Molecular Analysis of the Metabolic Rates of Discrete Subsurface Populations of Sulfate Reducers

ABSTRACTElucidating thein situmetabolic activity of phylogenetically diverse populations of sulfate-reducing microorganisms that populate anoxic sedimentary environments is key to understanding subsurface ecology. Previous pure culture studies have demonstrated that the transcript abundance of dissimilatory (bi)sulfite reductase genes is correlated with the sulfate-reducing activity of individual cells. To evaluate whether expression of these genes was diagnostic for subsurface communities, dissimilatory (bi)sulfite reductase gene transcript abundance in phylogenetically distinct sulfate-reducing populations was quantified during a field experiment in which acetate was added to uranium-contaminated groundwater. Analysis ofdsrABsequences prior to the addition of acetate indicated thatDesulfobacteraceae,Desulfobulbaceae, andSyntrophaceae-related sulfate reducers were the most abundant. QuantifyingdsrBtranscripts of the individual populations suggested thatDesulfobacteraceaeinitially had higherdsrBtranscripts per cell thanDesulfobulbaceaeorSyntrophaceaepopulations and that the activity ofDesulfobacteraceaeincreased further when the metabolism of dissimilatory metal reducers competing for the added acetate declined. In contrast,dsrBtranscript abundance inDesulfobulbaceaeandSyntrophaceaeremained relatively constant, suggesting a lack of stimulation by added acetate. The indication of higher sulfate-reducing activity in theDesulfobacteraceaewas consistent with the finding thatDesulfobacteraceaebecame the predominant component of the sulfate-reducing community. Discontinuing acetate additions resulted in a decline indsrBtranscript abundance in theDesulfobacteraceae. These results suggest that monitoring transcripts of dissimilatory (bi)sulfite reductase genes in distinct populations of sulfate reducers can provide insight into the relative rates of metabolism of different components of the sulfate-reducing community and their ability to respond to environmental perturbations.

Download Full-text

Simultaneous Catabolism of Plant-Derived Aromatic Compounds Results in Enhanced Growth for Members of the Roseobacter Lineage

Applied and Environmental Microbiology ◽

10.1128/aem.00405-13 ◽

2013 ◽

Vol 79 (12) ◽

pp. 3716-3723 ◽

Cited By ~ 15

Author(s):

Christopher A. Gulvik ◽

Alison Buchan

Keyword(s):

Salt Marshes ◽

Aromatic Compounds ◽

Soil Bacteria ◽

Transcript Abundance ◽

Gene Transcript ◽

Content Type ◽

Coastal Salt Marshes ◽

Metabolic Versatility ◽

Organic Carbon Pool ◽

Ruegeria Pomeroyi

ABSTRACTPlant-derived aromatic compounds are important components of the dissolved organic carbon pool in coastal salt marshes, and their mineralization by resident bacteria contributes to carbon cycling in these systems. Members of the roseobacter lineage of marine bacteria are abundant in coastal salt marshes, and several characterized strains, includingSagittula stellataE-37, utilize aromatic compounds as primary growth substrates. The genome sequence ofS. stellatacontains multiple, potentially competing, aerobic ring-cleaving pathways. Preferential hierarchies in substrate utilization and complex transcriptional regulation have been demonstrated to be the norm in many soil bacteria that also contain multiple ring-cleaving pathways. The purpose of this study was to ascertain whether substrate preference exists inS. stellatawhen the organism is provided a mixture of aromatic compounds that proceed through different ring-cleaving pathways. We focused on the protocatechuate (pca) and the aerobic benzoyl coenzyme A (box) pathways and the substrates known to proceed through them,p-hydroxybenzoate (POB) and benzoate, respectively. When these two substrates were provided at nonlimiting carbon concentrations, temporal patterns of cell density, gene transcript abundance, enzyme activity, and substrate concentrations indicated thatS. stellatasimultaneously catabolized both substrates. Furthermore, enhanced growth rates were observed whenS. stellatawas provided both compounds simultaneously compared to the rates of cells grown singly with an equimolar concentration of either substrate alone. This simultaneous-catabolism phenotype was also demonstrated in another lineage member,Ruegeria pomeroyiDSS-3. These findings challenge the paradigm of sequential aromatic catabolism reported for soil bacteria and contribute to the growing body of physiological evidence demonstrating the metabolic versatility of roseobacters.

Download Full-text

Outer Cell Surface Components Essential for Fe(III) Oxide Reduction by Geobacter metallireducens

Applied and Environmental Microbiology ◽

10.1128/aem.02954-12 ◽

2012 ◽

Vol 79 (3) ◽

pp. 901-907 ◽

Cited By ~ 55

Author(s):

Jessica A. Smith ◽

Derek R. Lovley ◽

Pier-Luc Tremblay

Keyword(s):

Outer Surface ◽

Surface Protein ◽

Transcript Abundance ◽

Geobacter Sulfurreducens ◽

Extracellular Electron Transfer ◽

Outer Cell ◽

Gene Transcript ◽

Oxide Reduction ◽

Geobacter Metallireducens ◽

Content Type

ABSTRACTGeobacterspecies are important Fe(III) reducers in a diversity of soils and sediments. Mechanisms for Fe(III) oxide reduction have been studied in detail inGeobacter sulfurreducens, but a number of the most thoroughly studied outer surface components ofG. sulfurreducens, particularlyc-type cytochromes, are not well conserved amongGeobacterspecies. In order to identify cellular components potentially important for Fe(III) oxide reduction inGeobacter metallireducens, gene transcript abundance was compared in cells grown on Fe(III) oxide or soluble Fe(III) citrate with whole-genome microarrays. Outer-surface cytochromes were also identified. Deletion of genes forc-type cytochromes that had higher transcript abundance during growth on Fe(III) oxides and/or were detected in the outer-surface protein fraction identified sixc-type cytochrome genes, that when deleted removed the capacity for Fe(III) oxide reduction. Several of thec-type cytochromes which were essential for Fe(III) oxide reduction inG. metallireducenshave homologs inG. sulfurreducensthat are not important for Fe(III) oxide reduction. Other genes essential for Fe(III) oxide reduction included a gene predicted to encode an NHL (Ncl-1–HT2A–Lin-41) repeat-containing protein and a gene potentially involved in pili glycosylation. Genes associated with flagellum-based motility, chemotaxis, and pili had higher transcript abundance during growth on Fe(III) oxide, consistent with the previously proposed importance of these components in Fe(III) oxide reduction. These results demonstrate that there are similarities in extracellular electron transfer betweenG. metallireducensandG. sulfurreducensbut the outer-surfacec-type cytochromes involved in Fe(III) oxide reduction are different.

Download Full-text

Nitrogen Utilization and Metabolism in Ruminococcus albus 8

Applied and Environmental Microbiology ◽

10.1128/aem.00029-14 ◽

2014 ◽

Vol 80 (10) ◽

pp. 3095-3102 ◽

Cited By ~ 12

Author(s):

Jong Nam Kim ◽

Emily DeCrescenzo Henriksen ◽

Isaac K. O. Cann ◽

Roderick I. Mackie

Keyword(s):

Growth Rate ◽

Nitrogen Source ◽

Nitrogen Metabolism ◽

Enzyme Activities ◽

Transcript Abundance ◽

Gene Transcript ◽

Sole Nitrogen Source ◽

Ruminococcus Albus ◽

Content Type ◽

Maximum Cell

ABSTRACTThe model rumenFirmicutesorganismRuminococcus albus8 was grown using ammonia, urea, or peptides as the sole nitrogen source; growth was not observed with amino acids as the sole nitrogen source. Growth ofR. albus8 on ammonia and urea showed the same growth rate (0.08 h−1) and similar maximum cell densities (for ammonia, the optical density at 600 nm [OD600] was 1.01; and for urea, the OD600was 0.99); however, growth on peptides resulted in a nearly identical growth rate (0.09 h−1) and a lower maximum cell density (OD600= 0.58). To identify differences in gene expression and enzyme activities, the transcript abundances of 10 different genes involved in nitrogen metabolism and specific enzyme activities were analyzed by harvesting mRNA and crude protein from cells at the mid- and late exponential phases of growth on the different N sources. Transcript abundances and enzyme activities varied according to nitrogen source, ammonia concentration, and growth phase. Growth ofR. albus8 on ammonia and urea was similar, with the only observed difference being an increase in urease transcript abundance and enzyme activity in urea-grown cultures. Growth ofR. albus8 on peptides showed a different nitrogen metabolism pattern, with higher gene transcript abundance levels ofgdhA,glnA,gltB,amtB,glnK, andureC, as well as higher activities of glutamate dehydrogenase and urease. These results demonstrate that ammonia, urea, and peptides can all serve as nitrogen sources forR. albusand that nitrogen metabolism genes and enzyme activities ofR. albus8 are regulated by nitrogen source and the level of ammonia in the growth medium.

Download Full-text

Functional Genomics with a Comprehensive Library of Transposon Mutants for the Sulfate-Reducing Bacterium Desulfovibrio alaskensis G20

mBio ◽

10.1128/mbio.01041-14 ◽

2014 ◽

Vol 5 (3) ◽

Cited By ~ 33

Author(s):

Jennifer V. Kuehl ◽

Morgan N. Price ◽

Jayashree Ray ◽

Kelly M. Wetmore ◽

Zuelma Esquivel ◽

...

Keyword(s):

Petroleum Industry ◽

Sulfate Reducing Bacteria ◽

Methionine Biosynthesis ◽

Data Set ◽

Protein Coding ◽

Content Type ◽

Sulfate Reducing ◽

Transposon Mutants ◽

The Individual ◽

Reducing Bacteria

ABSTRACTThe genomes of sulfate-reducing bacteria remain poorly characterized, largely due to a paucity of experimental data and genetic tools. To meet this challenge, we generated an archived library of 15,477 mapped transposon insertion mutants in the sulfate-reducing bacteriumDesulfovibrio alaskensisG20. To demonstrate the utility of the individual mutants, we profiled gene expression in mutants of six regulatory genes and used these data, together with 1,313 high-confidence transcription start sites identified by tiling microarrays and transcriptome sequencing (5′ RNA-Seq), to update the regulons of Fur and Rex and to confirm the predicted regulons of LysX, PhnF, PerR, and Dde_3000, a histidine kinase. In addition to enabling single mutant investigations, theD. alaskensisG20 transposon mutants also contain DNA bar codes, which enables the pooling and analysis of mutant fitness for thousands of strains simultaneously. Using two pools of mutants that represent insertions in 2,369 unique protein-coding genes, we demonstrate that the hypothetical geneDde_3007is required for methionine biosynthesis. Using comparative genomics, we propose that Dde_3007 performs a missing step in methionine biosynthesis by transferring a sulfur group toO-phosphohomoserine to form homocysteine. Additionally, we show that the entire choline utilization cluster is important for fitness in choline sulfate medium, which confirms that a functional microcompartment is required for choline oxidation. Finally, we demonstrate that Dde_3291, a MerR-like transcription factor, is a choline-dependent activator of the choline utilization cluster. Taken together, our data set and genetic resources provide a foundation for systems-level investigation of a poorly studied group of bacteria of environmental and industrial importance.IMPORTANCESulfate-reducing bacteria contribute to global nutrient cycles and are a nuisance for the petroleum industry. Despite their environmental and industrial significance, the genomes of sulfate-reducing bacteria remain poorly characterized. Here, we describe a genetic approach to fill gaps in our knowledge of sulfate-reducing bacteria. We generated a large collection of archived, transposon mutants inDesulfovibrio alaskensisG20 and used the phenotypes of these mutant strains to infer the function of genes involved in gene regulation, methionine biosynthesis, and choline utilization. Our findings and mutant resources will enable systematic investigations into gene function, energy generation, stress response, and metabolism for this important group of bacteria.

Download Full-text

Multiple Lateral Transfers of Dissimilatory Sulfite Reductase Genes between Major Lineages of Sulfate-Reducing Prokaryotes

Journal of Bacteriology ◽

10.1128/jb.183.20.6028-6035.2001 ◽

2001 ◽

Vol 183 (20) ◽

pp. 6028-6035 ◽

Cited By ~ 239

Author(s):

Michael Klein ◽

Michael Friedrich ◽

Andrew J. Roger ◽

Philip Hugenholtz ◽

Susan Fishbain ◽

...

Keyword(s):

Sulfite Reductase ◽

Beta Subunits ◽

Transfer Event ◽

Sulfate Reducers ◽

Sulfate Reducing ◽

Dissimilatory Sulfite Reductase ◽

Rrna Phylogeny ◽

Diversity Studies ◽

Reducing Bacteria ◽

Reference Strains

ABSTRACT A large fragment of the dissimilatory sulfite reductase genes (dsrAB) was PCR amplified and fully sequenced from 30 reference strains representing all recognized lineages of sulfate-reducing bacteria. In addition, the sequence of thedsrAB gene homologs of the sulfite reducerDesulfitobacterium dehalogenans was determined. In contrast to previous reports, comparative analysis of all available DsrAB sequences produced a tree topology partially inconsistent with the corresponding 16S rRNA phylogeny. For example, the DsrAB sequences of several Desulfotomaculum species (low G+C gram-positive division) and two members of the genusThermodesulfobacterium (a separate bacterial division) were monophyletic with δ-proteobacterial DsrAB sequences. The most parsimonious interpretation of these data is thatdsrAB genes from ancestors of as-yet-unrecognized sulfate reducers within the δ-Proteobacteria were laterally transferred across divisions. A number of insertions and deletions in the DsrAB alignment independently support these inferred lateral acquisitions of dsrAB genes. Evidence for adsrAB lateral gene transfer event also was found within the δ-Proteobacteria, affecting Desulfobacula toluolica. The root of the dsr tree was inferred to be within the Thermodesulfovibrio lineage by paralogous rooting of the alpha and beta subunits. This rooting suggests that the dsrAB genes inArchaeoglobus species also are the result of an ancient lateral transfer from a bacterial donor. Although these findings complicate the use of dsrAB genes to infer phylogenetic relationships among sulfate reducers in molecular diversity studies, they establish a framework to resolve the origins and diversification of this ancient respiratory lifestyle among organisms mediating a key step in the biogeochemical cycling of sulfur.

Download Full-text

Transcriptomic and Genetic Analysis of Direct Interspecies Electron Transfer

Applied and Environmental Microbiology ◽

10.1128/aem.03837-12 ◽

2013 ◽

Vol 79 (7) ◽

pp. 2397-2404 ◽

Cited By ~ 96

Author(s):

Pravin Malla Shrestha ◽

Amelia-Elena Rotaru ◽

Zarath M. Summers ◽

Minita Shrestha ◽

Fanghua Liu ◽

...

Keyword(s):

Electron Transfer ◽

Expression Patterns ◽

Transcript Abundance ◽

Geobacter Sulfurreducens ◽

Acetate Metabolism ◽

Gene Transcript ◽

Content Type ◽

Direct Interspecies Electron Transfer ◽

Interspecies Electron Transfer ◽

Pilin Gene

ABSTRACTThe possibility that metatranscriptomic analysis could distinguish between direct interspecies electron transfer (DIET) and H2interspecies transfer (HIT) in anaerobic communities was investigated by comparing gene transcript abundance in cocultures in whichGeobacter sulfurreducenswas the electron-accepting partner for eitherGeobacter metallireducens, which performs DIET, orPelobacter carbinolicus, which relies on HIT. Transcript abundance forG. sulfurreducensuptake hydrogenase genes was 7-fold lower in cocultures withG. metallireducensthan in cocultures withP. carbinolicus, consistent with DIET and HIT, respectively, in the two cocultures. Transcript abundance for the pilus-associated cytochrome OmcS, which is essential for DIET but not for HIT, was 240-fold higher in the cocultures withG. metallireducensthan in cocultures withP. carbinolicus. The pilin genepilAwas moderately expressed despite a mutation that might be expected to represspilAexpression. Lower transcript abundance forG. sulfurreducensgenes associated with acetate metabolism in the cocultures withP. carbinolicuswas consistent with the repression of these genes by H2during HIT. Genes for the biogenesis of pili and flagella and severalc-type cytochrome genes were among the most highly expressed inG. metallireducens. Mutant strains that lacked the ability to produce pili, flagella, or the outer surfacec-type cytochrome encoded by Gmet_2896 were not able to form cocultures withG. sulfurreducens. These results demonstrate that there are unique gene expression patterns that distinguish DIET from HIT and suggest that metatranscriptomics may be a promising route to investigate interspecies electron transfer pathways in more-complex environments.

Download Full-text

Syntrophic Growth of Desulfovibrio alaskensis Requires Genes for H2and Formate Metabolism as Well as Those for Flagellum and Biofilm Formation

Applied and Environmental Microbiology ◽

10.1128/aem.03358-14 ◽

2015 ◽

Vol 81 (7) ◽

pp. 2339-2348 ◽

Cited By ~ 20

Author(s):

Lee R. Krumholz ◽

Peter Bradstock ◽

Cody S. Sheik ◽

Yiwei Diao ◽

Ozcan Gazioglu ◽

...

Keyword(s):

Energy Metabolism ◽

Biofilm Formation ◽

Membrane Surface ◽

Transcript Abundance ◽

Content Type ◽

Sulfate Reducing ◽

Syntrophomonas Wolfei ◽

Flagellar Biosynthesis ◽

Metabolic Interactions ◽

Membrane Components

ABSTRACTIn anaerobic environments, mutually beneficial metabolic interactions between microorganisms (syntrophy) are essential for oxidation of organic matter to carbon dioxide and methane. Syntrophic interactions typically involve a microorganism degrading an organic compound to primary fermentation by-products and sources of electrons (i.e., formate, hydrogen, or nanowires) and a partner producing methane or respiring the electrons via alternative electron accepting processes. Using a transposon gene mutant library of the sulfate-reducingDesulfovibrio alaskensisG20, we screened for mutants incapable of serving as the electron-accepting partner of the butyrate-oxidizing bacterium,Syntrophomonas wolfei. A total of 17 gene mutants ofD. alaskensiswere identified as incapable of serving as the electron-accepting partner. The genes identified predominantly fell into three categories: membrane surface assembly, flagellum-pilus synthesis, and energy metabolism. Among these genes required to serve as the electron-accepting partner, the glycosyltransferase, pilus assembly protein (tadC), and flagellar biosynthesis protein showed reduced biofilm formation, suggesting that each of these components is involved in cell-to-cell interactions. Energy metabolism genes encoded proteins primarily involved in H2uptake and electron cycling, including a rhodanese-containing complex that is phylogenetically conserved among sulfate-reducingDeltaproteobacteria. Utilizing an mRNA sequencing approach, analysis of transcript abundance in wild-type axenic and cocultures confirmed that genes identified as important for serving as the electron-accepting partner were more highly expressed under syntrophic conditions. The results imply that sulfate-reducing microorganisms require flagellar and outer membrane components to effectively couple to their syntrophic partners; furthermore, H2metabolism is essential for syntrophic growth ofD. alaskensisG20.

Download Full-text

In VitroAnalyses of the Effects of Heparin and Parabens on Candida albicans Biofilms and Planktonic Cells

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.05061-11 ◽

2011 ◽

Vol 56 (1) ◽

pp. 148-153 ◽

Cited By ~ 15

Author(s):

Marisa H. Miceli ◽

Stella M. Bernardo ◽

T. S. Neil Ku ◽

Carla Walraven ◽

Samuel A. Lee

Keyword(s):

Candida Albicans ◽

Metabolic Activity ◽

Biofilm Formation ◽

High Dose ◽

Dependent Manner ◽

Planktonic Cells ◽

Content Type ◽

Heparin Sodium ◽

The Individual

ABSTRACTInfections and thromboses are the most common complications associated with central venous catheters. Suggested strategies for prevention and management of these complications include the use of heparin-coated catheters, heparin locks, and antimicrobial lock therapy. However, the effects of heparin onCandida albicansbiofilms and planktonic cells have not been previously studied. Therefore, we sought to determine thein vitroeffect of a heparin sodium preparation (HP) on biofilms and planktonic cells ofC. albicans. Because HP contains two preservatives, methyl paraben (MP) and propyl paraben (PP), these compounds and heparin sodium without preservatives (Pure-H) were also tested individually. The metabolic activity of the mature biofilm after treatment was assessed using XTT [2,3-bis-(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide] reduction and microscopy. Pure-H, MP, and PP caused up to 75, 85, and 60% reductions of metabolic activity of the mature preformedC. albicansbiofilms, respectively. Maximal efficacy against the mature biofilm was observed with HP (up to 90%) compared to the individual compounds (P< 0.0001). Pure-H, MP, and PP each inhibitedC. albicansbiofilm formation up to 90%. A complete inhibition of biofilm formation was observed with HP at 5,000 U/ml and higher. When tested against planktonic cells, each compound inhibited growth in a dose-dependent manner. These data indicated that HP, MP, PP, and Pure-H havein vitroantifungal activity againstC. albicansmature biofilms, formation of biofilms, and planktonic cells. Investigation of high-dose heparin-based strategies (e.g., heparin locks) in combination with traditional antifungal agents for the treatment and/or prevention ofC. albicansbiofilms is warranted.

Download Full-text

Gender bias in hospital leadership: a qualitative study on the experiences of women CEOs

Journal of Health Organization and Management ◽

10.1108/jhom-12-2016-0243 ◽

2017 ◽

Vol 31 (2) ◽

pp. 253-268 ◽

Cited By ~ 5

Author(s):

Sophie Soklaridis ◽

Ayelet Kuper ◽

Cynthia R. Whitehead ◽

Genevieve Ferguson ◽

Valerie H. Taylor ◽

...

Keyword(s):

Qualitative Study ◽

Gender Bias ◽

Female Leaders ◽

Content Type ◽

Hospital Leadership ◽

Purposeful Sampling ◽

Women Ceos ◽

Hospital Ceos ◽

The Individual ◽

Systemic Discrimination

Purpose The purpose of this paper is to examine the experiences of gender bias among women hospital CEOs and explore to what these female leaders attribute their success within a male-dominated hospital executive leadership milieu. Design/methodology/approach This qualitative study involved 12 women hospital CEOs from across Ontario, Canada. Purposeful sampling techniques and in-depth qualitative interview methods were used to facilitate discussion around experiences of gender and leadership. Findings Responses fell into two groups: the first group represented the statement “Gender inequality is alive and well”. The second group reflected the statement “Gender inequity is not significant, did not happen to me, and things are better now”. This group contained a sub-group with no consciousness of systemic discrimination and that claimed having no gendered experiences in their leadership journey. The first group described gender issues in various contexts, from the individual to the systemic. The second group was ambivalent about gender as a factor impacting leadership trajectories. Originality/value Representations of women’s leadership have become detached from feminism, with major consequences for women. This study reveals how difficult it is for some women CEOs to identify gender bias. The subtle everyday norms and practices within the workplace make it difficult to name and explain gender bias explicitly and may explain the challenges in understanding how it might affect a woman’s career path.

Download Full-text

Two Marine Desulfotomaculum spp. of Different Origin are Capable of Utilizing Acetone and Higher Ketones

Current Microbiology ◽

10.1007/s00284-021-02441-9 ◽

2021 ◽

Author(s):

Jasmin Frey ◽

Sophie Kaßner ◽

Bernhard Schink

Keyword(s):

Sulfate Reducing Bacteria ◽

Thiamine Diphosphate ◽

Sulfate Reducers ◽

Sulfate Reducing ◽

Reducing Bacteria ◽

Nitrate Reducing Bacteria ◽

Different Origin

AbstractDegradation of acetone and higher ketones has been described in detail for aerobic and nitrate-reducing bacteria. Among sulfate-reducing bacteria, degradation of acetone and other ketones is still an uncommon ability and has not been understood completely yet. In the present work, we show that Desulfotomaculum arcticum and Desulfotomaculum geothermicum are able to degrade acetone and butanone. Total proteomics of cell-free extracts of both organisms indicated an involvement of a thiamine diphosphate-dependent enzyme, a B12-dependent mutase, and a specific dehydrogenase during acetone degradation. Similar enzymes were recently described to be involved in acetone degradation by Desulfococcus biacutus. As there are so far only two described sulfate reducers able to degrade acetone, D. arcticum and D. geothermicum represent two further species with this capacity. All these bacteria appear to degrade acetone via the same set of enzymes and therefore via the same pathway.

Download Full-text