Functional mononuclear molybdenum enzymes: challenges and triumphs in molecular cloning, expression, and isolation.

Mononuclear molybdenum enzymes catalyze a variety of reactions that are essential in the cycling of nitrogen, carbon, arsenic, and sulfur. For decades, the structure and function of these crucial enzymes have been investigated to develop a fundamental knowledge for this vast family of enzymes and the chemistries they carry out. Therefore, obtaining abundant quantities of active enzyme is necessary for exploring this family's biochemical capability. This mini-review summarizes the methods for overexpressing mononuclear molybdenum enzymes in the context of the challenges encountered in the process. Effective methods for molybdenum cofactor synthesis and incorporation, optimization of expression conditions, improving isolation of active vs. inactive enzyme, incorporation of additional prosthetic groups, and inclusion of redox enzyme maturation protein chaperones are discussed in relation to the current molybdenum enzyme literature. This article summarizes the heterologous and homologous expression studies providing underlying patterns and potential future directions.

Determining conventional and unconventional oil and gas well brines in natural samples III: mass ratio analyses using both anions and cations.

Identifying the types of contamination and their sources in surface and groundwater is fundamental for effective protection of private and public source waters. Here we employed mass ratio analyses of a variety of anion and cation pairs to characterize flowback, produced water, and mine drainage. These endmembers were used to evaluate the source contributions of natural surface and ground water samples. A total of 1,177 ground water and surface water samples were analyzed including high-quality source waters and waters suspected of being impacted by drilling and mining activity. We found the following chemical ratios resolved different sources of contamination: Mg/Na vs SO4/Cl; SO4/Cl vs Mg/Li; Br/SO4 vs Ba/Cl; and Br vs Mg/Li. While no single parameter or mass ratio pairing by itself was definitive it was possible to converge on a likely source of contamination using multiple lines of analytical evidence. Further, this process clarified sources in impacted samples where one or more parameters commonly considered diagnostic of specific sources (e.g., Br, Ba), were below detection limits (e.g., too dilute) or not tested for. Ultimately, movement of sample values within the mass ratio space allows tracking of changes in water quality and contamination source dynamics as the water chemistry evolves.

Determining conventional and unconventional oil and gas well brines in natural samples I: Anion analysis with ion chromatography.

Unconventional natural gas extraction by hydraulic fracturing requires millions of gallons of water and generates flowback water, produced water and recycled fluids of varying chemical composition. Ion chromatography (IC) is a relatively low cost and efficient means to determine the anionic composition, however, the wide range in anionic content of these fluids poses a challenge to analytical methods developed for "natural" waters. We report here that the combination of UV and conductivity detectors increased detection sensitivity (e.g., 10-50 ppb) and expanded the number of anions detectable in a single sample run. Samples from four unconventional shale gas wells, two impoundments, nine conventional oil wells, two freshwater streams and mine drainage samples were analyzed in this study. All produced water samples and impoundment samples had high chloride (17,500-103,000 mg L-1, 93,900 to 134,000 mg L-1, 27,700 and 30,700 mg L-1), bromide (178-996 mg L-1, 183-439 mg L-1, 230 and 260 mg L-1) and conductivity (38,500-160,000 µS/cm3, 95,300 to 183,000 µS/cm3, 61,500 and 103,000 µS/cm3), respectively, relative to mine drainage and freshwater stream samples. Molar ratio analysis using Cl-/Br- to Cl- and SO42-/Cl- to Br- revealed significant differences between the samples, providing a simple means for distinguishing water impacted by different sources of contamination.

Determining conventional and unconventional oil and gas well brines in natural sample II: Cation analyses with ICP-MS and ICP-OES.

Flowback and produced water generated by the hydraulic fracturing of unconventional oil and gas plays contain a suite of cations (e.g., metals) typically in a high salt (e.g., NaCl) matrix. Here, we analyzed the chemical (cation) composition of production fluids associated with natural gas and oil development (e.g., flowback, produced water, impoundment fluids), along with mine drainage, and surface and ground water samples using ICP-OES and ICP-MS. ICP-MS and ICP-OES analytical performance and interference effects were evaluated. Both platforms exhibited excellent analytical spike recoveries, detection limits for blank and spiked solutions, and accuracy for standard certified reference materials. Mass ratio analyses using Ca/Sr, Ca/Mg, Ba/Sr, Mg/Sr, and B and Li, were assessed for their efficacy in differentiation among brines from conventional oil wells, produced water from unconventional oil and gas wells and impoundments, mine drainage treatment pond water, groundwater, and surface water. Examination of Mg/Sr ratios when compared with Li concentrations provide clear separation among the different types of samples, while Ca/Mg versus Ca/Sr correlations were useful for distinguishing between conventional and unconventional oil and gas fluids.

Respiratory Selenite Reductase from Bacillus selenitireducens Strain MLS10.

The putative respiratory selenite [Se(IV)] reductase (Srr) from Bacillus selenitireducens MLS10 has been identified through a polyphasic approach involving genomics, proteomics, and enzymology. Nondenaturing gel assays were used to identify Srr in cell fractions, and the active band was shown to contain a single protein of 80 kDa. The protein was identified through liquid chromatography-tandem mass spectrometry (LC-MS/MS) as a homolog of the catalytic subunit of polysulfide reductase (PsrA). It was found to be encoded as part of an operon that contains six genes that we designated srrE, srrA, srrB, srrC, srrD, and srrF SrrA is the catalytic subunit (80 kDa), with a twin-arginine translocation (TAT) leader sequence indicative of a periplasmic protein and one putative 4Fe-4S binding site. SrrB is a small subunit (17 kDa) with four putative 4Fe-4S binding sites, SrrC (43 kDa) is an anchoring subunit, and SrrD (24 kDa) is a chaperon protein. Both SrrE (38 kDa) and SrrF (45 kDa) were annotated as rhodanese domain-containing proteins. Phylogenetic analysis revealed that SrrA belonged to the PsrA/PhsA clade but that it did not define a distinct subgroup, based on the putative homologs that were subsequently identified from other known selenite-respiring bacteria (e.g., Desulfurispirillum indicum and Pyrobaculum aerophilum). The enzyme appeared to be specific for Se(IV), showing no activity with selenate, arsenate, or thiosulfate, with a Km of 145 ± 53 µM, a Vmax of 23 ± 2.5 µM min-1, and a kcat of 23 ± 2.68 s-1 These results further our understanding of the mechanisms of selenium biotransformation and its biogeochemical cycle.IMPORTANCE Selenium is an essential element for life, with Se(IV) reduction a key step in its biogeochemical cycle. This report identifies for the first time a dissimilatory Se(IV) reductase, Srr, from a known selenite-respiring bacterium, the haloalkalophilic Bacillus selenitireducens strain MLS10. The work extends the versatility of the complex iron-sulfur molybdoenzyme (CISM) superfamily in electron transfer involving chalcogen substrates with different redox potentials. Further, it underscores the importance of biochemical and enzymological approaches in establishing the functionality of these enzymes.

Arsenic induces structural and compositional colonic microbiome change and promotes host nitrogen and amino acid metabolism.

Chronic exposure to arsenic in drinking water causes cancer and non-cancer diseases. However, mechanisms for chronic arsenic-induced pathogenesis, especially in response to lower exposure levels, are unclear. In addition, the importance of health impacts from xeniobiotic-promoted microbiome changes is just being realized and effects of arsenic on the microbiome with relation to disease promotion are unknown. To investigate impact of arsenic exposure on both microbiome and host metabolism, the stucture and composition of colonic microbiota, their metabolic phenotype, and host tissue and plasma metabolite levels were compared in mice exposed for 2, 5, or 10weeks to 0, 10 (low) or 250 (high) ppb arsenite (As(III)). Genotyping of colonic bacteria revealed time and arsenic concentration dependent shifts in community composition, particularly the Bacteroidetes and Firmicutes, relative to those seen in the time-matched controls. Arsenic-induced erosion of bacterial biofilms adjacent to the mucosal lining and changes in the diversity and abundance of morphologically distinct species indicated changes in microbial community structure. Bacterical spores increased in abundance and intracellular inclusions decreased with high dose arsenic. Interestingly, expression of arsenate reductase (arsA) and the As(III) exporter arsB, remained unchanged, while the dissimilatory nitrite reductase (nrfA) gene expression increased. In keeping with the change in nitrogen metabolism, colonic and liver nitrite and nitrate levels and ratios changed with time. In addition, there was a concomitant increase in pathogenic arginine metabolites in the mouse circulation. These data suggest that arsenic exposure impacts the microbiome and microbiome/host nitrogen metabolism to support disease enhancing pathogenic phenotypes.

Nitrate and periplasmic nitrate reductases.

The nitrate anion is a simple, abundant and relatively stable species, yet plays a significant role in global cycling of nitrogen, global climate change, and human health. Although it has been known for quite some time that nitrate is an important species environmentally, recent studies have identified potential medical applications. In this respect the nitrate anion remains an enigmatic species that promises to offer exciting science in years to come. Many bacteria readily reduce nitrate to nitrite via nitrate reductases. Classified into three distinct types--periplasmic nitrate reductase (Nap), respiratory nitrate reductase (Nar) and assimilatory nitrate reductase (Nas), they are defined by their cellular location, operon organization and active site structure. Of these, Nap proteins are the focus of this review. Despite similarities in the catalytic and spectroscopic properties Nap from different Proteobacteria are phylogenetically distinct. This review has two major sections: in the first section, nitrate in the nitrogen cycle and human health, taxonomy of nitrate reductases, assimilatory and dissimilatory nitrate reduction, cellular locations of nitrate reductases, structural and redox chemistry are discussed. The second section focuses on the features of periplasmic nitrate reductase where the catalytic subunit of the Nap and its kinetic properties, auxiliary Nap proteins, operon structure and phylogenetic relationships are discussed.

Current perspectives on unconventional shale gas extraction in the Appalachian Basin.

The Appalachian Basin is home to three major shales, the Upper Devonian, Marcellus, and Utica. Together, they contain significant quantities of tight oil, gas, and mixed hydrocarbons. The Marcellus alone is estimated to contain upwards of 500 trillion cubic feet of natural gas. The extraction of these deposits is facilitated by a combination of horizontal drilling and slick water stimulation (e.g., hydraulic fracturing) or "fracking." The process of fracking requires large volumes of water, proppant, and chemicals as well as a large well pad (3-7 acres) and an extensive network of gathering and transmission pipelines. Drilling can generate about 1,000 tons of drill cuttings depending on the depth of the formation and the length of the horizontal bore. The flowback and produced waters that return to the surface during production are high in total dissolved solids (TDS, 60,000-350,000 mg L(-1)) and contain halides (e.g., chloride, bromide, fluoride), strontium, barium, and often naturally occurring radioactive materials (NORMs) as well as organics. The condensate tanks used to store these fluids can off gas a plethora of volatile organic compounds. The waste water, with its high TDS may be recycled, treated, or disposed of through deep well injection. Where allowed, open impoundments used for recycling are a source of air borne contamination as they are often aerated. The gas may be "dry" (mostly methane) or "wet," the latter containing a mixture of light hydrocarbons and liquids that need to be separated from the methane. Although the wells can produce significant quantities of natural gas, from 2-7 bcf, their initial decline rates are significant (50-75%) and may cease to be economic within a few years. This review presents an overview of unconventional gas extraction highlighting the environmental impacts and challenges.

Scintillation gamma spectrometer for analysis of hydraulic fracturing waste products.

Flowback and produced wastewaters from unconventional hydraulic fracturing during oil and gas explorations typically brings to the surface Naturally Occurring Radioactive Materials (NORM), predominantly radioisotopes from the U238 and Th232 decay chains. Traditionally, radiological sampling are performed by sending collected small samples for laboratory tests either by radiochemical analysis or measurements by a high-resolution High-Purity Germanium (HPGe) gamma spectrometer. One of the main isotopes of concern is Ra226 which requires an extended 21-days quantification period to allow for full secular equilibrium to be established for the alpha counting of its progeny daughter Rn222. Field trials of a sodium iodide (NaI) scintillation detector offers a more economic solution for rapid screenings of radiological samples. To achieve the quantification accuracy, this gamma spectrometer must be efficiency calibrated with known standard sources prior to field deployments to analyze the radioactivity concentrations in hydraulic fracturing waste products.

Well water contamination in a rural community in southwestern Pennsylvania near unconventional shale gas extraction.

Reports of ground water contamination in a southwestern Pennsylvania community coincided with unconventional shale gas extraction activities that started late 2009. Residents participated in a survey and well water samples were collected and analyzed. Available pre-drill and post-drill water test results and legacy operations (e.g., gas and oil wells, coal mining) were reviewed. Fifty-six of the 143 respondents indicated changes in water quality or quantity while 63 respondents reported no issues. Color change (brown, black, or orange) was the most common (27 households). Well type, when known, was rotary or cable tool, and depths ranged from 19 to 274 m. Chloride, sulfate, nitrate, sodium, calcium, magnesium, iron, manganese and strontium were commonly found, with 25 households exceeding the secondary maximum contaminate level (SMCL) for manganese. Methane was detected in 14 of the 18 houses tested. The 26 wells tested for total coliforms (2 positives) and E. coli (1 positive) indicated that septic contamination was not a factor. Repeated sampling of two wells in close proximity (204 m) but drawing from different depths (32 m and 54 m), revealed temporal variability. Since 2009, 65 horizontal wells were drilled within a 4 km (2.5 mile) radius of the community, each well was stimulated on average with 3.5 million gal of fluids and 3.2 million lbs of proppant. PA DEP cited violations included an improperly plugged well and at least one failed well casing. This study underscores the need for thorough analyses of data, documentation of legacy activity, pre-drill testing, and long term monitoring.

Impact of the Dimethyl Sulfoxide Reductase Superfamily on the Evolution of Biogeochemical Cycles.

The dimethyl sulfoxide reductase (or MopB) family is a diverse assemblage of enzymes found throughout Bacteria and Archaea. Many of these enzymes are believed to have been present in the last universal common ancestor (LUCA) of all cellular lineages. However, gaps in knowledge remain about how MopB enzymes evolved and how this diversification of functions impacted global biogeochemical cycles through geologic time. In this study, we perform maximum likelihood phylogenetic analyses on manually curated comparative genomic and metagenomic data sets containing over 47,000 distinct MopB homologs. We demonstrate that these enzymes constitute a catalytically and mechanistically diverse superfamily defined not by the molybdopterin- or tungstopterin-containing [molybdopterin or tungstopterin bis(pyranopterin guanine dinucleotide) (Mo/W-bisPGD)] cofactor but rather by the structural fold that binds it in the protein. Our results suggest that major metabolic innovations were the result of the loss of the metal cofactor or the gain or loss of protein domains. Phylogenetic analyses also demonstrated that formate oxidation and CO2 reduction were the ancestral functions of the superfamily, traits that have been vertically inherited from the LUCA. Nearly all of the other families, which drive all other biogeochemical cycles mediated by this superfamily, originated in the bacterial domain. Thus, organisms from Bacteria have been the key drivers of catalytic and biogeochemical innovations within the superfamily. The relative ordination of MopB families and their associated catalytic activities emphasize fundamental mechanisms of evolution in this superfamily. Furthermore, it underscores the importance of prokaryotic adaptability in response to the transition from an anoxic to an oxidized atmosphere. IMPORTANCE The MopB superfamily constitutes a repertoire of metalloenzymes that are central to enduring mysteries in microbiology, from the origin of life and how microorganisms and biogeochemical cycles have coevolved over deep time to how anaerobic life adapted to increasing concentrations of O2 during the transition from an anoxic to an oxic world. Our work emphasizes that phylogenetic analyses can reveal how domain gain or loss events, the acquisition of novel partner subunits, and the loss of metal cofactors can stimulate novel radiations of enzymes that dramatically increase the catalytic versatility of superfamilies. We also contend that the superfamily concept in protein evolution can uncover surprising kinships between enzymes that have remarkably different catalytic and physiological functions.

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.

The microbial carbonate factory of Hamelin Pool, Shark Bay, Western Australia.

Microbialites and peloids are commonly associated throughout the geologic record. Proterozoic carbonate megafacies are composed predominantly of micritic and peloidal limestones often interbedded with stromatolitic textures. The association is also common throughout carbonate ramps and platforms during the Phanerozoic. Recent investigations reveal that Hamelin Pool, located in Shark Bay, Western Australia, is a microbial carbonate factory that provides a modern analog for the microbialite-micritic sediment facies associations that are so prevalent in the geologic record. Hamelin Pool contains the largest known living marine stromatolite system in the world. Although best known for the constructive microbial processes that lead to formation of these stromatolites, our comprehensive mapping has revealed that erosion and degradation of weakly lithified microbial mats in Hamelin Pool leads to the extensive production and accumulation of sand-sized micritic grains. Over 40 km2 of upper intertidal shoreline in the pool contain unlithified to weakly lithified microbial pustular sheet mats, which erode to release irregular peloidal grains. In addition, over 20 km2 of gelatinous microbial mats, with thin brittle layers of micrite, colonize subtidal pavements. When these gelatinous mats erode, the micritic layers break down to form platey, micritic intraclasts with irregular boundaries. Together, the irregular micritic grains from pustular sheet mats and gelatinous pavement mats make up nearly 26% of the total sediment in the pool, plausibly producing ~ 24,000 metric tons of microbial sediment per year. As such, Hamelin Pool can be seen as a microbial carbonate factory, with construction by lithifying microbial mats forming microbialites, and erosion and degradation of weakly lithified microbial mats resulting in extensive production of sand-sized micritic sediments. Insight from these modern examples may have direct applicability for recognition of sedimentary deposits of microbial origin in the geologic record.

Discovery of Chlorophyll d: Isolation and Characterization of a Far-Red Cyanobacterium from the Original Site of Manning and Strain (1943) at Moss Beach, California.

We have isolated a chlorophyll-d-containing cyanobacterium from the intertidal field site at Moss Beach, on the coast of Central California, USA, where Manning and Strain (1943) originally discovered this far-red chlorophyll. Here, we present the cyanobacterium's environmental description, culturing procedure, pigment composition, ultrastructure, and full genome sequence. Among cultures of far-red cyanobacteria obtained from red algae from the same site, this strain was an epiphyte on a brown macroalgae. Its Qyin vivo absorbance peak is centered at 704-705 nm, the shortest wavelength observed thus far among the various known Acaryochloris strains. Its Chl a/Chl d ratio was 0.01, with Chl d accounting for 99% of the total Chl d and Chl a mass. TEM imagery indicates the absence of phycobilisomes, corroborated by both pigment spectra and genome analysis. The Moss Beach strain codes for only a single set of genes for producing allophycocyanin. Genomic sequencing yielded a 7.25 Mbp circular chromosome and 10 circular plasmids ranging from 16 kbp to 394 kbp. We have determined that this strain shares high similarity with strain S15, an epiphyte of red algae, while its distinct gene complement and ecological niche suggest that this strain could be the closest known relative to the original Chl d source of Manning and Strain (1943). The Moss Beach strain is designated Acaryochloris sp. (marina) strain Moss Beach.

The physiology and evolution of microbial selenium metabolism.

Selenium is an essential trace element whose compounds are widely metabolized by organisms from all three domains of life. Moreover, phylogenetic evidence indicates that selenium species, along with iron, molybdenum, tungsten, and nickel, were metabolized by the last universal common ancestor of all cellular lineages, primarily for the synthesis of the 21st amino acid selenocysteine. Thus, selenium metabolism is both environmentally ubiquitous and a physiological adaptation of primordial life. Selenium metabolic reactions comprise reductive transformations both for assimilation into macromolecules and dissimilatory reduction of selenium oxyanions and elemental selenium during anaerobic respiration. This review offers a comprehensive overview of the physiology and evolution of both assimilatory and dissimilatory selenium metabolism in bacteria and archaea, highlighting mechanisms of selenium respiration. This includes a thorough discussion of our current knowledge of the physiology of selenocysteine synthesis and incorporation into proteins in bacteria obtained from structural biology. Additionally, this is the first comprehensive discussion in a review of the incorporation of selenium into the tRNA nucleoside 5-methylaminomethyl-2-selenouridine and as an inorganic cofactor in certain molybdenum hydroxylase enzymes. Throughout, conserved mechanisms and derived features of selenium metabolism in both domains are emphasized and discussed within the context of the global selenium biogeochemical cycle.

Microbial selenium metabolism: a brief history, biogeochemistry and ecophysiology.

Selenium is an essential trace element for organisms from all three domains of life. Microorganisms, in particular, mediate reductive transformations of selenium that govern the element's mobility and bioavailability in terrestrial and aquatic environments. Selenium metabolism is not just ubiquitous but an ancient feature of life likely extending back to the universal common ancestor of all cellular lineages. As with the sulfur biogeochemical cycle, reductive transformations of selenium serve two metabolic functions: assimilation into macromolecules and dissimilatory reduction during anaerobic respiration. This review begins with a historical overview of how research in both aspects of selenium metabolism has developed. We then provide an overview of the global selenium biogeochemical cycle, emphasizing the central role of microorganisms in the cycle. This serves as a basis for a robust discussion of current models for the evolution of the selenium biogeochemical cycle over geologic time, and how knowledge of the evolution and ecophysiology of selenium metabolism can enrich and refine these models. We conclude with a discussion of the ecophysiological function of selenium-respiring prokaryotes within the cycle, and the tantalizing possibility of oxidative selenium transformations during chemolithoautotrophic growth.