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L.G. Miller

Publications and source records attributed to L.G. Miller.

At least 19 recordsLinked to original sources
USGS2008

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

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.

Extremophiles↗
USGS2008

Arsenic(III) fuels anoxygenic photosynthesis in hot spring biofilms from Mono Lake, California

Phylogenetic analysis indicates that microbial arsenic metabolism is ancient and probably extends back to the primordial Earth. In microbial biofilms growing on the rock surfaces of anoxic brine pools fed by hot springs containing arsenite and sulfide at high concentrations, we discovered light-dependent oxidation of arsenite [As(III)] to arsenate [As(V)] occurring under anoxic conditions. The communities were composed primarily of Ectothiorhodospira-like purple bacteria or Oscillatoria-like cyanobacteria. A pure culture of a photosynthetic bacterium grew as a photoautotroph when As(III) was used as the sole photosynthetic electron donor. The strain contained genes encoding a putative As(V) reductase but no detectable homologs of the As(III) oxidase genes of aerobic chemolithotrophs, suggesting a reverse functionality for the reductase. Production of As(V) by anoxygenic photosynthesis probably opened niches for primordial Earth's first As(V)-respiring prokaryotes.

Science↗
USGS2006

Dissimilatory arsenate and sulfate reduction in sediments of two hypersaline, arsenic-rich soda lakes: Mono and Searles Lakes, California

A radioisotope method was devised to study bacterial respiratory reduction of arsenate in sediments. The following two arsenic-rich soda lakes in California were chosen for comparison on the basis of their different salinities: Mono Lake (∼90 g/liter) and Searles Lake (∼340 g/liter). Profiles of arsenate reduction and sulfate reduction were constructed for both lakes. Reduction of [ 73 As]arsenate occurred at all depth intervals in the cores from Mono Lake (rate constant [ k ] = 0.103 to 0.04 h −1 ) and Searles Lake ( k = 0.012 to 0.002 h −1 ), and the highest activities occurred in the top sections of each core. In contrast, [ 35 S]sulfate reduction was measurable in Mono Lake ( k = 7.6 ×10 4 to 3.2 × 10 −6 h −1 ) but not in Searles Lake. Sediment DNA was extracted, PCR amplified, and separated by denaturing gradient gel electrophoresis (DGGE) to obtain phylogenetic markers (i.e., 16S rRNA genes) and a partial functional gene for dissimilatory arsenate reduction ( arrA ). The amplified arrA gene product showed a similar trend in both lakes; the signal was strongest in surface sediments and decreased to undetectable levels deeper in the sediments. More arrA gene signal was observed in Mono Lake and was detectable at a greater depth, despite the higher arsenate reduction activity observed in Searles Lake. A partial sequence (about 900 bp) was obtained for a clone (SLAS-3) that matched the dominant DGGE band found in deeper parts of the Searles Lake sample (below 3 cm), and this clone was found to be closely related to SLAS-1, a novel extremophilic arsenate respirer previously cultivated from Searles Lake.

Applied and Environmental Microbiology↗
USGS2005

Laboratory determination of the carbon kinetic isotope effects (KIEs) for reactions of methyl halides with various nucleophiles in solution

Large carbon kinetic isotope effects (KIEs) were measured for reactions of methyl bromide (MeBr), methyl chloride (MeCl), and methyl iodide (MeI) with various nucleophiles at 287 and 306 K in aqueous solutions. Rates of reaction of MeBr and MeI with H 2 O (neutral hydrolysis) or Cl − (halide substitution) were consistent with previous measurements. Hydrolysis rates increased with increasing temperature or pH (base hydrolysis). KIEs for hydrolysis were 51 ± 6% 0 for MeBr and 38 ± 8% 0 for MeI. Rates of halide substitution increased with increasing temperature and greater reactivity of the attacking nucleophile, with the fastest reaction being that of MeI with Br − . KIEs for halide substitution were independent of temperature but varied with the reactant methyl halide and the attacking nucleophile. KIEs were similar for MeBr substitution with Cl − and MeCl substitution with Br − (57 ± 5 and 60 ± 9% 0 , respectively). The KIE for halide exchange of MeI was lower overall (33 ± 8% 0 ) and was greater for substitution with Br − (46 ± 6% 0 ) than with Cl − (29 ± 6% 0 ).

Journal of Atmospheric Chemistry↗
USGS2005

Aminobacter ciceronei sp. nov. and Aminobacter lissarensis sp. nov., isolated from various terrestrial environments

The bacterial strains IMB-1 T and CC495 T , which are capable of growth on methyl chloride (CH 3 Cl, chloromethane) and methyl bromide (CH 3 Br, bromomethane), were isolated from agricultural soil in California fumigated with CH 3 Br, and woodland soil in Northern Ireland, respectively. Two pesticide-/herbicide-degrading bacteria, strains ER2 and C147, were isolated from agricultural soil in Canada. Strain ER2 degrades N -methyl carbamate insecticides, and strain C147 degrades triazine herbicides widely used in agriculture. On the basis of their morphological, physiological and genotypic characteristics, these four strains are considered to represent two novel species of the genus Aminobacter , for which the names Aminobacter ciceronei sp. nov. (type strain IMB-1 T =ATCC 202197 T =CIP 108660 T =CCUG 50580 T ; strains ER2 and C147) and Aminobacter lissarensis sp. nov. (type strain CC495 T =NCIMB 13798 T =CIP 108661 T =CCUG 50579 T ) are proposed.

International Journal of Systematic and Evolutiona↗
USGS2005

Microbiology: A microbial arsenic cycle in a salt-saturated, extreme environment

Searles Lake is a salt-saturated, alkaline brine unusually rich in the toxic element arsenic. Arsenic speciation changed from arsenate [As(V)] to arsenite [As(III)] with sediment depth. Incubated anoxic sediment slurries displayed dissimilatory As(V)-reductase activity that was markedly stimulated by H2 or sulfide, whereas aerobic slurries had rapid As(III)-oxidase activity. An anaerobic, extremely haloalkaliphilic bacterium was isolated from the sediment that grew via As(V) respiration, using either lactate or sulfide as its electron donor. Hence, a full biogeochemical cycle of arsenic occurs in Searles Lake, driven in part by inorganic electron donors.

Science↗
USGS2004

Degradation of methyl bromide and methyl chloride in soil microcosms: Use of stable C isotope fractionation and stable isotope probing to identify reactions and the responsible microorganisms

Bacteria in soil microcosm experiments oxidized elevated levels of methyl chloride (MeCl) and methyl bromide (MeBr), the former compound more rapidly than the latter. MeBr was also removed by chemical reactions while MeCl was not. Chemical degradation dominated the early removal of MeBr and accounted for more than half of its total loss. Fractionation of stable carbon isotopes during chemical degradation of MeBr resulted in a kinetic isotope effect (KIE) of 59 ± 7‰. Soil bacterial oxidation dominated the later removal of MeBr and MeCl and was characterized by different KIEs for each compound. The KIE for MeBr oxidation was 69 ± 9‰ and the KIE for MeCl oxidation was 49 ± 3‰. Stable isotope probing revealed that different populations of soil bacteria assimilated added 13 C-labeled MeBr and MeCl. The identity of the active MeBr and MeCl degrading bacteria in soil was determined by analysis of 16S rRNA gene sequences amplified from 13 C-DNA fractions, which identified a number of sequences from organisms not previously thought to be involved in methyl halide degradation. These included Burkholderia , the major clone type in the 13 C-MeBr fraction, and Rhodobacter, Lysobacter and Nocardioides the major clone types in the 13 C-MeCl fraction. None of the 16S rRNA gene sequences for methyl halide oxidizing bacteria currently in culture (including Aminobacter strain IMB-1 isolated from fumigated soil) were identified. Functional gene clone types closely related to Aminobacter spp. were identified in libraries containing the sequences for the cmuA gene, which codes for the enzyme known to catalyze the initial step in the oxidation of MeBr and MeCl. The cmuA gene was limited to members of the alpha-Proteobacteria whereas the greater diversity demonstrated by the 16S rRNA gene may indicate that other enzymes catalyze methyl halide oxidation in different groups of bacteria.

Geochimica et Cosmochimica Acta↗
USGS2002

Carbon isotope fractionation of methyl bromide during agricultural soil fumigations

The isotopic composition of methyl bromide (CH3Br) has been suggested to be a potentially useful tracer for constraining the global CH3Br budget. In order to determine the carbon isotopic composition of CH3Br emitted from the most significant anthropogenic application (pre-plant fumigation) we directly measured the ??13C of CH3Br released during commercial fumigation. We also measured the isotopic fractionation associated with degradation in agricultural soil under typical field fumigation conditions. The isotopic composition of CH3Br collected in soil several hours after injection of the fumigant was -44.5??? and this value increased to -20.7??? over the following three days. The mean kinetic isotope effect (KIE) associated with degradation of CH3Br in agricultural soil (12???) was smaller than the reported value for methylotrophic bacterial strain IMB-1, isolated from previously fumigated agricultural soil, but was similar to methylotrophic bacterial strain CC495, isolated from a pristine forest litter zone. Using this fractionation associated with the degradation of CH3Br in agricultural soil and the mean ??13C of the industrially manufactured CH3Br (-54.4???), we calculate that the agricultural soil fumigation source has a carbon isotope signature that ranges from -52.8??? to -42.0???. Roughly 65% of industrially manufactured CH3Br is used for field fumigations. The remaining 35% is used for structural and post-harvest fumigations with a minor amount used during industrial chemical manufacturing. Assuming that the structural and post-harvest fumigation sources of CH3Br are emitted without substantial fractionation, we calculate that the ??13C of anthropogenically emitted CH3Br ranges from -53.2??? to -47.5???.

Conference Paper↗
USGS2001

Large carbon isotope fractionation associated with oxidation of methyl halides by methylotrophic bacteria

The largest biological fractionations of stable carbon isotopes observed in nature occur during production of methane by methanogenic archaea. These fractionations result in substantial (as much as ≈70‰) shifts in δ 13 C relative to the initial substrate. We now report that a stable carbon isotopic fractionation of comparable magnitude (up to 70‰) occurs during oxidation of methyl halides by methylotrophic bacteria. We have demonstrated biological fractionation with whole cells of three methylotrophs (strain IMB-1, strain CC495, and strain MB2) and, to a lesser extent, with the purified cobalamin-dependent methyltransferase enzyme obtained from strain CC495. Thus, the genetic similarities recently reported between methylotrophs, and methanogens with respect to their pathways for C 1 -unit metabolism are also reflected in the carbon isotopic fractionations achieved by these organisms. We found that only part of the observed fractionation of carbon isotopes could be accounted for by the activity of the corrinoid methyltransferase enzyme, suggesting fractionation by enzymes further along the degradation pathway. These observations are of potential biogeochemical significance in the application of stable carbon isotope ratios to constrain the tropospheric budgets for the ozone-depleting halocarbons, methyl bromide and methyl chloride. Methyl bromide (MeBr) and methyl chloride (MeCl) are, respectively, the most abundant volatile bromo- and chlorocarbons in the troposphere and are major contributors to stratospheric ozone destruction (1). Both compounds have natural and human-influenced sources and a predominant sink by reaction with OH in the troposphere (2–4). MeBr also has a bacterial soil sink (5) that represents about 20% of the estimated total removal from the troposphere, and it is likely that a soil sink of similar magnitude exists for MeCl (6). Hence, if an isotopic fractionation is associated with the soil sink, it will influence the isotopic compositions of MeBr and MeCl in the lower atmosphere (7). The δ 13 C value of industrially produced MeBr ranges between −43.5‰ and −66.4‰ (7), but δ 13 C values of tropospheric MeBr and natural sources are not yet known. The δ 13 C of atmospheric MeCl has been measured from −22‰ to −45‰ (8, 9). If carbon isotope ratios are to be used to constrain the budgets of these methyl halides, it is essential to determine the extent of carbon isotope fractionation that occurs during biological degradation of these compounds. Methylotrophic bacteria use C 1 compounds, which are simple organic molecules that contain no carbon–carbon bonds. Strains IMB-1, CC495, and MB2 are as-yet-unnamed facultative methylotrophs isolated from agricultural soil, woodland leaf litter, and coastal seawater, respectively (10–13), environments where methyl halides are produced. They are members of the α subgroup of the Proteobacteria . On the basis of 16S rRNA gene sequences, strains IMB-1 and CC495 show some phylogenetic alignment with the genus Rhizobium (10, 11) and are very closely related to the new genus Pseudoaminobacte r (I. McDonald, personal communication). Strain MB2 aligns within the Ruegeria clade [J. K. Schaefer, K. D. Goodwin, I. R. McDonald, J. C. Murrell and R.S.O., unpublished work]. All of these aerobic bacteria are methylotrophs in that they can grow by using MeBr or MeCl as their sole carbon source, but they do not metabolize methane. They oxidize MeBr, MeCl, and methyl iodide (MeI) to CO 2 . Soil bacteria are known to consume MeBr at the ambient tropospheric mixing ratio of around 10 parts per trillion by volume (5). Preliminary experiments with strain IMB-1 indicate that it can oxidize MeBr at these mixing ratios** and is therefore likely to be characteristic of bacteria associated with MeBr uptake by soils. We examined δ 13 C of MeCl, MeBr, and MeI during oxidation by whole-cell suspensions of IMB-1 and CC495 and also the change in δ 13 C values of the three methyl halides during oxidation by the marine strain MB2. In addition, we measured the fractionation of carbon isotopes during formation of methane thiol (MeSH) from MeCl by the purified cobalamin-dependent enzyme, halomethane:bisulphide/halide ion methyltransferase (11) from CC495, to determine whether this initial step in MeCl degradation could account for the observed fractionation by whole cells. Finally, we determined the fractionation associated with the degradation of MeBr during field studies with agricultural soil by monitoring MeBr concentration and δ 13 C of MeBr in the headspace of flux chambers under fumigation conditions.

Proceedings of the National Academy of Sciences of↗
USGS2000

Bacterial dissimilatory reduction of arsenate and sulfate in meromictic Mono Lake, California

The stratified (meromictic) water column of alkaline and hypersaline Mono Lake, California, contains high concentrations of dissolved inorganic arsenic (~200 ??mol/L). Arsenic speciation changes from arsenate [As (V)] to arsenite [As (III)] with the transition from oxic surface waters (misolimnion) to anoxic bottom waters (monimolimnion). A radioassay was devised to measure the reduction of 73As (V) to 73As (III) and tested using cell suspensions of the As (V)-respiring Bacillus selenitireducens, which completely reduced the 73As (V). In field experiments, no significant activity was noted in the aerobic mixolimnion waters, but reduction of 73As (V) to 73As (III) was observed in all the monimolimnion samples. Rate constants ranged from 0.02 to 0.3/day, with the highest values in the samples from the deepest depths (24 and 28 m). The highest activities occurred between 18 and 21 m, where As (V) abundant (rate, ~5.9 ??mol/L per day). In contrast, sulfate reduction occurred at depths below 21 m, with the highest rates attained at 28 m (rate, ~2.3 ??mol/L per day). These results indicate that As (V) ranks second in importance, after sulfate, as an electron acceptor for anaerobic bacterial respiration in the water column. Annual arsenate respiration may mineralize as much as 14.2% of the pelagic photosynthetic carbon fixed during meromixis. When combined with sulfate-reduction data, anaerobic respiration in the water column can mineralize 32-55% of this primary production. As lakes of this type approach salt saturation, As (V) can become the most important electron acceptor for the biogeochemical cycling of carbon.

California↗
USGS1999

Oxidation of ammonia and methane in an alkaline, saline lake

The oxidation of ammonia (NH 3 ) and methane (CH 4 ) was investigated in an alkaline saline lake, Mono Lake, California (U.S.A.). Ammonia oxidation was examined in April and July 1995 by comparing dark 14 CO 2 fixation rates in the presence or absence of methyl fluoride (MeF), an inhibitor of NH 3 oxidation. Ammonia oxidizer‐mediated dark 14 CO 2 fixation rates were similar in surface (5–7 m) and oxycline (11–15 m) waters, ranging between 70–340 and 89–186 nM d −1 , respectively, or 1–7% of primary production by phytoplankton. Ammonia oxidation rates ranged between 580–2,830 nM d −1 in surface waters and 732–1,548 nM d −1 in oxycline waters. Methane oxidation was examined using a 14 CH 4 tracer technique in July 1994, April 1995, and July 1995. Methane oxidation rates were consistently higher in July, and rates in oxycline and anaerobic bottom waters (0.5–37 and 7–48 nM d −1 , respectively) were 10‐fold higher than those in aerobic surface waters (0.04–3.8 nM d −1 ). The majority of CH 4 oxidation, in terms of integrated activity, occurred within anoxic bottom waters. Water column oxidation reduced the potential lake‐atmosphere CH 4 flux by a factor of two to three. Measured oxidation rates and water column concentrations were used to estimate the biological turnover times of NH 3 and CH 4 . The NH 3 pool turns over rapidly, on time scales of 0.8 d in surface waters and 10 d within the oxycline, while CH 4 is cycled on 10 3 ‐d time scales in surface waters and 10 −2 time scales within oxycline and bottom waters. Our data suggest an important role for NH 3 oxidation in alkaline, saline lakes since the process converts volatile NH 3 to soluble NO 2 − , thereby reducing loss via lake‐atmosphere exchange and maintaining nitrogen in a form that is readily available to phyto‐plankton.

Limnology and Oceanography↗
USGS1998

Difluoromethane, a new and improved inhibitor of methanotrophy

Difluoromethane (HFC-32; DFM) is compared to acetylene and methyl fluoride as an inhibitor of methanotrophy in cultures and soils. DFM was found to be a reversible inhibitor of CH 4 oxidation by Methylococcus capsulatus (Bath). Consumption of CH 4 in soil was blocked by additions of low levels of DFM (0.03 kPa), and this inhibition was reversed by DFM removal. Although a small quantity of DFM was consumed during these incubations, its remaining concentration was sufficiently elevated to sustain inhibition. Methanogenesis in anaerobic soil slurries, including acetoclastic methanogenesis, was unaffected by levels of DFM which inhibit methanotrophy. Low levels of DFM (0.03 kPa) also inhibited nitrification and N 2 O production by soils. DFM is proposed as an improved inhibitor of CH 4 oxidation over acetylene and/or methyl fluoride on the basis of its reversibility, its efficacy at low concentrations, its lack of inhibition of methanogenesis, and its low cost.

Applied and Environmental Microbiology↗
USGS1997

Bacterial oxidation of methyl bromide in Mono Lake, California

The oxidation of methyl bromide (MeBr) in the water column of Mono Lake, CA, was studied by measuring the formation of H14CO3 from [14C]MeBr. Potential oxidation was detected throughout the water column, with highest rates occurring in the epilimnion (5-12 m depth). The oxidation of MeBr was eliminated by filter-sterilization, thereby demonstrating the involvement of bacteria. Vertical profiles of MeBr activity differed from those obtained for nitrification and methane oxidation, indicating that MeBr oxidation is not simply a co-oxidation process by either nitrifiers or methanotrophs. Furthermore, specific inhibitors of methane oxidation and/or nitrification (e.g., methyl fluoride, acetylene, allyl sulfide) had no effect upon the rate of MeBr oxidation in live samples. Of a variety of potential electron donors added to Mono Lake water, only trimethylamine resulted in the stimulation of MeBr oxidation. Cumulatively, these results suggest that the oxidation of MeBr in Mono Lake waters is attributable to trimethylamine-degrading methylotrophs. Neither methyl chloride nor methanol inhibited the oxidation of [14C]MeBr in live samples, indicating that these bacteria directly oxidized MeBr rather than the products of MeBr nucleophilic substitution reactions.

Environmental Science & Technology↗
USGS1997

Bacterial oxidation of methyl bromide in fumigated agricultural soils

The oxidation of [ 14 C]methyl bromide ([ 14 C]MeBr) to 14 CO 2 was measured in field experiments with soils collected from two strawberry plots fumigated with mixtures of MeBr and chloropicrin (CCl 3 NO 2 ). Although these fumigants are considered potent biocides, we found that the highest rates of MeBr oxidation occurred 1 to 2 days after injection when the fields were tarped, rather than before or several days after injection. No oxidation of MeBr occurred in heat-killed soils, indicating that microbes were the causative agents of the oxidation. Degradation of MeBr by chemical and/or biological processes accounted for 20 to 50% of the loss of MeBr during fumigation, with evasion to the atmosphere inferred to comprise the remainder. In laboratory incubations, complete removal of [ 14 C]MeBr occurred within a few days, with 47 to 67% of the added MeBr oxidized to 14 CO 2 and the remainder of counts associated with the solid phase. Chloropicrin inhibited the oxidation of MeBr, implying that use of this substance constrains the extent of microbial degradation of MeBr during fumigation. Oxidation was by direct bacterial attack of MeBr and not of methanol, a product of the chemical hydrolysis of MeBr. Neither nitrifying nor methane-oxidizing bacteria were sufficiently active in these soils to account for the observed oxidation of MeBr, nor could the microbial degradation of MeBr be linked to cooxidation with exogenously supplied electron donors. However, repeated addition of MeBr to live soils resulted in higher rates of its removal, suggesting that soil bacteria used MeBr as an electron donor for growth. To support this interpretation, we isolated a gram-negative, aerobic bacterium from these soils which grew with MeBr as a sole source of carbon and energy.

California↗
USGS1996

Effects of glacial meltwater inflows and moat freezing on mixing in an ice-covered antarctic lake as interpreted from stable isotope and tritium distributions

Perennially ice-covered lakes in the McMurdo Dry Valleys have risen several meters over the past two decades due to climatic warming and increased glacial meltwater inflow. To elucidate the hydrologic responses to changing climate and the effects on lake mixing processes we measured the stable isotope (??18O and ??D) and tritium concentrations of water and ice samples collected in the Lake Fryxell watershed from 1987 through 1990. Stable isotope enrichment resulted from evaporation in stream and moat samples and from sublimation in surface lake-ice samples. Tritium enrichment resulted from exchange with the postnuclear atmosphere in stream and moat samples. Rapid injection of tritiated water into the upper water column of the make and incorporation of this water into the ice cover resulted in uniformly elevated tritium contents (> 3.0 TU) in these reservoirs. Tritium was also present in deep water, suggesting that a component of bottom water was recently at the surface. During summer, melted lake ice and stream water forms the moat. Water excluded from ice formation during fall moat freezing (enriched in solutes and tritium, and depleted in 18O and 2H relative to water below 15-m depth) may sink as density currents to the bottom of the lake. Seasonal lake circulation, in response to climate-driven surface inflow, is therefore responsible for the distribution of both water isotopes and dissolved solutes in Lake Fryxell.

Limnology and Oceanography↗