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At least 343 records · Page 19Linked to original sources

Deferrisoma paleochoriense sp. nov., a thermophilic, iron(III)-reducing bacterium from a shallow-water hydrothermal vent in the Mediterranean Sea

A novel thermophilic, anaerobic, mixotrophic bacterium, designated strain MAG-PB1 T , was isolated from a shallow-water hydrothermal vent system in Palaeochori Bay off the coast of the island of Milos, Greece. The cells were Gram-negative, rugose, short rods, approximately 1.0 μm long and 0.5 μm wide. Strain MAG-PB1 T grew at 30–70 °C (optimum 60 °C), 0–50 g NaCl l − 1 (optimum 15–20 g l − 1 ) and pH 5.5–8.0 (optimum pH 6.0). Generation time under optimal conditions was 2.5 h. Optimal growth occurred under chemolithoautotrophic conditions with H 2 as the energy source and CO 2 as the carbon source. Fe(III), Mn(IV), arsenate and selenate were used as electron acceptors. Peptone, tryptone, Casamino acids, sucrose, yeast extract, d -fructose, α- d -glucose and ( − )- d -arabinose also served as electron donors. No growth occurred in the presence of lactate or formate. The G+C content of the genomic DNA was 66.7 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that this organism is closely related to Deferrisoma camini , the first species of a recently described genus in the Deltaproteobacteria . Based on the 16S rRNA gene phylogenetic analysis and on physiological, biochemical and structural characteristics, the strain was found to represent a novel species, for which the name Deferrisoma palaeochoriense sp. nov. is proposed. The type strain is MAG-PB1 T ( = JCM 30394 T  = DSM 29363 T ).

Mediterranean Sea, Milos Island, Paleochori Bay↗

Efficacy of detection canines for avian botulism surveillance and mitigation

Hawai'i's endangered waterbirds have experienced epizootics caused by ingestion of prey that accumulated a botulinum neurotoxin produced by the anaerobic bacterium Clostridium botulinum (avian botulism; Type C). Waterbird carcasses, necrophagous flies, and their larvae initiate and spread avian botulism, a food-borne paralytic disease lethal to waterbirds. Each new carcass has potential to develop toxin-accumulating necrophagous vectors amplifying outbreaks and killing hundreds of endangered waterbirds. Early carcass removal is an effective mitigation strategy for preventing avian intoxication, toxin concentration in necrophagous and secondary food webs, and reducing the magnitude of epizootics. However, rapid detection of carcasses can be problematic and labor intensive. Therefore, we tested a new method using scent detection canines for avian botulism surveillance on Kaua'i Island. During operational surveillance and a randomized double-blind field trial, trained detector canines with experienced field handlers improved carcass detection probability, especially in dense vegetation. Detector canines could be combined with conventional surveillance to optimize search strategies for carcass removal and are a useful tool to reduce risks of the initiation and propagation of avian botulism.

Hawaii↗

Arsenic cycling in hydrocarbon plumes: secondary effects of natural attenuation

Monitored natural attenuation is widely applied as a remediation strategy at hydrocarbon spill sites. Natural attenuation relies on biodegradation of hydrocarbons coupled with reduction of electron acceptors, including solid phase ferric iron (Fe(III)). Because arsenic (As) adsorbs to Fe-hydroxides, a potential secondary effect of natural attenuation of hydrocarbons coupled with Fe(III) reduction is a release of naturally occurring As to groundwater. At a crude-oil-contaminated aquifer near Bemidji, Minnesota, anaerobic biodegradation of hydrocarbons coupled to Fe(III) reduction has been well documented. We collected groundwater samples at the site annually from 2009 to 2013 to examine if As is released to groundwater and, if so, to document relationships between As and Fe inside and outside of the dissolved hydrocarbon plume. Arsenic concentrations in groundwater in the plume reached 230 µg/L, whereas groundwater outside the plume contained less than 5 µg/L As. Combined with previous data from the Bemidji site, our results suggest that (1) naturally occurring As is associated with Fe-hydroxides present in the glacially derived aquifer sediments; (2) introduction of hydrocarbons results in reduction of Fe-hydroxides, releasing As and Fe to groundwater; (3) at the leading edge of the plume, As and Fe are removed from groundwater and retained on sediments; and (4) downgradient from the plume, patterns of As and Fe in groundwater are similar to background. We develop a conceptual model of secondary As release due to natural attenuation of hydrocarbons that can be applied to other sites where an influx of biodegradable organic carbon promotes Fe(III) reduction.

Minnesota↗

Effect of hydrological conditions on nitrous oxide, methane, and carbon dioxide dynamics in a bottomland hardwood forest and its implication for soil carbon sequestration

This study was conducted at three locations in a bottomland hardwood forest with a distinct elevation and hydrological gradient: ridge (high, dry), transition, and swamp (low, wet). At each location, concentrations of soil greenhouse gases (N 2 O, CH 4 , and CO 2 ), their fluxes to the atmosphere, and soil redox potential (Eh) were measured bimonthly, while the water table was monitored every day. Results show that soil Eh was significantly ( P < 0.001) correlated with water table: a negative correlation at the ridge and transition locations, but a positive correlation at the permanently flooded swamp location. Both soil gas profile analysis and surface gas flux measurements indicated that the ridge and transition locations could be a sink of atmospheric CH 4 , especially in warm seasons, but generally functioned as a minor source of CH 4 in cool seasons. The swamp location was a major source of CH 4 , and the emission rate was higher in the warm seasons (mean 28 and median 23 mg m −2 h −1 ) than in the cool seasons (both mean and median 13 mg m −2 h −1 ). Average CO 2 emission rate was 251, 380 and 52 mg m −2 h −1 for the ridge, transition and swamp location, respectively. At each location, higher CO 2 emission rates were also found in the warm seasons. The lowest CO 2 emission rate was found at the swamp location, where soil C content was the highest, due to less microbial biomass, less CO 2 production in such an anaerobic environment, and greater difficulty of CO 2 diffusion to the atmosphere. Cumulative global warming potential emission from these three greenhouse gases was in an order of swamp > transition > ridge location. The ratio CO 2 /CH 4 production in soil is a critical factor for evaluating the overall benefit of soil C sequestration, which can be greatly offset by CH 4 production and emission.

Global Change Biology↗

Microbial community structure of hydrothermal deposits from geochemically different vent fields along the Mid-Atlantic Ridge

To evaluate the effects of local fluid geochemistry on microbial communities associated with active hydrothermal vent deposits, we examined the archaeal and bacterial communities of 12 samples collected from two very different vent fields: the basalt-hosted Lucky Strike (37&deg;17'N, 32&deg;16.3'W, depth 1600-1750m) and the ultramafic-hosted Rainbow (36&deg;13'N, 33&deg;54.1'W, depth 2270-2330m) vent fields along the Mid-Atlantic Ridge (MAR). Using multiplexed barcoded pyrosequencing of the variable region 4 (V4) of the 16S rRNA genes, we show statistically significant differences between the archaeal and bacterial communities associated with the different vent fields. Quantitative polymerase chain reaction (qPCR) assays of the functional gene diagnostic for methanogenesis ( mcr A), as well as geochemical modelling to predict pore fluid chemistries within the deposits, support the pyrosequencing observations. Collectively, these results show that the less reduced, hydrogen-poor fluids at Lucky Strike limit colonization by strict anaerobes such as methanogens, and allow for hyperthermophilic microaerophiles, like Aeropyrum . In contrast, the hydrogen-rich reducing vent fluids at the ultramafic-influenced Rainbow vent field support the prevalence of methanogens and other hydrogen-oxidizing thermophiles at this site. These results demonstrate that biogeographical patterns of hydrothermal vent microorganisms are shaped in part by large scale geological and geochemical processes.

Environmental Microbiology↗

Soil magnetic susceptibility: A quantitative proxy of soil drainage for use in ecological restoration

Flooded, saturated, or poorly drained soils are commonly anaerobic, leading to microbially induced magnetite/maghemite dissolution and decreased soil magnetic susceptibility (MS). Thus, MS is considerably higher in well-drained soils (MS typically 40-80 ?? 10-5 standard international [SI]) compared to poorly drained soils (MS typically 10-25 ?? 10-5 SI) in Illinois, other soil-forming factors being equal. Following calibration to standard soil probings, MS values can be used to rapidly and precisely delineate hydric from nonhydric soils in areas with relatively uniform parent material. Furthermore, soil MS has a moderate to strong association with individual tree species' distribution across soil moisture regimes, correlating inversely with independently reported rankings of a tree species' flood tolerance. Soil MS mapping can thus provide a simple, rapid, and quantitative means for precisely guiding reforestation with respect to plant species' adaptations to soil drainage classes. For instance, in native woodlands of east-central Illinois, Quercus alba , Prunus serotina, and Liriodendron tulipifera predominantly occur in moderately well-drained soils (MS 40-60 ?? 10-5 SI), whereas Acer saccharinum, Carya laciniosa, and Fraxinus pennsylvanica predominantly occur in poorly drained soils (MS <20 ?? 10-5 SI). Using a similar method, an MS contour map was used to guide restoration of mesic, wet mesic, and wet prairie species to pre-settlement distributions at Meadowbrook Park (Urbana, IL, U.S.A.). Through use of soil MS maps calibrated to soil drainage class and native vegetation occurrence, restoration efforts can be conducted more successfully and species distributions more accurately reconstructed at the microecosystem level. ?? 2008 Society for Ecological Restoration International.

Restoration Ecology↗

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

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.

FEMS Microbiology Ecology↗

When a habitat freezes solid: Microorganisms over-winter within the ice column of a coastal Antarctic lake

A major impediment to understanding the biology of microorganisms inhabiting Antarctic environments is the logistical constraint of conducting field work primarily during the summer season. However, organisms that persist throughout the year encounter severe environmental changes between seasons. In an attempt to bridge this gap, we collected ice core samples from Pony Lake in early November 2004 when the lake was frozen solid to its base, providing an archive for the biological and chemical processes that occurred during winter freezeup. The ice contained bacteria and virus-like particles, while flagellated algae and ciliates over-wintered in the form of inactive cysts and spores. Both bacteria and algae were metabolically active in the ice core melt water. Bacterial production ranged from 1.8 to 37.9 μg C L −1 day −1 . Upon encountering favorable growth conditions in the melt water, primary production ranged from 51 to 931 μg C L −1 day −1 . Because of the strong H 2 S odor and the presence of closely related anaerobic organisms assigned to Pony Lake bacterial 16S rRNA gene clones, we hypothesize that the microbial assemblage was strongly affected by oxygen gradients, which ultimately restricted the majority of phylotypes to distinct strata within the ice column. This study provides evidence that the microbial community over-winters in the ice column of Pony Lake and returns to a highly active metabolic state when spring melt is initiated.

FEMS Microbiology Ecology↗

Natural controls involved in shallow aquifer contamination

Shallow aquifers, commonly the most important sources of ground water, are also those most susceptible to contamination . The mode of entry of contaminants to shallow aquifers is (1) directly, via wells or secondary openings in consolidated rocks, (2) percolation through the zone of aeration, (3) induced infiltration through the zone of saturation, and (4) interaquifer leakage or flow through open holes. Natural removal or degradation of contaminants is by filtration, dispersion, sorption, ion exchange, oxidation, and various biochemical processes. These phenomena are controlled by the physical environment, structure; mineralogy, and hydraulic characteristics of the earth materials contacted by the liquid wastes. When liquid wastes enter an aquifer directly, there is little or no natural treatment by filtration, sorption, or oxidation. Purification is only by those processes that operate within the aquifer under anaerobic conditions. Contaminants from natural sources that enter aquifers under saturated‐flow conditions are degraded primarily by dilution. The natural processes effective in reducing contamination from surface‐water sources depend on the hydraulic regimen involved , which vary with individual cases. Liquid wastes percolating through the zone of aeration are those most likely to be purified by natural environment processes. Natural processes, however, do not effectively remove or degrade all contaminants, especially some of the many highly stable compounds that have gained widespread use in recent years, such as synthetic detergents. Comprehensive interdisciplinary research into the ability of various earth materials to remove many types of contaminants under varying hydrologic conditions is needed.

Groundwater↗

Chemical changes in an industrial waste liquid during post-injection movement in a limestone aquifer, Pensacola, Florida

An industrial waste liquid containing organonitrile compounds and nitrate ion has been injected into the lower limestone of the Floridan aquifer near Pensacola, Florida since June 1975. Chemical analyses of water from monitor wells and backflow from the injection well indicate that organic carbon compounds are converted to CO 2 and nitrate is converted to N 2 . These transformations are caused by bacteria immediately after injection, and are virtually completed within 100 m of the injection well. The zone near the injection well behaves like an anaerobic filter with nitrate respiring bacteria dominating the microbial flora in this zone. Sodium thiocyanate contained in the waste is unaltered during passage through the injection zone and is used to detect the degree of mixing of injected waste liquid with native water at a monitor well 312 m (712 ft) from the injection well. The dispersivity of the injection zone was calculated to be 10 m (33 ft). Analyses of samples from the monitor well indicate 80 percent reduction in chemical oxygen demand and virtually complete loss of organonitriles and nitrate from the waste liquid during passage from the injection well to the monitor well. Bacterial densities were much lower at the monitor well than in backflow from the injection well.

Florida↗

Dichlorobenzene in ground water: Evidence for long-term persistence

Hydrologic and geochemical evidence were used to establish the long-term persistence of dichlorobenzene in ground water that has been contaminated from 50 years of rapid-infiltration sewage disposal. An extensive plume of dichlorobenzene extends more than 3,500 meters downgradient from the disposal beds, with concentrations of the combined isomers ranging from less than 0.01 to over 1.0 ??g/l. Based on estimates of maximum ground-water flow velocities, a minimum age of 20 years was established for the farthest downgradient zone of dichlorobenzene contamination. Branched-chained, alkylbenzenesulfonic acid surfactants, that were introduced into the ground water prior to 1966, occur along with dichlorobenzene in the downgradient part of the plume, further establish residence of the compounds in the aquifer for at least 20 years. Although dichlorobenzene can be biologically degraded under aerobic conditions, its persistence at this field site is attributed to the dynamics of the ground-water system. Denitrifying conditions, resulting from the degradation of organic compounds in the aquifer near the disposal beds, appear to have enhanced the persistence of dichlorobenzene, which is not degraded by anaerobic bacteria. Biological degradation of dichlorobenzene in the aerobic part of the plume downgradient from the source is probably limited by the paucity of a suitable organic-carbon substrate and the low concentrations of dissolved oxygen in the contaminated ground water.

Ground Water↗

Influence of environmental factors on denitrification in sediment contaminated with JP-4 jet fuel

In 1975, the loss of approximately 83,000 gallons of JP-4 grade jet fuel resulted in contamination of the shallow aquifer near North Charleston, South Carolina. To identify those factors likely to influence microbial activity under denitrifying conditions, we examined the fate of amended NO 3 , the effect of pH, NO 3 , and PO 4 on denitrification, and the variability of denitrification in sediments collected at the site. Denitrification (N 2 O-N production) accounted for 98% of the depletion of NO 3 -N under anaerobic conditions. Both carbon mineralization and denitrification rates increased asymptotically with increasing NO 3 to a maximum at approximately 1 mM NO 3 . Addition of up to 1 mM PO 4 did not significantly increase N 2 O and CO 2 production. Denitrification rates were at least 38% lower at p H = 4 than observed at p H = 7. Comparison of samples with differing degrees of hydrocarbon contamination indicated that at least a tenfold variation in sediment denitrification occurs at the North Charleston site.

Groundwater↗

Ground water age and nitrate distribution within a glacial aquifer beneath a thick unsaturated zone

The impact on ground water quality from increasing fertilizer application rates over the past 40 years is evaluated within a glacial aquifer system beneath a thick unsaturated zone. Ground water ages within the aquifer could not be accurately determined from the measured distribution of 3 H and as a result, chlorofluorocarbon (CFC) and 3 H/ 3 He dating techniques were applied. Beneath a 25 m thick unsaturated zone, ground water ages based on CFC‐11 concentrations were greater than 3 H/ 3 He ground water ages by 6 to 10 years, due to the time lag associated with the diffusion of CFCs through the unsaturated zone. Using the corrected CFC‐11 and 3 H/ 3 He ground water ages and the estimated travel time of 3H within the unsaturated zone, the approximate position of ground water recharged since the mid‐1960s was determined. Nitrate concentrations within post mid‐1960s recharge were generally elevated and near or above the drinking water limit of 10 mg‐N/L. In comparison, pre mid‐1960s recharge had nitrate concentrations <2.5 mg‐N/L. The elevated NO 3 − concentrations in post mid‐1960s recharge are attributed mainly to increasing fertilizer application rates between 1970 and the mid‐ to late 1980s. Anaerobic conditions suitable for denitrifkation are present within pre mid‐1960s recharge indicating that removal of DO is a slow process taking tens of years. Over the next 10 to 20 years, nitrate concentrations at municipal well fields that are currently capturing aerobic ground water recharged near the mid‐1960s are expected to increase because of the higher fertilizer application rates beginning in the 1970s and 1980s.

Groundwater↗

Crude oil at the Bemidji Site: 25 years of monitoring, modeling, and understanding

The fate of hydrocarbons in the subsurface near Bemidji, Minnesota, has been investigated by a multidisciplinary group of scientists for over a quarter century. Research at Bemidji has involved extensive investigations of multiphase flow and transport, volatilization, dissolution, geochemical interactions, microbial populations, and biodegradation with the goal of providing an improved understanding of the natural processes limiting the extent of hydrocarbon contamination. A considerable volume of oil remains in the subsurface today despite 30 years of natural attenuation and 5 years of pump‐and‐skim remediation. Studies at Bemidji were among the first to document the importance of anaerobic biodegradation processes for hydrocarbon removal and remediation by natural attenuation. Spatial variability of hydraulic properties was observed to influence subsurface oil and water flow, vapor diffusion, and the progression of biodegradation. Pore‐scale capillary pressure‐saturation hysteresis and the presence of fine‐grained sediments impeded oil flow, causing entrapment and relatively large residual oil saturations. Hydrocarbon attenuation and plume extent was a function of groundwater flow, compound‐specific volatilization, dissolution and biodegradation rates, and availability of electron acceptors. Simulation of hydrocarbon fate and transport affirmed concepts developed from field observations, and provided estimates of field‐scale reaction rates and hydrocarbon mass balance. Long‐term field studies at Bemidji have illustrated that the fate of hydrocarbons evolves with time, and a snap‐shot study of a hydrocarbon plume may not provide information that is of relevance to the long‐term behavior of the plume during natural attenuation.

Minnesota↗

Fate of MTBE relative to benzene in a gasoline-contaminated aquifer (1993-98):

Methyl tert -butyl ether (MTBE) and benzene have been measured since 1993 in a shallow, sandy aquifer contaminated by a mid-1980s release of gasoline containing fuel oxygenates. In wells downgradient of the release area, MTBK was detected before benzene, reflecting a chromatographic-like separation of these compounds in the direction of ground water flow. Higher concentrations of MTBE and benzene were measured in the deeper sampling ports of multilevel sampling wells located near the release area, and also up to 10 feet (3 m) below the water table surface in nested wells located farther from the release area. This distribution of higher concentrations at depth is caused by recharge events that deflect originally horizontal ground water flowlines. In the laboratory, microcosms containing aquifer material incubated with uniformly labeled 14 C-MTBE under aerobic and anaerobic. Fe(III)-reducing conditions indicated a low but measurable biodegradation potential (<3% 14 C-MTBW as 14 CO 2 ) after a seven-month incubation period, Tert -butyl alcohol (TBA), a proposed microbial-MTBE transformation intermediate, was detected in MTBE-contaminated wells, but TBA was also measured in unsaturated release area sediments. This suggests that TBA may have been present in the original fuel spilled and does not necessarily reflect microbial degradation of MTBE. Combined, these data suggest that milligram per liter to microgram per liter decreases in MTBE concentrations relative to benzene are caused by the natural attenuation processes of dilution and dispersion with less-contaminated ground water in the direction of flow rather than biodegradation at this point source gasoline release site.

Groundwater Monitoring & Remediation↗

Influence of dissolved oxygen convection on well sampling

Convective transport of dissolved oxygen (D.O.) from shallow to deeper parts of wells was observed as the shallow water in wells in South Carolina became cooler than the deeper water in the wells due to seasonal changes. Wells having a relatively small depth to water were more susceptible to thermally induced convection than wells where the depth to water was greater because the shallower water levels were more influenced by air temperature. The potential for convective transport of D.O. to maintain oxygenated conditions in a well screened in an anaerobic aquifer was diminished as ground water exchange through the well screen increased and as oxygen demand increased. Transport of D.O. to the screened interval can adversely affect the ability of passive samplers to produce accurate concentrations of oxygen-sensitive solutes such as iron, other redox indicators, and microbiological data. A comparison of passive sampling to low-flow sampling in a well undergoing convection, however, showed general agreement of volatile organic compound concentrations. During low-flow sampling, the pumped water may be a mixture of convecting water from within the well casing and aquifer water moving inward through the screen. This mixing of water during low-flow sampling can substantially increase equilibration times, can cause false stabilization of indicator parameters, can give false indications of the redox state, and can provide microbiological data that are not representative of the aquifer conditions. Data from this investigation show that simple in-well devices can effectively mitigate convective transport of oxygen. The devices can range from inflatable packers to simple, inexpensive baffle systems. ?? 2007 National Ground Water Association.

Ground Water Monitoring and Remediation↗

Oxygen and iron isotope studies of magnetite produced by magnetotactic bacteria

A series of carefully controlled laboratory studies was carried out to investigate oxygen and iron isotope fractionation during the intracellular production of magnetite (Fe3O4) by two different species of magnetotactic bacteria at temperatures between 4??and 35??C under microaerobic and anaerobic conditions. No detectable fractionation of iron isotopes in the bacterial magnetites was observed. However, oxygen isotope measurements indicated a temperature-dependent fractionation for Fe3O4 and water that is consistent with that observed for Fe3O4 produced extracellularly by thermophilic Fe3+-reducing bacteria. These results contrast with established fractionation curves estimated from either high-temperature experiments or theoretical calculations. With the fractionation curve established in this report, oxygen-18 isotope values of bacterial Fe3O4 may be useful in paleoenvironmental studies for determining the oxygen-18 isotope values of formation waters and for inferring paleotemperatures.

Science↗

Dissimilatory reduction of selenate and arsenate in nature

This chapter discusses the biogeochemical reduction of selenate (Se(VI)) and arsenate (As(V)) when they enter anoxic environments and are used as electron acceptors for the oxidation of organic matter. These reductions are of a dissimilative nature and support the anaerobic growth of selected bacteria which conserve energy from this process. The chapter summarizes what is known about the bacteria's taxonomy, physiology, and biochemistry. Reduction to the solid, relatively unreactive Se(0) represents a mechanism for the removal of toxic Se(VI) and Se(IV) from natural waters. The environmental ramifications of these issues are also discussed in the chapter. The number of bacterial species known to respire selenate and arsenate continues to increase. The biological reduction of selenate and arsenate occurs for a number of reasons. In general, these are assimilation, regulation of reducing equivalents, detoxification, and dissimilation. Each is discussed in detail in the chapter. The realization that arsenate and selenate are indeed suitable electron acceptors and are readily available in both natural and contaminated environments suggests that even more unrelated species will be discovered. The initial biochemical studies also suggest that there may be different pathways for selenate and arsenate reduction, with specific terminal reductases and cytochromes.

Book chapter↗