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Thomas R. Kulp

Publications and source records attributed to Thomas R. Kulp.

11 recordsLinked to original sources

Arsenic accumulation in Sonora Mud Turtles (Kinosternon sonoriense) in an unusual freshwater food web

Montezuma Well is an unusual fishless, spring-fed, desert wetland in central Arizona. Water in the wetland is naturally enriched with > 100 µg/l dissolved geogenic arsenic (As) and supports a simple aquatic food web dominated by a small number of endemic invertebrate species that achieve high abundances. Previous studies of As among various environmental compartments and organisms in Montezuma Well did not include omnivorous Sonora Mud turtles ( Kinosternon sonoriense ) despite their potential importance in the As cycle by virtue of their substantial biomass and role as top predators. We measured As concentrations in water, sediment, and organisms (macrophytes, amphipods, insects, leeches, and turtles) representing a range of trophic levels in order to document the importance of turtles at the apex of the Montezuma Well food web and in the As cycle. Concentrations of As in turtles varied according to tissue type. The greatest values (up to 26.77 mg/kg dry weight) were in the scutes of 1 of our oldest turtles (31.5 yrs). These elevated concentrations may be due to the affinity of As to react with sulfur in the keratin of scutes, and therefore might reflect duration of exposure in long-lived turtles. Although As concentrations generally tend to decrease when moving up to higher trophic levels in a food web, our results were different. Relatively elevated concentrations reported in sediments by us and a previous study declined in plant samples as expected. Amphipod concentrations increased but then decreased again in 3 of their invertebrate predators. Arsenic concentrations in endemic leeches were extremely elevated with a mean value of 72.2 mg/kg. The mean concentration of As in turtles was 7.08 mg/kg across tissue types and was greater than the plants or invertebrates they eat, with the notable exception of leeches, which have been proposed to be part of their diet.

Arizona

Microbial antimony biogeochemistry: Enzymes, regulation, and related metabolic pathways

Antimony (Sb) is a toxic metalloid that occurs widely at trace concentrations in soil, aquatic systems, and the atmosphere. Nowadays, with the development of its new industrial applications and the corresponding expansion of antimony mining activities, the phenomenon of antimony pollution has become an increasingly serious concern. In recent years, research interest in Sb has been growing and reflects a fundamental scientific concern regarding Sb in the environment. In this review, we summarize the recent research on bacterial antimony transformations, especially those regarding antimony uptake, efflux, antimonite oxidation, and antimonate reduction. We conclude that our current understanding of antimony biochemistry and biogeochemistry is roughly equivalent to where that of arsenic was some 20 years ago. This portends the possibility of future discoveries with regard to the ability of microorganisms to conserve energy for their growth from antimony redox reactions and the isolation of new species of “antimonotrophs.”

Applied and Environmental Microbiology

Bioaccumulation trends of arsenic and antimony in a freshwater ecosystem affected by mine drainage

We compared As and Sb bioaccumulation and biomagnification when these metalloids co-occurred at varying environmental concentrations in a stream and wetlands near a contaminated mine site in Idaho (USA). We measured As and Sb concentrations in water and substrate samples, and in tissues of organisms representing several trophic levels. Bioaccumulation of both As and Sb was observed in stream organisms with the following trend of bio-diminution with increasing trophic level: primary producers > tadpoles > macroinvertebrates > trout. We also note reductions in metalloid concentrations in one of two stream remediation reaches engineered within the past 17 years to ameliorate metalloid contamination in the stream. Several wetlands contained thick microbial mats and were highly populated with boreal toad tadpoles that fed on them. The mats were extremely contaminated (up to 76 564 mg kg –1 As and 675 mg kg –1 Sb) with amorphous As- and Sb-bearing minerals that we interpret as biogenic precipitates from geomicrobiological As- and Sb-cycling. Ingested mat material provided a direct source of metalloids to tadpoles, and concentrations of 3867 mg kg –1 (As) and 375 mg kg –1 (Sb) reported here represent the highest whole body As and Sb levels ever reported in living tadpoles. The bulk of tadpole metalloid burden remained in the gut despite attempts to purge the tadpoles prior to analysis. This study adds to a number of recent investigations reporting bioaccumulation, but not biomagnification, of As and Sb in food webs. Moreover, our results suggest that tadpoles, in particular, may be more resistant to metalloid contamination than previously assumed.

Environmental Chemistry

Microbiological oxidation of antimony(III) with oxygen or nitrate by bacteria isolated from contaminated mine sediments

Bacterial oxidation of arsenite [As(III)] is a well-studied and important biogeochemical pathway that directly influences the mobility and toxicity of arsenic in the environment. In contrast, little is known about microbiological oxidation of the chemically similar anion antimonite [Sb(III)]. In this study, two bacterial strains, designated IDSBO-1 and IDSBO-4, which grow on tartrate compounds and oxidize Sb(III) using either oxygen or nitrate, respectively, as a terminal electron acceptor, were isolated from contaminated mine sediments. Both isolates belonged to the Comamonadaceae family and were 99% similar to previously described species. We identify these novel strains as Hydrogenophaga taeniospiralis strain IDSBO-1 and Variovorax paradoxus strain IDSBO-4. Both strains possess a gene with homology to the aioA gene, which encodes an As(III)-oxidase, and both oxidize As(III) aerobically, but only IDSBO-4 oxidized Sb(III) in the presence of air, while strain IDSBO-1 could achieve this via nitrate respiration. Our results suggest that expression of aioA is not induced by Sb(III) but may be involved in Sb(III) oxidation along with an Sb(III)-specific pathway. Phylogenetic analysis of proteins encoded by the aioA genes revealed a close sequence similarity (90%) among the two isolates and other known As(III)-oxidizing bacteria, particularly Acidovorax sp. strain NO1. Both isolates were capable of chemolithoautotrophic growth using As(III) as a primary electron donor, and strain IDSBO-4 exhibited incorporation of radiolabeled [ 14 C]bicarbonate while oxidizing Sb(III) from Sb(III)-tartrate, suggesting possible Sb(III)-dependent autotrophy. Enrichment cultures produced the Sb(V) oxide mineral mopungite and lesser amounts of Sb(III)-bearing senarmontite as precipitates.

Idaho

Microbiological reduction of Sb(V) in anoxic freshwater sediments

Microbiological reduction of millimolar concentrations of Sb(V) to Sb(III) was observed in anoxic sediments from two freshwater settings: (1) a Sb- and As-contaminated mine site (Stibnite Mine) in central Idaho and 2) an uncontaminated suburban lake (Searsville Lake) in the San Francisco Bay Area. Rates of Sb(V) reduction in anoxic sediment microcosms and enrichment cultures were enhanced by amendment with lactate or acetate as electron donors but not by H2, and no reduction occurred in sterilized controls. Addition of 2- 14 C-acetate to Stibnite Mine microcosms resulted in the production of 14 CO 2 coupled to Sb(V) reduction, suggesting that this process proceeds by a dissimilatory respiratory pathway in those sediments. Antimony(V) reduction in Searsville Lake sediments was not coupled to acetate mineralization and may be associated with Sb-resistance. The microcosms and enrichment cultures also reduced sulfate, and the precipitation of insoluble Sb(III)-sulfide complexes was a major sink for reduced Sb. The reduction of Sb(V) by Stibnite Mine sediments was inhibited by As(V), suggesting that As(V) is a preferred electron acceptor for the indigenous community. These findings indicate a novel pathway for anaerobic microbiological respiration and suggest that communities capable of reducing high concentrations of Sb(V) commonly occur naturally in the environment.

Environmental Science & Technology

Desulfohalophilus alkaliarsenatis gen. nov., sp. nov., an extremely halophilic sulfate- and arsenate-respiring bacterium from Searles Lake, California

A haloalkaliphilic sulfate-respiring bacterium, strain SLSR-1, was isolated from a lactate-fed stable enrichment culture originally obtained from the extreme environment of Searles Lake, California. The isolate proved capable of growth via sulfate-reduction over a broad range of salinities (125–330 g/L), although growth was slowest at salt-saturation. Strain SLSR-1 was also capable of growth via dissimilatory arsenate-reduction and displayed an even broader range of salinity tolerance (50–330 g/L) when grown under these conditions. Strain SLSR-1 could also grow via dissimilatory nitrate reduction to ammonia. Growth experiments in the presence of high borate concentrations indicated a greater sensitivity of sulfate-reduction than arsenate-respiration to this naturally abundant anion in Searles Lake. Strain SLSR-1 contained genes involved in both sulfate-reduction ( dsrAB ) and arsenate respiration ( arrA ). Amplicons of 16S rRNA gene sequences obtained from DNA extracted from Searles Lake sediment revealed the presence of close relatives of strain SLSR-1 as part of the flora of this ecosystem despite the fact that sulfate-reduction activity could not be detected in situ. We conclude that strain SLSR-1 can only achieve growth via arsenate-reduction under the current chemical conditions prevalent at Searles Lake. Strain SLSR-1 is a deltaproteobacterium in the family Desulfohalobiacea of anaerobic, haloalkaliphilic bacteria, for which we propose the name Desulfohalophilus alkaliarsenatis gen. nov., sp. nov.

California

Response to comments on "A bacterium that can grow using arsenic instead of phosphorus"

Concerns have been raised about our recent study suggesting that arsenic (As) substitutes for phosphorus in major biomolecules of a bacterium that tolerates extreme As concentrations. We welcome the opportunity to better explain our methods and results and to consider alternative interpretations. We maintain that our interpretation of As substitution, based on multiple congruent lines of evidence, is viable.

Science

Coupled arsenotrophy in a hot spring photosynthetic biofilm at Mono Lake, California

Red-pigmented biofilms grow on rock and cobble surfaces present in anoxic hot springs located on Paoha Island in Mono Lake. The bacterial community was dominated (∼ 85% of 16S rRNA gene clones) by sequences from the photosynthetic Ectothiorhodospira genus. Scraped biofilm materials incubated under anoxic conditions rapidly oxidized As(III) to As(V) in the light via anoxygenic photosynthesis but could also readily reduce As(V) to As(III) in the dark at comparable rates. Back-labeling experiments with 73 As(V) demonstrated that reduction to 73 As(III) also occurred in the light, thereby illustrating the cooccurrence of these two anaerobic processes as an example of closely coupled arsenotrophy. Oxic biofilms also oxidized As(III) to As(V). Biofilms incubated with [ 14 C]acetate oxidized the radiolabel to 14 CO 2 in the light but not the dark, indicating a capacity for photoheterotrophy but not chemoheterotrophy. Anoxic, dark-incubated samples demonstrated As(V) reduction linked to additions of hydrogen or sulfide but not acetate. Chemoautotrophy linked to As(V) as measured by dark fixation of [ 14 C]bicarbonate into cell material was stimulated by either H 2 or HS − . Functional genes for the arsenate respiratory reductase ( arrA ) and arsenic resistance ( arsB ) were detected in sequenced amplicons of extracted DNA, with about half of the arrA sequences closely related (∼98% translated amino acid identity) to those from the family Ectothiorhodospiraceae . Surprisingly, no authentic PCR products for arsenite oxidase ( aoxB ) were obtained, despite observing aerobic arsenite oxidation activity. Collectively, these results demonstrate close linkages of these arsenic redox processes occurring within these biofilms. Oxyanions of the group 15 element arsenic, arsenate [As(V)] and arsenite [As(III)], have been known for millennia to be potent poisons. Despite its well-established toxicity to life, the phenomenon of arsenic resistance was discovered whereby some microorganisms maintain an otherwise “normal” existence in the presence of high concentrations of As(V) or As(III) (17, 29, 31). More recently it has become recognized that certain representatives from the bacterial and archaeal domains can actually exploit the electrochemical potential of the As(V)/As(III) redox couple (+130 mV) to gain energy for growth. This can be achieved either by employing As(III) as an autotrophic electron donor or by using As(V) as a respiratory electron acceptor (18, 21, 34). The latter phenomenon, although most commonly associated with chemoheterotrophy, can also employ inorganic substances like sulfide or H 2 . Indeed, As(V)-respiring anaerobes displaying a capacity for chemoautotrophy with these electron donors have been isolated and described (5, 7, 16). We recently reported that photoautotrophy is supported by As(III) in anoxic biofilms located in hot springs on Paoha Island in Mono Lake, CA (15). This process represented a novel means of As(III) oxidation achieved via anoxygenic photosynthesis occurring in certain photosynthetic bacteria (i.e., Ectothiorhodospira ) and possibly within some cyanobacteria as well (e.g., “ Oscillatoria ”). Whether or not a microbial habitat is overtly oxic or anoxic, or temporally shifts between these two states over a diel cycle, critical energy linkages between aerobes and anaerobes have long been known for the biogeochemical cycles of key elements, such as sulfur, iron, and nitrogen. Most prominently studied is the case of nitrogen, whereby an ecological coupling exists between the processes of nitrification and denitrification (9, 10, 28). The former process provides energy to aerobic nitrifiers, while the latter process consumes the nitrate produced by this reaction, thereby meeting the energy needs of the denitrifiers. For arsenic, the detection of both As(III) oxidation and As(V) reduction in oxic and anoxic incubations of freshly collected periphyton suggested that an analogous coupled process may also occur for this element (12). Similarly, several uncontaminated soils in Japan displayed a capacity for either As(V) reduction or As(III) oxidation upon arsenic oxyanion amendment and whether they were incubated under oxic or anoxic conditions (39). A defined coculture consisting of an aerobic As(III) oxidizer (strain OL1) and an anaerobic As(V) respirer (strain Y5) was shown to function in this fashion under manipulated laboratory conditions of oxygen tension (26). We pursued the phenomenon of coupled arsenic metabolism further by using materials collected from the hot spring biofilms in Mono Lake, but we focused on examination of the cycling of arsenic under anoxic conditions. In this paper we report results obtained by manipulated incubations of red-pigmented biofilms found in the hot springs of Paoha Island. Preliminary community characterizations of these biofilms show that they are dominated by B acteria from the genus Ectothiorhodospira but also harbor an assemblage of Archaea related to the Halobacteriacaea . Incubation results have demonstrated the presence of the following arsenic metabolic activities: respiratory As(V) reduction, photosynthetic anaerobic As(III) oxidation, and aerobic As(III) oxidation, along with the ecophysiological conditions under which they occur. Surprisingly, we were unable to obtain authentic PCR products for arsenite oxidase genes ( aoxB ), despite observing aerobic As(III) oxidation activity. These biofilms serve as a model system for how anaerobic cycling of arsenic can be sustained with oxidation of As(III) by anoxygenic photosynthesis coupled to regeneration of this electron donor via dissimilatory As(V) reduction. The significance that such a light-driven anaerobic ecosystem may have played in the Archean Earth is discussed.

California

Source, Distribution, and Management of Arsenic in Water from Wells, Eastern San Joaquin Ground-Water Subbasin, California

Between 1974 and 2001 water from as many as one-third of wells in the Eastern San Joaquin Ground Water Subbasin, about 80 miles east of San Francisco, had arsenic concentrations greater than the U.S. Environmental Protection Agency Maximum Contaminant Level (MCL) for arsenic of 10 micrograms per liter (ug/L). Water from some wells had arsenic concentrations greater than 60 ug/L. The sources of arsenic in the study area include (1) weathering of arsenic bearing minerals, (2) desorption of arsenic associated with iron and manganese oxide coatings on the surfaces of mineral grains at pH's greater than 7.6, and (3) release of arsenic through reductive dissolution of iron and manganese oxide coatings in the absence of oxygen. Reductive dissolution is responsible for arsenic concentrations greater than the MCL. The distribution of arsenic varied areally and with depth. Concentrations were lower near ground-water recharge areas along the foothills of the Sierra Nevada; whereas, concentrations were higher in deeper wells at the downgradient end of long flow paths near the margin of the San Joaquin Delta (fig. 1). Management opportunities to control high arsenic concentrations are present because water from the surface discharge of wells is a mixture of water from the different depths penetrated by wells. On the basis of well-bore flow and depth-dependent water-quality data collected as part of this study, the screened interval of a public-supply well having arsenic concentrations that occasionally exceed the MCL was modified to reduce arsenic concentrations in the surface discharge of the well. Arsenic concentrations from the modified well were about 7 ug/L. Simulations of ground-water flow to the well showed that although upward movement of high-arsenic water from depth within the aquifer occurred, arsenic concentrations from the well are expected to remain below the MCL.

Open-File Report

Dissimilatory arsenate reduction with sulfide as the electron donor--Experiments with Mono Lake water and isolation of strain MLMS-1, a chemoautotrophic arsenate-respirer

Anoxic bottom water from Mono Lake, California, can biologically reduce added arsenate without any addition of electron donors. Of the possible in situ inorganic electron donors present, only sulfide was sufficiently abundant to drive this reaction. We tested the ability of sulfide to serve as an electron donor for arsenate reduction in experiments with lake water. Reduction of arsenate to arsenite occurred simultaneously with the removal of sulfide. No loss of sulfide occurred in controls without arsenate or in sterilized samples containing both arsenate and sulfide. The rate of arsenate reduction in lake water was dependent on the amount of available arsenate. We enriched for a bacterium that could achieve growth with sulfide and arsenate in a defined, mineral medium and purified it by serial dilution. The isolate, strain MLMS-1, is a gram-negative, motile curved rod that grows by oxidizing sulfide to sulfate while reducing arsenate to arsenite. Chemoautotrophy was confirmed by the incorporation of H 14 CO 3 − into dark-incubated cells, but preliminary gene probing tests with primers for ribulose-1,5-biphosphate carboxylase/oxygenase did not yield PCR-amplified products. Alignment of 16S rRNA sequences indicated that strain MLMS-1 was in the δ- Proteobacteria , located near sulfate reducers like Desulfobulbus sp. (88 to 90% similarity) but more closely related (97%) to unidentified sequences amplified previously from Mono Lake. However, strain MLMS-1 does not grow with sulfate as its electron acceptor.

California