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At least 307 records · Page 17Linked to original sources

USGS2011

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°17'N, 32°16.3'W, depth 1600-1750m) and the ultramafic-hosted Rainbow (36°13'N, 33°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↗

USGS2008

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↗

USGS2011

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↗

USGS2006

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↗

USGS2006

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↗

USGS2006

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↗

USGS2009

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↗

USGS2007

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↗

USGS2007

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↗

USGS1999

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↗

USGS2014

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↗

USGS2008

Subsurface microbial diversity in deep-granitic-fracture water in Colorado

A microbial community analysis using 16S rRNA gene sequencing was performed on borehole water and a granite rock core from Henderson Mine, a >1,000-meter-deep molybdenum mine near Empire, CO. Chemical analysis of borehole water at two separate depths (1,044 m and 1,004 m below the mine entrance) suggests that a sharp chemical gradient exists, likely from the mixing of two distinct subsurface fluids, one metal rich and one relatively dilute; this has created unique niches for microorganisms. The microbial community analyzed from filtered, oxic borehole water indicated an abundance of sequences from iron-oxidizing bacteria ( Gallionella spp.) and was compared to the community from the same borehole after 2 weeks of being plugged with an expandable packer. Statistical analyses with UniFrac revealed a significant shift in community structure following the addition of the packer. Phospholipid fatty acid (PLFA) analysis suggested that Nitrosomonadales dominated the oxic borehole, while PLFAs indicative of anaerobic bacteria were most abundant in the samples from the plugged borehole. Microbial sequences were represented primarily by Firmicutes , Proteobacteria , and a lineage of sequences which did not group with any identified bacterial division; phylogenetic analyses confirmed the presence of a novel candidate division. This “Henderson candidate division” dominated the clone libraries from the dilute anoxic fluids. Sequences obtained from the granitic rock core (1,740 m below the surface) were represented by the divisions Proteobacteria (primarily the family Ralstoniaceae ) and Firmicutes . Sequences grouping within Ralstoniaceae were also found in the clone libraries from metal-rich fluids yet were absent in more dilute fluids. Lineage-specific comparisons, combined with phylogenetic statistical analyses, show that geochemical variance has an important effect on microbial community structure in deep, subsurface systems.

Applied and Environmental Microbiology↗

USGS2025

Comparative assessment of a restored and natural wetland using 13C-DNA SIP reveals a higher potential for methane production in the restored wetland

Wetlands are the largest natural source of methane (CH 4 ), a potent greenhouse gas produced by methanogens. Methanogenesis rates are controlled by environmental factors such as redox potential, temperature, and carbon and electron acceptor availability and are presumably dependent on the composition of the active methanogen community. We collected intact soil cores from a restored and natural freshwater depressional wetland on Maryland’s Delmarva Peninsula (USA) to assess the effects of wetland restoration and redox shifts on microbial processes. Intact soil cores were incubated under either saturated (anoxic) or unsaturated (oxic) conditions and amended with 13 C-acetate for quantitative stable isotope probing (qSIP) of the 16S rRNA gene. Restored wetland cores supported a distinct community of methanogens compared to natural cores, and acetoclastic methanogens putatively identified in the genus Methanosarcina were among the most abundant taxa in restored anoxic and oxic cores. The active microbial communities in the restored wetland cores were also distinguished by the unique presence of facultatively anaerobic bacteria belonging to the orders Firmicutes and Bacteroidetes . In natural wetland incubations, methanogen populations were not among the most abundant taxa, and these communities were instead distinguished by the unique presence of aerobic bacteria in the phyla Acidobacteria , Actinobacteria , and class Alphaproteobacteria . Iron-reducing bacteria, in the genus Geobacter , were active across all redox conditions in both the restored and the natural cores, except the natural oxic–anoxic condition. These findings suggest an overall higher potential for methanogenesis in the restored wetland site compared to the natural wetland site, even when there is evidence of Fe reduction.

Maryland↗

USGS2009

Ecophysiology of "halarsenatibacter silvermanii" strain SLAS-1 T , gen. nov., sp. nov., a facultative chemoautotrophic arsenate respirer from salt-saturated Searles Lake, California

Searles Lake occupies a closed basin harboring salt-saturated, alkaline brines that have exceptionally high concentrations of arsenic oxyanions. Strain SLAS-1 T was previously isolated from Searles Lake (R. S. Oremland, T. R. Kulp, J. Switzer Blum, S. E. Hoeft, S. Baesman, L. G. Miller, and J. F. Stolz, Science 308:1305-1308, 2005). We now describe this extremophile with regard to its substrate affinities, its unusual mode of motility, sequenced arrABD gene cluster, cell envelope lipids, and its phylogenetic alignment within the order Halanaero-bacteriales, assigning it the name "Halarsenatibacter silvermanii" strain SLAS-1 T . We also report on the substrate dynamics of an anaerobic enrichment culture obtained from Searles Lake that grows under conditions of salt saturation and whose members include a novel sulfate reducer of the order Desulfovibriales, the archaeon Halorhabdus utahensis, as well as a close homolog of strain SLAS-1 T . Copyright ?? 2009, American Society for Microbiology. All Rights Reserved.

Applied and Environmental Microbiology↗

USGS2015

Large fractions of CO 2 -fixing microorganisms in pristine limestone aquifers appear to be involved in the oxidation of reduced sulfur and nitrogen compounds

The traditional view of the dependency of subsurface environments on surface-derived allochthonous carbon inputs is challenged by increasing evidence for the role of lithoautotrophy in aquifer carbon flow. We linked information on autotrophy (Calvin-Benson-Bassham cycle) with that from total microbial community analysis in groundwater at two superimposed—upper and lower—limestone groundwater reservoirs (aquifers). Quantitative PCR revealed that up to 17% of the microbial population had the genetic potential to fix CO 2 via the Calvin cycle, with abundances of cbbM and cbbL genes, encoding RubisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) forms I and II, ranging from 1.14 × 10 3 to 6 × 10 6 genes liter −1 over a 2-year period. The structure of the active microbial communities based on 16S rRNA transcripts differed between the two aquifers, with a larger fraction of heterotrophic, facultative anaerobic, soil-related groups in the oxygen-deficient upper aquifer. Most identified CO 2 -assimilating phylogenetic groups appeared to be involved in the oxidation of sulfur or nitrogen compounds and harbored both RubisCO forms I and II, allowing efficient CO 2 fixation in environments with strong oxygen and CO 2 fluctuations. The genera Sulfuricella and Nitrosomonas were represented by read fractions of up to 78 and 33%, respectively, within the cbbM and cbbL transcript pool and accounted for 5.6 and 3.8% of 16S rRNA sequence reads, respectively, in the lower aquifer. Our results indicate that a large fraction of bacteria in pristine limestone aquifers has the genetic potential for autotrophic CO 2 fixation, with energy most likely provided by the oxidation of reduced sulfur and nitrogen compounds.

Applied and Environmental Microbiology↗

USGS1981

Microbial formation of ethane in anoxic estuarine sediments

Estuarine sediment slurries produced methane and traces of ethane when incubated under hydrogen. Formation of methane occurred over a broad temperature range with an optimum above 65°C. Ethane formation had a temperature optimum at 40°C. Formation of these two gases was inhibited by air, autoclaving, incubation at 4 and 80°C, and by the methanogenic inhibitor, 2-bromoethanesulfonic acid. Ethane production was stimulated by addition of ethylthioethanesulfonic acid, and production from ethylthioethanesulfonic acid was blocked by 2-bromoethanesulfonic acid. A highly purified enrichment culture of a methanogenic bacterium obtained from sediments produced traces of ethane from ethylthioethanesulfonic acid. These results indicate that the small quantities of ethane found in anaerobic sediments can be formed by certain methanogenic bacteria.

Applied and Environmental Microbiology↗

USGS1986

Formation of methane and carbon dioxide from dimethylselenide in anoxic sediments and by a methanogenic bacterium

Anaerobic San Francisco Bay salt marsh sediments rapidly metabolized [ 14 C]dimethylselenide (DMSe) to 14 CH 4 and 14 CO 2 . Addition of selective inhibitors (2-bromoethanesulfonic acid or molybdate) to these sediments indicated that both methanogenic and sulfate-respiring bacteria could degrade DMSe to gaseous products. However, sediments taken from the selenium-contaminated Kesterson Wildlife Refuge produced only 14 CO 2 from [ 14 C]DMSe, implying that methanogens were not important in the Kesterson samples. A pure culture of a dimethylsulfide (DMS)-grown methylotrophic methanogen converted [ 14 C]DMSe to 14 CH 4 and 14 CO 2 . However, the organism could not grow on DMSe. Addition of DMS to either sediments or the pure culture retarded the metabolism of DMSe. This effect appeared to be caused by competitive inhibition, thereby indicating a common enzyme system for DMS and DMSe metabolism. DMSe appears to be degraded as part of the DMS pool present in anoxic environments. These results suggest that methylotrophic methanogens may demethylate methylated forms of other metals and metalloids found in nature.

California↗

USGS1988

Microbial hydroxylation of quinoline in contaminated groundwater: evidence for incorporation of the oxygen atom of water.

Studies conducted in an aquifer contaminated by creosote suggest that quinoline is converted to 2(1H)quinolinone by an indigenous consortium of microorganisms. Laboratory microbial experiments using H 2 18 O indicate that water is the source of the oxygen atom for this hydroxylation reaction under aerobic and anaerobic conditions.

Applied and Environmental Microbiology↗