes. Their activity has been measured by the use of fluorogenic model substrates e.g. methylumbelliferyl (MUF) substrates for a number of enzymes involved in the degradation of polysacharides as cellulose, hemicellulose...

Community Composition of Nitrous Oxide-Related Genes in Salt Marsh Sediments Exposed to Nitrogen Enrichment.

Science.gov (United States)

Angell, John H; Peng, Xuefeng; Ji, Qixing; Craick, Ian; Jayakumar, Amal; Kearns, Patrick J; Ward, Bess B; Bowen, Jennifer L

2018-01-01

Salt marshes provide many key ecosystem services that have tremendous ecological and economic value. One critical service is the removal of fixed nitrogen from coastal waters, which limits the negative effects of eutrophication resulting from increased nutrient supply. Nutrient enrichment of salt marsh sediments results in higher rates of nitrogen cycling and, commonly, a concurrent increase in the flux of nitrous oxide, an important greenhouse gas. Little is known, however, regarding controls on the microbial communities that contribute to nitrous oxide fluxes in marsh sediments. To address this disconnect, we generated profiles of microbial communities and communities of micro-organisms containing specific nitrogen cycling genes that encode several enzymes ( amoA, norB, nosZ) related to nitrous oxide flux from salt marsh sediments. We hypothesized that communities of microbes responsible for nitrogen transformations will be structured by nitrogen availability. Taxa that respond positively to high nitrogen inputs may be responsible for the elevated rates of nitrogen cycling processes measured in fertilized sediments. Our data show that, with the exception of ammonia-oxidizing archaea, the community composition of organisms involved in the production and consumption of nitrous oxide was altered under nutrient enrichment. These results suggest that previously measured rates of nitrous oxide production and consumption are likely the result of changes in community structure, not simply changes in microbial activity.

Application of Biofilm Covered Activated Carbon Particles as a Microbial Inoculum Delivery System for Enhanced Bioaugmentation of PCBs in Contaminated Sediment

Science.gov (United States)

2013-09-01

after anaerobic digestion at thermophilic conditions (60- 70C). Application of biofilm covered activated carbon particles as a microbial inoculum...Sludge Thickener; Sludge = Sludge after anaerobic digestion at thermophilic conditions (60- 70C). C3. Microscopic evaluation of dechlorinating...associated enzymes are capable of opening the biphenyl ring structure and transform the molecule into a linear structure, this changed structure was not

Distinct microbial communities in the active and permafrost layers on the Tibetan Plateau.

Science.gov (United States)

Chen, Yong-Liang; Deng, Ye; Ding, Jin-Zhi; Hu, Hang-Wei; Xu, Tian-Le; Li, Fei; Yang, Gui-Biao; Yang, Yuan-He

2017-12-01

Permafrost represents an important understudied genetic resource. Soil microorganisms play important roles in regulating biogeochemical cycles and maintaining ecosystem function. However, our knowledge of patterns and drivers of permafrost microbial communities is limited over broad geographic scales. Using high-throughput Illumina sequencing, this study compared soil bacterial, archaeal and fungal communities between the active and permafrost layers on the Tibetan Plateau. Our results indicated that microbial alpha diversity was significantly higher in the active layer than in the permafrost layer with the exception of fungal Shannon-Wiener index and Simpson's diversity index, and microbial community structures were significantly different between the two layers. Our results also revealed that environmental factors such as soil fertility (soil organic carbon, dissolved organic carbon and total nitrogen contents) were the primary drivers of the beta diversity of bacterial, archaeal and fungal communities in the active layer. In contrast, environmental variables such as the mean annual precipitation and total phosphorus played dominant roles in driving the microbial beta diversity in the permafrost layer. Spatial distance was important for predicting the bacterial and archaeal beta diversity in both the active and permafrost layers, but not for fungal communities. Collectively, these results demonstrated different driving factors of microbial beta diversity between the active layer and permafrost layer, implying that the drivers of the microbial beta diversity observed in the active layer cannot be used to predict the biogeographic patterns of the microbial beta diversity in the permafrost layer. © 2017 John Wiley & Sons Ltd.

Unraveling the relationship between microbial translocation and systemic immune activation in HIV infection

Science.gov (United States)

Shan, Liang; Siliciano, Robert F.

2014-01-01

Chronic immune activation is a key factor in HIV-1 disease progression. The translocation of microbial products from the intestinal lumen into the systemic circulation occurs during HIV-1 infection and is associated closely with immune activation; however, it has not been determined conclusively whether microbial translocation drives immune activation or occurs as a consequence of HIV-1 infection. In an important study in this issue of the JCI, Kristoff and colleagues describe the role of microbial translocation in producing immune activation in an animal model of HIV-1 infection, SIV infection of pigtailed macaques. Blocking translocation of intestinal bacterial LPS into the circulation dramatically reduced T cell activation and proliferation, production of proinflammatory cytokines, and plasma SIV RNA levels. This study directly demonstrates that microbial translocation promotes the systemic immune activation associated with HIV-1/SIV infection. PMID:24837427

Effects of Sediment Chemical Properties on Phosphorus Release Rates in the Sediment-Water Interface of the Steppe Wetlands

Directory of Open Access Journals (Sweden)

Jing He

2017-11-01

Full Text Available Rising temperature causes a process of phosphorus release, which can be characterized well using phosphorus release rates (VP. The objective of the present study was to investigate the major factors affecting sediment phosphorus release rates through a wetland habitat simulation experiment. The results showed that the VP of different wetland sediments were different and changed with the order of W–R (river wetland > W–L (lake wetland > W–M (grassy marsh wetland > W–A (reservoir wetland. The main driving factors which influenced sediment phosphorus flux velocity in the sediment–water interface were sediment B-SO42−, B-MBN and A-MBP content. Path analysis and determination coefficient analysis indicated the standard multiple regression equation for sediment phosphorus release rates in the sediment–water interface, and each main factor was Y = −0.105 + 0.096X1 + 0.275X2 − 0.010X3 (r = 0.416, p < 0.01, n = 144, where Y is sediment phosphorus release rates; X1 is sediment B-SO42− content; X2 is sediment B-MBN; and X3 is sediment A-MBP content. Sediment B-SO42−, B-MBN and A-MBP content and the interaction between them were the main factors affecting sediment phosphorus release rates in the sediment–water interface. Therefore, these results suggest that soil chemical properties and microbial activities likely play an important role in phosphorus release rates in the sediment–water interface. We hope to provide effective scientific management and control methods for relevant environmental protection departments.

Reductive immobilization of U(VI) in Fe(III) oxide-reducing subsurface sediments: Analysis of coupled microbial-geochemical processes in experimental reactive transport systems. Final Scientific/Technical Report-EMSP 73914

International Nuclear Information System (INIS)

Eric E. Roden Matilde M. Urrutia Mark O. Barnett Clifford R. Lange

2005-01-01

(VI) reduction is likely to be less efficient in natural soils and sediments than would be inferred from studies with synthetic Fe(III) oxides. A key implication of these findings is that production of Fe(II)-enriched sediments during one-time (or periodic) stimulation of DMRB activity is not likely to permit efficient long-term abiotic conversion of U(VI) to U(IV) in biogenic redox barriers designed to prevent far-field subsurface U(VI) migration. Instead our results suggest that ongoing DMRB activity will be required to achieve maximal U(VI) reduction efficiency, and emphasize the need for detailed understanding of patterns of DMRB growth, colonization, and maintenance in physically and chemically heterogeneous subsurface environments in order to predict the effectiveness of subsurface U(VI) bioremediation operations. A final ''capstone'' aspect of experimental work on the project was to examine the potential for sustained coupled Fe(III) oxide and U(VI) reduction in experimental flow-through reactor systems (i.e. sediment columns and ''semicontinuous culture'' systems) that are conceptually analogous to hydrologically-open subsurface environments. The results conclusively demonstrated the potential for sustained removal of U(VI) from solution via DMRB activity in excess of the U(VI) sorption capacity of the natural mineral assemblages as determined in abiotic controls. In addition, the abundance of sorbed U(VI) (a potential long-term source of U(VI) to the aqueous phase) was much lower in the biotic vs. abiotic systems. The latter results agree with other project findings which demonstrated the capacity for G. sulfurreducens to reduce sorbed U(VI). Throughout the project we have developed and refined a variety of reaction-based models of coupled Fe(III) oxide/U(VI) reduction, including a generalized model which accounts for the population dynamics of various respiratory microbial functional groups. These models have been employed in numerical simulations of both batch bench

Nutrient enrichment induces dormancy and decreases diversity of active bacteria in salt marsh sediments

Science.gov (United States)

Kearns, Patrick J.; Angell, John H.; Howard, Evan M.; Deegan, Linda A.; Stanley, Rachel H. R.; Bowen, Jennifer L.

2016-09-01

Microorganisms control key biogeochemical pathways, thus changes in microbial diversity, community structure and activity can affect ecosystem response to environmental drivers. Understanding factors that control the proportion of active microbes in the environment and how they vary when perturbed is critical to anticipating ecosystem response to global change. Increasing supplies of anthropogenic nitrogen to ecosystems globally makes it imperative that we understand how nutrient supply alters active microbial communities. Here we show that nitrogen additions to salt marshes cause a shift in the active microbial community despite no change in the total community. The active community shift causes the proportion of dormant microbial taxa to double, from 45 to 90%, and induces diversity loss in the active portion of the community. Our results suggest that perturbations to salt marshes can drastically alter active microbial communities, however these communities may remain resilient by protecting total diversity through increased dormancy.

Effect of salinity on nitrogenase activity and composition of the active diazotrophic community in intertidal microbial mats

NARCIS (Netherlands)

Severin, I.; Confurius-Guns, V.; Stal, L.J.

2012-01-01

Microbial mats are often found in intertidal areas experiencing a large range of salinities. This study investigated the effect of changing salinities on nitrogenase activity and on the composition of the active diazotrophic community ( transcript libraries) of three types of microbial mats situated

Compositional Characteristics of Dissolved Organic Matter released from the sediment of Han river in Korea.

Science.gov (United States)

Oh, H.; Choi, J. H.

2017-12-01

The dissolved organic matter (DOM) has variable characteristics depending on the sources. The DOM of a river is affected by rain water, windborne material, surface and groundwater flow, and sediments. In particular, sediments are sources and sinks of nutrients and pollutants in aquatic ecosystems by supplying large amounts of organic matter. The DOM which absorbs ultraviolet and visible light is called colored dissolved organic matter (CDOM). CDOM is responsible for the optical properties of natural waters in several biogeochemical and photochemical processes and absorbs UV-A (315-400 nm) and UV-B (280-315), which are harmful to aquatic ecosystems (Helms et al., 2008). In this study, we investigated the quantity and quality of DOM and CDOM released from the sediments of Han river which was impacted by anthropogenic activities and hydrologic alternation of 4 Major River Restoration Project. The target area of this study is Gangchenbo (GC), Yeojubo (YJ), and Ipobo(IP) of the Han River, Korea. Sediments and water samples were taken on July and August of 2016 and were incubated at 20° up to 7 days. Absorbance was measured with UV-visible spectrophotometer (Libra S32 PC, Biochrom). Fluorescence intensity determined with Fluorescence EEMs (F-7000, Hitachi). Absorbance and fluorescence intensity were used to calculate Specific Ultraviolet Absorbance (SUVA254), Humification index (HIX), Biological index (BIX), Spectral slope (SR) and component analysis. The DOC concentration increased after 3 days of incubation. According to the SUVA254 analysis, the microbial activity is highest in the initial overlying water of IP. HIX have range of 1.35-4.08, and decrease poly aromatic structures of organic matter during incubation. From the results of the BIX, autochthonous organic matter was released from the sediments. In all sites, Humic-like DOM, Microbial humic-like DOM and Protein-like DOM increased significantly between Day 0 and 3(except Humic-like, Microbial humic-like DOM in

[Sanitary-hygienic assessment of microbial biofertilizer].

Science.gov (United States)

Arkhipchenko, N A; Akhtemava, G A; Lebedeva, T V; Voronina, A A; Makhan'kova, T I; Pavlova, M M; Shteĭntsaĭg, T A

1991-10-01

Biological treatment of sewage from pig-breeding complexes allowed to produce microbial biomass and primary sediments. The mixture of these components (1:1) after rendering harmless and drying out become the high effective biofertilizer. The results of chronic experiment on sanitary status of soil (microbial and helminthological indexes) under this biofertilizer usage are discussed, and the harmlessness of it is demonstrated.

Microbial activities at the benthic boundary layer in the Aegean Sea

Science.gov (United States)

Bianchi, A.; Tholosan, O.; Garcin, J.; Polychronaki, T.; Tselepides, A.; Buscail, R.; Duineveld, G.

2003-05-01

During the Aegean Sea component of the EU MTP-MATER project, benthic samples were acquired along a depth gradient from two continental margins in the Aegean Sea. Sampling was undertaken during spring and summer 1997 and the microbial metabolic activities measured (Vmax for aminopeptidase activity, 14C-glutamate respiration and assimilation) displayed seasonal variability even in deep-sea conditions. The metabolic rates encountered in the North Aegean (average depth 566±234 m), were approximately five-fold higher than in the deeper (1336±140 m) Southern part of the Aegean. The aminopeptidase rates, however, were the exception with higher values recorded in the more oligotrophic sediments of the Southern stations (1383±152 vs. 766±297 nmol MCA cm-2 h-1). A discrepancy in bacterial metabolism also appeared in the near bottom waters. In the Southern stations, 80% of the glutamate uptake was used for energy yielding processes and only 20% devoted to biomass production, while in the North Aegean, most of the used glutamate was incorporated into bacterial cells. During the early burial stages, bacterial mineralization rates estimated from 14C-glutamate respiration decreased drastically compared to the rates of biopolymer hydrolysis estimated by aminopeptidase assays. Thus, at the 2-cm depth layer, these rates were only 32 and up to 77% of the corresponding average values, respectively, in the superficial layer. Such a discrepancy between the evolution of these two metabolic activities is possibly due to the rapid removal of readily utilizable monomers in the surface deposits. The correlation between bacterial respiration and total organic carbon, or total organic nitrogen, is higher in the surficial sediment (0-2 and 2-4 cm) than in the underlying layer. Conversely, it is only at 4-cm depth layer that the hydrolysis rates appear correlated with organic carbon and nitrogen concentrations. This pattern confirms the drastic degradation of organic matter during the early

Phylogenetically distinct bacteria involve extensive dechlorination of aroclor 1260 in sediment-free cultures.

Directory of Open Access Journals (Sweden)

Shanquan Wang

Full Text Available Microbial reductive dechlorination of the persistent polychlorinated biphenyls (PCBs is attracting much attention in cleanup of the contaminated environment. Nevertheless, most PCB dechlorinating cultures require presence of sediment or sediment substitutes to maintain their dechlorination activities which hinders subsequent bacterial enrichment and isolation processes. The information on enriching sediment-free PCB dechlorinating cultures is still limited. In this study, 18 microcosms established with soils and sediments were screened for their dechlorination activities on a PCB mixture - Aroclor 1260. After one year of incubation, 10 out of 18 microcosms showed significant PCB dechlorination with distinct dechlorination patterns (e.g., Process H, N and T classified based on profiles of PCB congeners loss and new congeners formation. Through serial transfers in defined medium, six sediment-free PCB dechlorinating cultures (i.e., CW-4, CG-1, CG-3, CG-4, CG-5 and SG-1 were obtained without amending any sediment or sediment-substitutes. PCB dechlorination Process H was the most frequently observed dechlorination pattern, which was found in four sediment-free cultures (CW-4, CG-3, CG-4 and SG-1. Sediment-free culture CG-5 showed the most extensive PCB dechlorination among the six cultures, which was mediated by Process N, resulting in the accumulation of penta- (e.g., 236-24-CB and tetra-chlorobiphenyls (tetra-CBs (e.g., 24-24-CB, 24-25-CB, 24-26-CB and 25-26-CB via dechlorinating 30.44% hepta-CBs and 59.12% hexa-CBs after three months of incubation. For culture CG-1, dechlorinators mainly attacked double flanked meta-chlorines and partially ortho-chlorines, which might represent a novel dechlorination pattern. Phylogenetic analysis showed distinct affiliation of PCB dechlorinators in the microcosms, including Dehalogenimonas and Dehalococcoides species. This study broadens our knowledge in microbial reductive dechlorination of PCBs, and provides

Phylogenetic characterization of phosphatase-expressing bacterial communities in Baltic Sea sediments

NARCIS (Netherlands)

Steenbergh, Anne; Bodelier, Paul; Hoogveld, H.L.; Slomp, C.P; Laanbroek, H.J.

2015-01-01

Phosphate release from sediments hampers the remediation of aquatic systems from a eutrophic state. Microbial phosphatases in sediments release phosphorus during organic matter degradation. Despite the important role of phosphatase-expressing bacteria, the identity of these bacteria in sediments is

Limited recovery of soil microbial activity after transient exposure to gasoline vapors

DEFF Research Database (Denmark)

Modrzyński, Jakub J.; Christensen, Jan H.; Mayer, Philipp

2016-01-01

During gasoline spills complex mixtures of toxic volatile organic compounds (VOCs) are released to terrestrial environments. Gasoline VOCs exert baseline toxicity (narcosis) and may thus broadly affect soil biota. We assessed the functional resilience (i.e. resistance and recovery of microbial...... functions) in soil microbial communities transiently exposed to gasoline vapors by passive dosing via headspace for 40 days followed by a recovery phase of 84 days. Chemical exposure was characterized with GC-MS, whereas microbial activity was monitored as soil respiration (CO2 release) and soil bacterial...... microbial activity indicating residual soil toxicity, which could not be attributed to BTEX, but rather to mixture toxicity of more persistent gasoline constituents or degradation products. Our results indicate a limited potential for functional recovery of soil microbial communities after transient...

Microbial activities in soil near natural gas leaks

Energy Technology Data Exchange (ETDEWEB)

Adamse, A D; Hoeks, J; de Bont, J A.M.; van Kessel, J F

1972-01-01

From the present experiments it may be concluded that in the surroundings of natural gas leaks, methane, ethane and possibly some other components of the natural gas are oxidized by microbial activities as long as oxygen is available. This is demonstrated by an increased oxygen consumption and carbon dioxide production, as well as by increased numbers of different types of bacteria. The resulting deficiency of oxygen, the excess of carbon dioxide, and perhaps the formation of inhibitory amounts of ethylene, are considered to be mainly responsible for the death of trees near natural gas leaks. Also the long period of time needed by the soil to recover, may be due to prolonged microbial activities, as well as to the presence of e.g. ethylene. The present experiments suggest that especially methane-oxidizing bacteria of the Methylosinus trichosporium type were present in predominating numbers and consequently have mainly been responsible for the increased oxygen consumption. However, some fungi oxidizing components of natural gas, including methane and ethane may also have contributed to the increased microbial activities in the soil. The same will be true of a possible secondary microflora on products derived from microorganisms oxidizing natural gas components. 12 references, 9 figures, 7 tables.

Zonation of Microbial Communities by a Hydrothermal Mound in the Atlantis II Deep (the Red Sea)

KAUST Repository

Wang, Yong

2015-10-20

In deep-sea geothermal rift zones, the dispersal of hydrothermal fluids of moderately-high temperatures typically forms subseafloor mounds. Major mineral components of the crust covering the mound are barite and metal sulfides. As a result of the continental rifting along the Red Sea, metalliferous sediments accumulate on the seafloor of the Atlantis II Deep. In the present study, a barite crust was identified in a sediment core from the Atlantis II Deep, indicating the formation of a hydrothermal mound at the sampling site. Here, we examined how such a dense barite crust could affect the local environment and the distribution of microbial inhabitants. Our results demonstrate distinctive features of mineral components and microbial communities in the sediment layers separated by the barite crust. Within the mound, archaea accounted for 65% of the community. In contrast, the sediments above the barite boundary were overwhelmed by bacteria. The composition of microbial communities under the mound was similar to that in the sediments of the nearby Discovery Deep and marine cold seeps. This work reveals the zonation of microbial communities after the formation of the hydrothermal mound in the subsurface sediments of the rift basin.

Zonation of Microbial Communities by a Hydrothermal Mound in the Atlantis II Deep (the Red Sea.

Directory of Open Access Journals (Sweden)

Yong Wang

Full Text Available In deep-sea geothermal rift zones, the dispersal of hydrothermal fluids of moderately-high temperatures typically forms subseafloor mounds. Major mineral components of the crust covering the mound are barite and metal sulfides. As a result of the continental rifting along the Red Sea, metalliferous sediments accumulate on the seafloor of the Atlantis II Deep. In the present study, a barite crust was identified in a sediment core from the Atlantis II Deep, indicating the formation of a hydrothermal mound at the sampling site. Here, we examined how such a dense barite crust could affect the local environment and the distribution of microbial inhabitants. Our results demonstrate distinctive features of mineral components and microbial communities in the sediment layers separated by the barite crust. Within the mound, archaea accounted for 65% of the community. In contrast, the sediments above the barite boundary were overwhelmed by bacteria. The composition of microbial communities under the mound was similar to that in the sediments of the nearby Discovery Deep and marine cold seeps. This work reveals the zonation of microbial communities after the formation of the hydrothermal mound in the subsurface sediments of the rift basin.

Zonation of Microbial Communities by a Hydrothermal Mound in the Atlantis II Deep (the Red Sea)

KAUST Repository

Wang, Yong; Li, Jiang Tao; He, Li Sheng; Yang, Bo; Gao, Zhao Ming; Cao, Hui Luo; Batang, Zenon B.; Al-Suwailem, Abdulaziz M.; Qian, Pei-Yuan

2015-01-01

In deep-sea geothermal rift zones, the dispersal of hydrothermal fluids of moderately-high temperatures typically forms subseafloor mounds. Major mineral components of the crust covering the mound are barite and metal sulfides. As a result of the continental rifting along the Red Sea, metalliferous sediments accumulate on the seafloor of the Atlantis II Deep. In the present study, a barite crust was identified in a sediment core from the Atlantis II Deep, indicating the formation of a hydrothermal mound at the sampling site. Here, we examined how such a dense barite crust could affect the local environment and the distribution of microbial inhabitants. Our results demonstrate distinctive features of mineral components and microbial communities in the sediment layers separated by the barite crust. Within the mound, archaea accounted for 65% of the community. In contrast, the sediments above the barite boundary were overwhelmed by bacteria. The composition of microbial communities under the mound was similar to that in the sediments of the nearby Discovery Deep and marine cold seeps. This work reveals the zonation of microbial communities after the formation of the hydrothermal mound in the subsurface sediments of the rift basin.

The role of certain infauna and vascular plants in the mediation of redox reactions in marine sediments

Science.gov (United States)

Hines, Mark E.

1992-01-01

The mechanisms by which certain animals and plants affect redox processes in sediments was examined by studying three environments: (1) subtidal sediments dominated by the deposit-feeding polychaete Heteromastus filiformis; (2) a saltmarsh inhabited by the tall form of Spartina alterniflora; and (3) tropical carbonate sediments inhabited by three species of seagrasses. S-35-sulfide production rates were compared to pool sizes of dissolved sulfide and dissolved iron. In all of the sediments studied, rates of sulfide reduction were enhanced by macroorganisms while the rate of turnover of dissolved sulfide increased. The polychaete enhanced microbial activity and redox cycling primarily by subducting particles of organic matter and oxidized iron during sediment reworking. The Spartina species enhanced anaerobic activity by transporting primarily dissolved organic matter and oxidants. Although the final result of both animal and plant activities was the enhancement of sub-surface cycling of sulfur and iron, decreased dissolved sulfide and increased dissolved iron concentrations, the mechanisms which produced these results differed dramatically.

Microbial community in high arsenic shallow groundwater aquifers in Hetao Basin of Inner Mongolia, China.

Directory of Open Access Journals (Sweden)

Ping Li

Full Text Available A survey was carried out on the microbial community of 20 groundwater samples (4 low and 16 high arsenic groundwater and 19 sediments from three boreholes (two high arsenic and one low arsenic boreholes in a high arsenic groundwater system located in Hetao Basin, Inner Mongolia, using the 454 pyrosequencing approach. A total of 233,704 sequence reads were obtained and classified into 12-267 operational taxonomic units (OTUs. Groundwater and sediment samples were divided into low and high arsenic groups based on measured geochemical parameters and microbial communities, by hierarchical clustering and principal coordinates analysis. Richness and diversity of the microbial communities in high arsenic sediments are higher than those in high arsenic groundwater. Microbial community structure was significantly different either between low and high arsenic samples or between groundwater and sediments. Acinetobacter, Pseudomonas, Psychrobacter and Alishewanella were the top four genera in high arsenic groundwater, while Thiobacillus, Pseudomonas, Hydrogenophaga, Enterobacteriaceae, Sulfuricurvum and Arthrobacter dominated high arsenic sediments. Archaeal sequences in high arsenic groundwater were mostly related to methanogens. Biota-environment matching and co-inertia analyses showed that arsenic, total organic carbon, SO4(2-, SO4(2-/total sulfur ratio, and Fe(2+ were important environmental factors shaping the observed microbial communities. The results of this study expand our current understanding of microbial ecology in high arsenic groundwater aquifers and emphasize the potential importance of microbes in arsenic transformation in the Hetao Basin, Inner Mongolia.

Microbial community in high arsenic shallow groundwater aquifers in Hetao Basin of Inner Mongolia, China.

Science.gov (United States)

Li, Ping; Wang, Yanhong; Dai, Xinyue; Zhang, Rui; Jiang, Zhou; Jiang, Dawei; Wang, Shang; Jiang, Hongchen; Wang, Yanxin; Dong, Hailiang

2015-01-01

A survey was carried out on the microbial community of 20 groundwater samples (4 low and 16 high arsenic groundwater) and 19 sediments from three boreholes (two high arsenic and one low arsenic boreholes) in a high arsenic groundwater system located in Hetao Basin, Inner Mongolia, using the 454 pyrosequencing approach. A total of 233,704 sequence reads were obtained and classified into 12-267 operational taxonomic units (OTUs). Groundwater and sediment samples were divided into low and high arsenic groups based on measured geochemical parameters and microbial communities, by hierarchical clustering and principal coordinates analysis. Richness and diversity of the microbial communities in high arsenic sediments are higher than those in high arsenic groundwater. Microbial community structure was significantly different either between low and high arsenic samples or between groundwater and sediments. Acinetobacter, Pseudomonas, Psychrobacter and Alishewanella were the top four genera in high arsenic groundwater, while Thiobacillus, Pseudomonas, Hydrogenophaga, Enterobacteriaceae, Sulfuricurvum and Arthrobacter dominated high arsenic sediments. Archaeal sequences in high arsenic groundwater were mostly related to methanogens. Biota-environment matching and co-inertia analyses showed that arsenic, total organic carbon, SO4(2-), SO4(2-)/total sulfur ratio, and Fe(2+) were important environmental factors shaping the observed microbial communities. The results of this study expand our current understanding of microbial ecology in high arsenic groundwater aquifers and emphasize the potential importance of microbes in arsenic transformation in the Hetao Basin, Inner Mongolia.

Impact of repeated insecticide application on soil microbial activity

International Nuclear Information System (INIS)

Xu Bujin; Zhang Yongxi; Chen Meici; Zhu Nanwen; Ming Hong

2001-01-01

The effects of repeated insecticide application on soil microbial activity were studied both in a cotton field and in the laboratory. The results of experiment show that there are some effects on soil microbial activities, such as the population of soil microorganisms, soil respiration, dehydrogenase activity and nitrogen fixation. The degree of effects depends on the chemical dosage. Within the range of 0.5-10.0 μg/g air-dry-soil, the higher the concentration, the stronger effect. In this experiment, the effect disappeared within 4, 8 or 16 days after treatment, depending on the dose applied. In field conditions, the situation is more complex and the data of field experiment show greater fluctuation. (author)

Effective bioremediation strategy for rapid in situ cleanup of anoxic marine sediments in mesocosm oil spill simulation.

Directory of Open Access Journals (Sweden)

Maria eGenovese

2014-04-01

Full Text Available The purpose of present study was the simulation of an oil spill accompanied by burial of significant amount of petroleum hydrocarbons (PHs in coastal sediments. Approximately 1,000 kg of sediments collected in Messina harbor were spiked with Bunker C furnace fuel oil (6,500 ppm. The rapid consumption of oxygen by aerobic heterotrophs created highly reduced conditions in the sediments with subsequent recession of biodegradation rates. As follows, after three months of ageing, the anaerobic sediments did not exhibit any significant levels of biodegradation and more than 80% of added Bunker C fuel oil remained buried. Anaerobic microbial community exhibited a strong enrichment in sulfate-reducing PHs-degrading and PHs-associated Deltaproteobacteria. As an effective bioremediation strategy to clean up these contaminated sediments, we applied a Modular Slurry System (MSS allowing the containment of sediments and their physical-chemical treatment, e.g. aeration. Aeration for three months has increased the removal of main PHs contaminants up to 98%. As revealed by CARD-FISH, qPCR and 16S rRNA gene clone library analyses, addition of Bunker C fuel oil initially affected the activity of autochthonous aerobic obligate marine hydrocarbonoclastic bacteria (OMHCB, and after one month more than the third of microbial population was represented by Alcanivorax-, Cycloclasticus- and Marinobacter-related organisms. In the end of the experiment, the microbial community composition has returned to a status typically observed in pristine marine ecosystems with no detectable OMHCB present. Eco-toxicological bioassay revealed that the toxicity of sediments after treatment was substantially decreased. Thus, our studies demonstrated that petroleum-contaminated anaerobic marine sediments could efficiently be cleaned through an in situ oxygenation which stimulates their self-cleaning potential due to reawakening of allochtonous aerobic OMHCB.

Microbial habitat connectivity across spatial scales and hydrothermal temperature gradients at Guaymas Basin

Directory of Open Access Journals (Sweden)

Stefanie eMeyer

2013-07-01

Full Text Available The Guaymas Basin (Gulf of California hydrothermal vent area is known as a dynamic and hydrothermally vented sedimentary system, where the advection and production of a variety of different metabolic substrates support a high microbial diversity and activity in the seafloor. The main objective of our study was to explore the role of temperature and other environmental factors on community diversity, such as the presence of microbial mats and seafloor bathymetry within one hydrothermally vented field of 200 × 250 m dimension. In this field, temperature increased strongly with sediment depth reaching the known limit to life within a few decimeters. Potential sulfate reduction rate as a key community activity parameter was strongly affected by in situ temperature and sediment depth, declining from high rates of 1-5 μmol ml-1 d-1 at the surface to the detection limit below 5 cm sediment depth, despite the presence of sulfate and hydrocarbons. Automated Ribosomal Intergenic Spacer Analysis yielded a high-resolution fingerprint of the dominant members of the bacterial community. Our analyses showed strong temperature and sediment depth effects on bacterial cell abundance and Operational Taxonomic Units (OTUs number, both declining by more than one order of magnitude below the top 5 cm of the sediment surface. Another fraction of the variation in diversity and community structure was explained by differences in the local bathymetry and spatial position within the vent field. Nevertheless, more than 80% of all detected OTUs were shared among the different temperature realms and sediment depths, after being classified as cold (T<10°C, medium (10°C≤T<40°C or hot (T≥40°C temperature conditions, with significant OTU overlap with the richer surface communities. Overall, this indicates a high connectivity of benthic bacterial habitats in this dynamic and heterogeneous marine ecosystem influenced by strong hydrothermalism.

Extraction of sediment-associated polycyclic aromatic hydrocarbons with granular activated carbon

NARCIS (Netherlands)

Rakowska, M.I.; Kupryianchyk, D.; Grotenhuis, J.T.C.; Rijnaarts, H.H.M.; Koelmans, A.A.

2013-01-01

Addition of activated carbon (AC) to sediments has been proposed as a method to reduce ecotoxicological risks of sediment-bound contaminants. The present study explores the effectiveness of granular AC (GAC) in extracting polycyclic aromatic hydrocarbon (PAH) from highly contaminated sediments. Four

Effect of electrokinetic remediation on indigenous microbial activity and community within diesel contaminated soil.

Science.gov (United States)

Kim, Seong-Hye; Han, Hyo-Yeol; Lee, You-Jin; Kim, Chul Woong; Yang, Ji-Won

2010-07-15

Electrokinetic remediation has been successfully used to remove organic contaminants and heavy metals within soil. The electrokinetic process changes basic soil properties, but little is known about the impact of this remediation technology on indigenous soil microbial activities. This study reports on the effects of electrokinetic remediation on indigenous microbial activity and community within diesel contaminated soil. The main removal mechanism of diesel was electroosmosis and most of the bacteria were transported by electroosmosis. After 25 days of electrokinetic remediation (0.63 mA cm(-2)), soil pH developed from pH 3.5 near the anode to pH 10.8 near the cathode. The soil pH change by electrokinetics reduced microbial cell number and microbial diversity. Especially the number of culturable bacteria decreased significantly and only Bacillus and strains in Bacillales were found as culturable bacteria. The use of EDTA as an electrolyte seemed to have detrimental effects on the soil microbial activity, particularly in the soil near the cathode. On the other hand, the soil dehydrogenase activity was enhanced close to the anode and the analysis of microbial community structure showed the increase of several microbial populations after electrokinetics. It is thought that the main causes of changes in microbial activities were soil pH and direct electric current. The results described here suggest that the application of electrokinetics can be a promising soil remediation technology if soil parameters, electric current, and electrolyte are suitably controlled based on the understanding of interaction between electrokinetics, contaminants, and indigenous microbial community. Copyright 2010 Elsevier B.V. All rights reserved.

Enhanced phosphorus reduction in simulated eutrophic water: a comparative study of submerged macrophytes, sediment microbial fuel cells, and their combination.

Science.gov (United States)

Xu, Peng; Xiao, Enrong; Xu, Dan; Li, Juan; Zhang, Yi; Dai, Zhigang; Zhou, Qiaohong; Wu, Zhenbin

2018-05-01

The phosphorus reduction in water column was attempted by integrating sediment microbial fuel cells (SMFCs) with the submerged macrophyte Vallisneria spiralis. A comparative study was conducted to treat simulated water rich in phosphate with a control and three treatments: SMFC alone (SMFC), submerged macrophytes alone (macophyte), and combined macrophytes and fuel cells (M-SMFC). All treatments promoted phosphorus flux from the water column to sediments. Maximum phosphorus reduction was obtained in proportion to the highest stable phosphorus level in sediments in M-SMFC. For the initial phosphate concentrations of 0.2, 1, 2, and 4 mg/L, average phosphate values in the overlying water during four phases decreased by 33.3% (25.0%, 8.3%), 30.8% (5.1%, 17.9%), 36.5% (27.8%, 15.7%), and 36.2% (0.7%, 22.1%) for M-SMFC (macrophyte, SMFC), compared with the control. With macrophyte treatment, the obvious phosphorus release from sediments was observed during the declining period. However, such phenomenon was significantly inhibited with M-SMFC. The electrogenesis bacteria achieved stronger phosphorus adsorption and assimilation was significantly enriched on the closed-circuit anodes. The higher abundance of Geobacter and Pseudomonas in M-SMFC might in part explain the highest phosphorus reduction in the water column. M-SMFC treatment could be promising to control the phosphorus in eutrophic water bodies.

Effects of ultrasonic disintegration on sludge microbial activity and dewaterability

International Nuclear Information System (INIS)

Li Huan; Jin Yiying; Mahar, Rasool Bux; Wang Zhiyu; Nie Yongfeng

2009-01-01

Ultrasonic treatment can disintegrate sludge, enhance microbial activity and improve sludge dewaterability at different energy inputs. To find their relationship, the three phenomena during ultrasonic treatment were investigated synchronously, and an experimental model was established to describe the process of ultrasonic sludge disintegration. Analysis results showed that the changes of sludge microbial activity and dewaterability were dependent on sludge disintegration degree during ultrasonic treatment. When sludge disintegration degree was lower than 20%, sludge flocs were disintegrated into micro-floc aggregates and the microbial activity increased over 20%. When sludge disintegration degree was over 40%, most cells were destroyed at different degree, and sludge activity decreased drastically. Only when sludge disintegration degree was 2-5%, sludge dewaterability was improved with the conditioning of FeCl 3 . It was also found that the sonication with low density and long duration was more efficient than sonication with high density and short duration at the same energy input for sludge disintegration, and a transmutative power function model can be used to describe the process of ultrasonic disintegration

Effects of ultrasonic disintegration on sludge microbial activity and dewaterability.

Science.gov (United States)

Huan, Li; Yiying, Jin; Mahar, Rasool Bux; Zhiyu, Wang; Yongfeng, Nie

2009-01-30

Ultrasonic treatment can disintegrate sludge, enhance microbial activity and improve sludge dewaterability at different energy inputs. To find their relationship, the three phenomena during ultrasonic treatment were investigated synchronously, and an experimental model was established to describe the process of ultrasonic sludge disintegration. Analysis results showed that the changes of sludge microbial activity and dewaterability were dependent on sludge disintegration degree during ultrasonic treatment. When sludge disintegration degree was lower than 20%, sludge flocs were disintegrated into micro-floc aggregates and the microbial activity increased over 20%. When sludge disintegration degree was over 40%, most cells were destroyed at different degree, and sludge activity decreased drastically. Only when sludge disintegration degree was 2-5%, sludge dewaterability was improved with the conditioning of FeCl(3). It was also found that the sonication with low density and long duration was more efficient than sonication with high density and short duration at the same energy input for sludge disintegration, and a transmutative power function model can be used to describe the process of ultrasonic disintegration.

Effect of glyphosate on the microbial activity of two Romanian soils.

Science.gov (United States)

Sumalan, R M; Alexa, E; Negrea, M; Sumalan, R L; Doncean, A; Pop, G

2010-01-01

Glyphosate applied to soils potentially affect microbial activity. A series of field and laboratory experiments assessed the effect of this herbicide on soil microorganisms. The aim of experiments was to evaluate the effect of glyphosate application on the soil microbial community structure, function and their activity. We studied "in vitro", changes in the microbial activity of typical Chernozem and Gleysol soils, with and without applied glyphosate. The herbicide was applied at a rate of 2, respectively 4 mg kg(-1) of soil and microbial activity were measured by fluorescein diacetate (FDA) hydrolysis. We found an increase of 9 to 13% in FDA hydrolyses in the presence of glyphosate in rate of 2 mg kg (-1) compared with the same type of soil which had never received herbicide. The double quantity of glyphosate decrease soil microbial activity; the amount of hydrolyzed fluorescein is lower than the addition of 2 ppm. The greater decrease was observed in the Gleysol type where the fluorescein hydrolyzed is with 4, 85% lower than version control without glyphosate. Chemical characters of soil, influence soil biological activity when herbicide is added. In Chemozem case, rich in humus, whose predominant micro flora is represented by actinomycetes through glyphosate treatment these organisms growths of as major producers of antibiotics actinomycetes determine an inhibitory effect on eubacteria and micromycetes growth, which is highlighted by estimating a relatively small number of them. After 10 days, once with decreasing of glyphosate content in soil, decreases the number of active actinomycetes, therefore we are witnessing to a numerical growth of bacterial population. In Gleysol type the indigenous micro flora is represented by eubacteria, so when the glyphosate is added it was registered a high growth of these organisms fraction.

Necromass as a source of energy to microorganisms in marine sediments.

Science.gov (United States)

Bradley, J.; Amend, J.; LaRowe, D.

2017-12-01

Marine sediments constitute one of the largest, most energy-limited biospheres on Earth. Despite increasing exploration and interest characterizing microbial communities in marine sediments, the production and role of microbial dead-matter (necromass) has largely been overlooked. Necromass is produced on a global scale, yet its significance as a power source to heterotrophic microorganisms remains unknown. We developed a physical, bio-energetic and geochemical model to quantify the total power supply from necromass oxidation and the total power demand of living microorganisms in marine sediments. This model is first applied to sediments from the oligotrophic South Pacific Gyre (SPG), where organic carbon and biomass concentrations are extremely low, yet microorganisms persist for millions of years in some of the lowest energy states on Earth. We show that necromass does not supply sufficient power to support the total demands of the living community (maintenance demands of microorganisms in marine sediments for up to 60,000 years following burial. Our model assumes that all counted cells are viable. Yet, if only a fraction of counted cells are alive, the role of necromass as an electron donor in fueling microbial metabolisms is even greater. This new insight requires a reassessment of carbon fluxes in the deep biosphere. By extension, we also demonstrate a mechanism for microbial communities to persist by oxidizing necromass over geological timescales, and thereby endure unfavorable, low-energy settings that might be analogous to conditions on early Earth and on other planetary bodies.

The potential significance of microbial activity in radioactive waste disposal

International Nuclear Information System (INIS)

McCabe, A.M.

1987-12-01

The aim of this report is to assess the potential significance of microbial activity in radioactive waste disposal. It outlines the major factors which need to be considered in order to evaluate the importance of microbiological action. These include water and nutritional sources (particularly carbon) hostile conditions (particularly the effects of radiation and pH), the establishment of pH micro-environments and the degradative effect of microbial metabolic by-products on the disposed waste forms. Before an active microbial population can develop there are certain basic requirements for life. These are outlined and the possibility of colonisation occurring within the chemical, radiological and nutritional constraints of a repository are considered. Once colonisation is assumed, the effect of microbial activity is discussed under five headings, i.e. (i) direct attack, (ii) physical disruption (which includes consideration of fissuring processes and void formation), (iii) gas generation (which may be of particular importance), (iv) radionuclide uptake and finally (v) alteration of groundwater chemistry. Particular attention is paid to the possibility of environments becoming established both within the waste form itself (allowing microbes to attack from the inside of the repository outward) or attack on the encapsulant materials (microbes attacking from the outside inward). (author)

Nutrient limitation of soil microbial activity during the earliest stages of ecosystem development.

Science.gov (United States)

Castle, Sarah C; Sullivan, Benjamin W; Knelman, Joseph; Hood, Eran; Nemergut, Diana R; Schmidt, Steven K; Cleveland, Cory C

2017-11-01

A dominant paradigm in ecology is that plants are limited by nitrogen (N) during primary succession. Whether generalizable patterns of nutrient limitation are also applicable to metabolically and phylogenetically diverse soil microbial communities, however, is not well understood. We investigated if measures of N and phosphorus (P) pools inform our understanding of the nutrient(s) most limiting to soil microbial community activities during primary succession. We evaluated soil biogeochemical properties and microbial processes using two complementary methodological approaches-a nutrient addition microcosm experiment and extracellular enzyme assays-to assess microbial nutrient limitation across three actively retreating glacial chronosequences. Microbial respiratory responses in the microcosm experiment provided evidence for N, P and N/P co-limitation at Easton Glacier, Washington, USA, Puca Glacier, Peru, and Mendenhall Glacier, Alaska, USA, respectively, and patterns of nutrient limitation generally reflected site-level differences in soil nutrient availability. The activities of three key extracellular enzymes known to vary with soil N and P availability developed in broadly similar ways among sites, increasing with succession and consistently correlating with changes in soil total N pools. Together, our findings demonstrate that during the earliest stages of soil development, microbial nutrient limitation and activity generally reflect soil nutrient supply, a result that is broadly consistent with biogeochemical theory.