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John F. Stolz

Publications and source records attributed to John F. Stolz.

16 recordsLinked to original sources
USGS2023

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- bis PGD)] 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 CO 2 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.

Microbiology Spectrum↗
USGS2020

Arsenolipids in cultured Picocystis strain ML, and their occurrence in biota and sediment from Mono Lake, California

Primary production in Mono Lake, a hypersaline soda lake rich in dissolved inorganic arsenic, is dominated by Picocystis strain ML. We set out to determine if this photoautotrophic picoplankter could metabolize inorganic arsenic and in doing so form unusual arsenolipids (e.g., arsenic bound to 2- O -methyl ribosides) as reported in other saline ecosystems and by halophilic algae. We cultivated Picocystis strain ML on a seawater-based medium with either low (37 µM) or high (1000 µM) phosphate in the presence of arsenite (400 µM), arsenate (800 µM), or without arsenic additions (ca 0.025 µM). Cultivars formed a variety of organoarsenic compounds, including a phytyl 2- O -methyl arsenosugar, depending upon the cultivation conditions and arsenic exposure. When the cells were grown at low P, the organoarsenicals they produced when exposed to both arsenite and arsenate were primarily arsenolipids (~88%) with only a modest content of water-soluble organoarsenic compounds (e.g., arsenosugars). When grown at high P, sequestration shifted to primarily water-soluble, simple methylated arsenicals such as dimethylarsinate; arsenolipids still constituted ~32% of organoarsenic incorporated into cells exposed to arsenate but < 1% when exposed to arsenite. Curiously, Picocystis strain ML grown at low P and exposed to arsenate sequestered huge amounts of arsenic into the cells accounting for 13.3% of the dry biomass; cells grown at low P and arsenite exposure sequestered much lower amounts, equivalent to 0.35% of dry biomass. Extraction of a resistant phase with trifluoroacetate recovered most of the sequestered arsenic in the form of arsenate. Uptake of arsenate into low P-cultivated cells was confirmed by X-ray fluorescence, while XANES/EXAFS spectra indicated the sequestered arsenic was retained as an inorganic iron precipitate, similar to scorodite, rather than as an As-containing macromolecule. Samples from Mono Lake demonstrated the presence of a wide variety of organoarsenic compounds, including arsenosugar phospholipids, most prevalent in zooplankton ( Artemia ) and phytoplankton samples, with much lower amounts detected in the bottom sediments. These observations suggest a trophic transfer of organoarsenicals from the phytoplankton ( Picocystis ) to the zooplankton ( Artemia ) community, with efficient bacterial mineralization of any lysis-released organoarsenicals back to inorganic oxyanions before they sink to the sediments.

California↗
USGS2019

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 , s rrB , 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 K m of 145 ± 53 μM, a V max of 23 ± 2.5 μM min −1 , and a k cat of 23 ± 2.68 s −1 . These results further our understanding of the mechanisms of selenium biotransformation and its biogeochemical cycle.

Journal of Bacteriology↗
USGS2017

Autotrophic microbial arsenotrophy in arsenic-rich soda lakes

A number of prokaryotes are capable of employing arsenic oxy-anions as either electron acceptors [arsenate; As(V)] or electron donors [arsenite; As(III)] to sustain arsenic-dependent growth (‘arsenotrophy’). A subset of these microorganisms function as either chemoautotrophs or photoautotrophs, whereby they gain sufficient energy from their redox metabolism of arsenic to completely satisfy their carbon needs for growth by autotrophy, that is the fixation of inorganic carbon (e.g. HCO 3 − ) into their biomass. Here we review what has been learned of these processes by investigations we have undertaken in three soda lakes of the western USA and from the physiological characterizations of the relevant bacteria, which include the critical genes involved, such as respiratory arsenate reductase ( arrA ) and the discovery of its arsenite-oxidizing counterpart ( arxA ). When possible, we refer to instances of similar process occurring in other, less extreme ecosystems and by microbes other than haloalkaliphiles.

FEMS Microbiology Letters↗
USGS2016

Arsenite as an electron donor for anoxygenic photosynthesis: Description of three strains of Ectothiorhodospria from Mono Lake, California, and Big Soda Lake, Nevada

Three novel strains of photosynthetic bacteria from the family Ectothiorhodospiraceae were isolated from soda lakes of the Great Basin Desert, USA by employing arsenite (As(III)) as the sole electron donor in the enrichment/isolation process. Strain PHS-1 was previously isolated from a hot spring in Mono Lake, while strain MLW-1 was obtained from Mono Lake sediment, and strain BSL-9 was isolated from Big Soda Lake. Strains PHS-1, MLW-1, and BSL-9 were all capable of As(III)-dependent growth via anoxygenic photosynthesis and contained homologs of arxA, but displayed different phenotypes. Comparisons were made with three related species: Ectothiorhodospira shaposhnikovii DSM 2111, Ectothiorhodospira shaposhnikovii DSM 243 T , and Halorhodospira halophila DSM 244. All three type cultures oxidized arsenite to arsenate but did not grow with As(III) as the sole electron donor. DNA–DNA hybridization indicated that strain PHS-1 belongs to the same species as Ect. shaposhnikovii DSM 2111 (81.1% sequence similarity), distinct from Ect. shaposhnikovii DSM 243 T (58.1% sequence similarity). These results suggest that the capacity for light-driven As(III) oxidation is a common phenomenon among purple photosynthetic bacteria in soda lakes. However, the use of As(III) as a sole electron donor to sustain growth via anoxygenic photosynthesis is confined to novel isolates that were screened for by this selective cultivation criterion.

Life Sciences↗
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&ndash;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&ndash;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

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 &mu;M), 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

Arsenic

No abstract available.

Book chapter↗
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↗
USGS2007

Alkalilimnicola ehrlichii sp. nov., a novel, arsenite-oxidizing haloalkaliphilic gammaproteobacterium capable of chemoautotrophic or heterotrophic growth with nitrate or oxygen as the electron acceptor

A facultative chemoautotrophic bacterium, strain MLHE-1 T , was isolated from Mono Lake, an alkaline hypersaline soda lake in California, USA. Cells of strain MLHE-1 T were Gram-negative, short motile rods that grew with inorganic electron donors (arsenite, hydrogen, sulfide or thiosulfate) coupled with the reduction of nitrate to nitrite. No aerobic growth was attained with arsenite or sulfide, but hydrogen sustained both aerobic and anaerobic growth. No growth occurred when nitrite or nitrous oxide was substituted for nitrate. Heterotrophic growth was observed under aerobic and anaerobic (nitrate) conditions. Cells of strain MLHE-1 T could oxidize but not grow on CO, while CH 4 neither supported growth nor was it oxidized. When grown chemoautotrophically, strain MLHE-1 T assimilated inorganic carbon via the Calvin–Benson–Bassham reductive pentose phosphate pathway, with the activity of ribulose 1,5-bisphosphate carboxylase (RuBisCO) functioning optimally at 0.1 M NaCl and at pH 7.3. Strain MLHE-1 T grew over broad ranges of pH (7.3–10.0; optimum, 9.3), salinity (15–190 g l −1 ; optimum 30 g l −1 ) and temperature (13–40 °C; optimum, 30 °C). Phylogenetic analysis of 16S rRNA gene sequences placed strain MLHE-1 T in the class Gammaproteobacteria (family Ectothiorhodospiraceae ) and most closely related to Alkalispirillum mobile (98.5 %) and Alkalilimnicola halodurans (98.6 %), although none of these three haloalkaliphilic micro-organisms were capable of photoautotrophic growth and only strain MLHE-1 T was able to oxidize As(III). On the basis of physiological characteristics and DNA–DNA hybridization data, it is suggested that strain MLHE-1 T represents a novel species within the genus Alkalilimnicola for which the name Alkalilimnicola ehrlichii is proposed. The type strain is MLHE-1 T (=DSM 17681 T =ATCC BAA-1101 T ). Aspects of the annotated full genome of Alkalilimnicola ehrlichii are discussed in the light of its physiology.

California↗
USGS2006

Arsenic and selenium in microbial metabolism

Arsenic and selenium are readily metabolized by prokaryotes, participating in a full range of metabolic functions including assimilation, methylation, detoxification, and anaerobic respiration. Arsenic speciation and mobility is affected by microbes through oxidation/reduction reactions as part of resistance and respiratory processes. A robust arsenic cycle has been demonstrated in diverse environments. Respiratory arsenate reductases, arsenic methyltransferases, and new components in arsenic resistance have been recently described. The requirement for selenium stems primarily from its incorporation into selenocysteine and its function in selenoenzymes. Selenium oxyanions can serve as an electron acceptor in anaerobic respiration, forming distinct nanoparticles of elemental selenium that may be enriched in (76)Se. The biogenesis of selenoproteins has been elucidated, and selenium methyltransferases and a respiratory selenate reductase have also been described. This review highlights recent advances in ecology, biochemistry, and molecular biology and provides a prelude to the impact of genomics studies.

Annual Review of Microbiology↗
USGS2005

Arsenic, microbes and contaminated aquifers

The health of tens of millions of people world-wide is at risk from drinking arsenic-contaminated well water. In most cases this arsenic occurs naturally within the sub-surface aquifers, rather than being derived from identifiable point sources of pollution. The mobilization of arsenic into the aqueous phase is the first crucial step in a process that eventually leads to human arsenicosis. Increasing evidence suggests that this is a microbiological phenomenon.

Trends in Microbiology↗
USGS2004

The microbial arsenic cycle in Mono Lake, California

Significant concentrations of dissolved inorganic arsenic can be found in the waters of a number of lakes located in the western USA and in other water bodies around the world. These lakes are often situated in arid, volcanic terrain. The highest concentrations of arsenic occur in hypersaline, closed basin soda lakes and their remnant brines. Although arsenic is a well-known toxicant to eukaryotes and prokaryotes alike, some prokaryotes have evolved biochemical mechanisms to exploit arsenic oxyanions (i.e., arsenate and arsenite); they can use them either as an electron acceptor for anaerobic respiration (arsenate), or as an electron donor (arsenite) to support chemoautotrophic fixation of CO 2 into cell carbon. Unlike in freshwater or marine ecosystems, these processes may assume quantitative significance with respect to the carbon cycle in arsenic-rich soda lakes. For the past several years our research has focused on the occurrence and biogeochemical manifestations of these processes in Mono Lake, a particularly arsenic-rich environment. Herein we review some of our findings concerning the biogeochemical arsenic cycle in this lake, with the hope that it may broaden the understanding of the influence of microorganisms upon the speciation of arsenic in more common, less “extreme” environments, such as drinking water aquifers.

California↗
USGS2004

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↗