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Ronald S. Oremland

Publications and source records attributed to Ronald S. Oremland.

At least 37 records · Page 2Linked to original sources
USGS2016

Functional metagenomic selection of RubisCOs from uncultivated bacteria

Ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) is a critical yet severely inefficient enzyme that catalyses the fixation of virtually all of the carbon found on Earth. Here, we report a functional metagenomic selection that recovers physiologically active RubisCO molecules directly from uncultivated and largely unknown members of natural microbial communities. Selection is based on CO 2 -dependent growth in a host strain capable of expressing environmental deoxyribonucleic acid (DNA), precluding the need for pure cultures or screening of recombinant clones for enzymatic activity. Seventeen functional RubisCO-encoded sequences were selected using DNA extracted from soil and river autotrophic enrichments, a photosynthetic biofilm and a subsurface groundwater aquifer. Notably, three related form II RubisCOs were recovered which share high sequence similarity with metagenomic scaffolds from uncultivated members of the G allionellaceae family. One of the G allionellaceae RubisCOs was purified and shown to possess CO 2 /O 2 specificity typical of form II enzymes. X-ray crystallography determined that this enzyme is a hexamer, only the second form II multimer ever solved and the first RubisCO structure obtained from an uncultivated bacterium. Functional metagenomic selection leverages natural biological diversity and billions of years of evolution inherent in environmental communities, providing a new window into the discovery of CO 2 -fixing enzymes not previously characterized.

Environmental Microbiology↗
USGS2016

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↗
USGS2016

Genome sequence of the photoarsenotrophic bacterium Ectothiorhodospira sp. strain BSL-9, isolated from a hypersaline alkaline arsenic-rich extreme environment

The full genome sequence of Ectothiorhodospira sp. strain BSL-9 is reported here. This purple sulfur bacterium encodes an arxA -type arsenite oxidase within the arxB2AB1CD gene island and is capable of carrying out “photoarsenotrophy” anoxygenic photosynthetic arsenite oxidation. Its genome is composed of 3.5 Mb and has approximately 63% G+C content.

Genome Announcements↗
USGS2015

Methane oxidation and molecular characterization of methanotrophs from a former mercury mine impoundment

The Herman Pit, once a mercury mine, is an impoundment located in an active geothermal area. Its acidic waters are permeated by hundreds of gas seeps. One seep was sampled and found to be composed of mostly CO 2 with some CH 4 present. The δ 13 CH 4 value suggested a complex origin for the methane: i.e. , a thermogenic component plus a biological methanogenic portion. The relatively 12 C-enriched CO 2 suggested a reworking of the ebullitive methane by methanotrophic bacteria. Therefore, we tested bottom sediments for their ability to consume methane by conducting aerobic incubations of slurried materials. Methane was removed from the headspace of live slurries, and subsequent additions of methane resulted in faster removal rates. This activity could be transferred to an artificial, acidic medium, indicating the presence of acidophilic or acid-tolerant methanotrophs, the latter reinforced by the observation of maximum activity at pH = 4.5 with incubated slurries. A successful extraction of sterol and hopanoid lipids characteristic of methanotrophs was achieved, and their abundances greatly increased with increased sediment methane consumption. DNA extracted from methane-oxidizing enrichment cultures was amplified and sequenced for pmoA genes that aligned with methanotrophic members of the Gammaproteobacteria . An enrichment culture was established that grew in an acidic (pH 4.5) medium via methane oxidation.

California↗
USGS2015

Anaerobic chemolithotrophic growth of the haloalkaliphilic bacterium strain MLMS‑1 by disproportionation of monothioarsenate

A novel chemolithotrophic metabolism based on a mixed arsenic−sulfur species has been discovered for the anaerobic deltaproteobacterium, strain MLMS-1, a haloalkaliphile isolated from Mono Lake, California, U.S. Strain MLMS‑1 is the first reported obligate arsenate-respiring chemoautotroph which grows by coupling arsenate reduction to arsenite with the oxidation of sulfide to sulfate. In that pathway the formation of a mixed arsenic−sulfur species was reported. That species was assumed to be monothioarsenite ([H2AsIIIS−IIO2] −), formed as an intermediate by abiotic reaction of arsenite with sulfide. We now report that this species is monothioarsenate ([HAsVS−IIO3] 2−) as revealed by X-ray absorption spectroscopy. Monothioarsenate forms by abiotic reaction of arsenite with zerovalent sulfur. Monothioarsenate is kinetically stable under a wide range of pH and redox conditions. However, it was metabolized rapidly by strain MLMS-1 when incubated with arsenate. Incubations using monothioarsenate confirmed that strain MLMS-1 was able to grow (μ = 0.017 h−1 ) on this substrate via a disproportionation reaction by oxidizing the thio-group-sulfur (S−II) to zerovalent sulfur or sulfate while concurrently reducing the central arsenic atom (AsV) to arsenite. Monothioarsenate disproportionation could be widespread in nature beyond the already studied arsenic and sulfide rich hot springs and soda lakes where it was discovered.

Environmental Science & Technology↗
USGS2015

Characterization of the extremely arsenic-resistant Brevibacterium linens strain AE038-8 isolated from contaminated groundwater in Tucumán, Argentina

Brevibacterium linens AE038-8, isolated from As-contaminated groundwater in Tucumán (Argentina), is highly resistant to arsenic oxyanions, being able to tolerate up to 1 M As(V) and 75 mM As(III) in a complex medium. Strain AE038-8 was also able to reduce As(V) to As(III) when grown in complex medium but paradoxically it could not do this in a defined minimal medium with sodium acetate and ammonium sulfate as carbon and nitrogen sources, respectively. No oxidation of As(III) to As(V) was observed under any conditions. Three copies of the ars operon comprising arsenic resistance genes were found on B. linens AE038-8 genome. In addition to the well known arsC , ACR3 and arsR , two copies of the arsO gene of unknown function were detected.

Tucumán↗
USGS2015

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↗
USGS2015

Geomicrobial interactions with arsenic and antimony

Although arsenic and antimony are generally toxic to life, some microorganisms exist that can metabolize certain forms of these elements. Some can use arsenite or stibnite as potential or sole energy sources, whereas others can use aresenate and antimonite (as was discovered only recently) as terminal electron acceptors. Still other microbes can metabolize arsenic and antimony compounds to detoxify them. These reactions are important from a geomicrobial standpoint because they indicate that a number of microbes contribute to arsenic and antimony mobilization or immobilization in the environment and play a role in arsenic and antimony cycles. Recent reviews include five on prokaryotes and arsenic metabolism, a review with an arsenic perspective on biomining, and a series on environmental antimony, including one about antimony and its interaction with microbiota.

Book chapter↗
USGS2014

Methane oxidation linked to chlorite dismutation

We examined the potential for CH 4 oxidation to be coupled with oxygen derived from the dissimilatory reduction of perchlorate, chlorate, or via chlorite (ClO − 2 ) dismutation. Although dissimilatory reduction of ClO − 4 and ClO − 3 could be inferred from the accumulation of chloride ions either in spent media or in soil slurries prepared from exposed freshwater lake sediment, neither of these oxyanions evoked methane oxidation when added to either anaerobic mixed cultures or soil enriched in methanotrophs. In contrast, ClO − 2 amendment elicited such activity. Methane (0.2 kPa) was completely removed within several days from the headspace of cell suspensions of Dechloromonas agitata CKB incubated with either Methylococcus capsulatus Bath or Methylomicrobium album BG8 in the presence of 5 mM ClO − 2 . We also observed complete removal of 0.2 kPa CH 4 in bottles containing soil enriched in methanotrophs when co-incubated with D. agitata CKB and 10 mM ClO − 2 . However, to be effective these experiments required physical separation of soil from D. agitata CKB to allow for the partitioning of O 2 liberated from chlorite dismutation into the shared headspace. Although a link between ClO − 2 and CH 4 consumption was established in soils and cultures, no upstream connection with either ClO − 4 or ClO − 3 was discerned. This result suggests that the release of O 2 during enzymatic perchlorate reduction was negligible, and that the oxygen produced was unavailable to the aerobic methanotrophs.

Frontiers in Microbiology↗
USGS2013

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↗
USGS2013

A biogeochemical and genetic survey of acetylene fermentation by environmental samples and bacterial isolates

Anoxic samples (sediment and groundwater) from 13 chemically diverse field sites were assayed for their ability to consume acetylene (C 2 H 2 ). Over incubation periods ranging from ˜ 10 to 80 days, selected samples from 7 of the 13 tested sites displayed significant C2H2 removal. No significant formation of ethylene was noted in these incubations; therefore, C 2 H 2 consumption could be attributed to acetylene hydratase (AH) rather than nitrogenase activity. This putative AH (PAH) activity was observed in only 21% of the total of assayed samples, while amplification of AH genes from extracted DNA using degenerate primers derived from Pelobacter acetylenicus occurred in even fewer (9.8%) samples. Acetylene-fermenting bacteria were isolated as a pure culture from the sediments of a tidal mudflat in San Francisco Bay (SFB93) and as an enrichment culture from freshwater Searsville Lake (SV7). Comparison of 16S rDNA clone libraries revealed that SFB93 was closely related to P. carbolinicus, while SV7 consisted of several unrelated bacteria. AH gene was amplified from SFB93 but not SV7. The inability of the primers to generate amplicons in the SV7 enrichment, as well as from several of the environmental samples that displayed PAH activity, implied that either the primers were too highly constrained in their specificity or that there was a different type of AH gene in these environmental samples than occurs in P. acetylenicus. The significance of this work with regard to the search for life in the outer Solar System, where C 2 HL 2 is abundant, is discussed.

Geomicrobiology Journal↗
USGS2012

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↗
USGS2012

ArxA, a new clade of arsenite oxidase within the DMSO reductase family of molybdenum oxidoreductases

Arsenotrophy, growth coupled to autotrophic arsenite oxidation or arsenate respiratory reduction, occurs only in the prokaryotic domain of life. The enzymes responsible for arsenotrophy belong to distinct clades within the DMSO reductase family of molybdenum-containing oxidoreductases: specifically arsenate respiratory reductase, ArrA, and arsenite oxidase, AioA (formerly referred to as AroA and AoxB). A new arsenite oxidase clade, ArxA, represented by the haloalkaliphilic bacterium Alkalilimnicola ehrlichii strain MLHE-1 was also identified in the photosynthetic purple sulfur bacterium Ectothiorhodospira sp. strain PHS-1. A draft genome sequence of PHS-1 was completed and an arx operon similar to MLHE-1 was identified. Gene expression studies showed that arx A was strongly induced with arsenite. Microbial ecology investigation led to the identification of additional arx A-like sequences in Mono Lake and Hot Creek sediments, both arsenic-rich environments in California. Phylogenetic analyses placed these sequences as distinct members of the ArxA clade of arsenite oxidases. ArxA-like sequences were also identified in metagenome sequences of several alkaline microbial mat environments of Yellowstone National Park hot springs. These results suggest that ArxA-type arsenite oxidases appear to be widely distributed in the environment presenting an opportunity for further investigations of the contribution of Arx-dependent arsenotrophy to the arsenic biogeochemical cycle.

Environmental Microbiology↗
USGS2012

Anaerobic oxidation of arsenite by autotrophic bacteria: The view from Mono Lake, California

Introduction The phenomenon of arsenite [As(III)] oxidation by aerobic bacteria was first reported by Green (1918), and the many subsequent discoveries made in this realm, most occurring over the past three decades, are the primary focus of this book. In contrast, the fact that select anaerobes can also achieve this feat was an entirely serendipitous discovery. As often occurs in science, the intended path leading towards a stated goal can take an unexpected turn, ultimately leading to greater rewards than those originally anticipated. The intellectual freedom to meander such a path of curiosity-driven research is a great gift especially when one arrives at an unexpected revelation. It is perhaps the most rewarding aspect of a scientist's career. Such was the case when we first uncovered the phenomenon of anaerobic As(III) oxidation. Our arsenic-related field work focused on Mono Lake, California because of its exceptionally high levels of dissolved inorganic arsenic (~200 μM), and the fact that we had previously isolated two novel species of arsenate [As(V)]-respiring bacteria, Bacillus arseniciselenatis and B. selenitireducens from its bottom sediments(Switzer Blum et al. , 1998). Radiotracer investigations employing 73 As(V) measured high As(V) reductase activity in the anoxic water column of the lake, yielding an estimate that this electron sink could mineralize approximately 8-14% of annual phytoplankton productivity (Oremland et al. , 2000), a value confirmed independently on the basis of mass balance considerations (Hollibaugh et al. , 2005). In both studies both groups also used cultivation-based methods (Most-Probable-Numbers) to estimate the densities of As(V)-respiring bacteria in the anoxic water column, and arrived at similar low but detectable values (e.g. 10 2 -10 3 ml -1 ). The next goal was to determine what taxa of As(V)-respiring prokaryotes were involved in these water-column transformations, using culture-independent analyses (Denaturing Gradient Gel Electrophoresis) of As(V)-amended anoxic bottom water. We had expected to find 16S rRNA gene amplicon sequences similar to those from the bacilli we isolated from the sediments, but instead found a few rather unremarkable amplicons in the Epsilon, Gamma and Delta proteobacteria; yet these incubations showed a complete reduction of the added As(V), caused by sulfide-linked oxidation by resident chemoautotrophs of the Delta-proteobacteria (Hoeft et al. , 2004; Hollibaugh et al. , 2006). This As(V) reductase activity was inhibited by nitrate, while addition of As(III) to nitrate-amended waters resulted in the formation of As(V). This observation led us to conclude that there was anaerobic biological oxidation of As(III) to As(V), linked to the provided nitrate ions (Hoeft et al. , 2002).

California↗
USGS2011

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↗
USGS2011

Nanoparticles formed from bacterial oxyanion reduction of toxic Group 15 and 16 metalloids

This chapter presents some examples of nanoparticles formed by only a few microbial species that are cultivated in only a handful of laboratories worldwide. The investigations so far have just scratched the surface of the potential of the natural world to yield bionanomineral producers. While future research should involve screening surveys of the prokaryotes for this biomineralizing phenomenon, more detailed investigations are justified. The chapter discusses microbial Interaction with Group 15 and 16 Toxic Metalloids. The toxicity of the metalloids Se, Te, and As is due to the disruption of thiol intracellular biochemistry through the formation of stable, long-lived sulfur complexes. Selenium oxyanion reduction occurs in a wide range of microbes, including representatives of the Wolinella , Pseudomonas , Sulfurospirillum , Enterobacter , Thaurea , Bacillus , Shewanella , and Citrobacter genera. Technological applications of Se(0) and Te(0) nanoparticles include their use in photocopiers, microelectronic circuits, and solar cells as a result of their photo-optical and semiconducting physical properties. Nonetheless, once novel Se, Te, and As bionanoparticles are identified as having significant technical applications, applied research into their practical commercial production will without doubt ensue rapidly.

Book chapter↗