scholarly journals Effects of Genetic and Physiological Divergence on the Evolution of a Sulfate-Reducing Bacterium under Conditions of Elevated Temperature

mBio ◽  
2020 ◽  
Vol 11 (4) ◽  
Author(s):  
Megan L. Kempher ◽  
Xuanyu Tao ◽  
Rong Song ◽  
Bo Wu ◽  
David A. Stahl ◽  
...  
Keyword(s):  
Natural Selection ◽  
Elevated Temperature ◽  
Experimental Evolution ◽  
Evolutionary Biology ◽  
Desulfovibrio Vulgaris ◽  
Common Environment ◽  
Content Type ◽  
Sulfate Reducing ◽  
Evolution Study ◽  
The Impact

ABSTRACT Adaptation via natural selection is an important driver of evolution, and repeatable adaptations of replicate populations, under conditions of a constant environment, have been extensively reported. However, isolated groups of populations in nature tend to harbor both genetic and physiological divergence due to multiple selective pressures that they have encountered. How this divergence affects adaptation of these populations to a new common environment remains unclear. To determine the impact of prior genetic and physiological divergence in shaping adaptive evolution to accommodate a new common environment, an experimental evolution study with the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough (DvH) was conducted. Two groups of replicate populations with genetic and physiological divergence, derived from a previous evolution study, were propagated in an elevated-temperature environment for 1,000 generations. Ancestor populations without prior experimental evolution were also propagated in the same environment as a control. After 1,000 generations, all the populations had increased growth rates and all but one had greater fitness in the new environment than the ancestor population. Moreover, improvements in growth rate were moderately affected by the divergence in the starting populations, while changes in fitness were not significantly affected. The mutations acquired at the gene level in each group of populations were quite different, indicating that the observed phenotypic changes were achieved by evolutionary responses that differed between the groups. Overall, our work demonstrated that the initial differences in fitness between the starting populations were eliminated by adaptation and that phenotypic convergence was achieved by acquisition of mutations in different genes. IMPORTANCE Improving our understanding of how previous adaptation influences evolution has been a long-standing goal in evolutionary biology. Natural selection tends to drive populations to find similar adaptive solutions for the same selective conditions. However, variations in historical environments can lead to both physiological and genetic divergence that can make evolution unpredictable. Here, we assessed the influence of divergence on the evolution of a model sulfate-reducing bacterium, Desulfovibrio vulgaris Hildenborough, in response to elevated temperature and found a significant effect at the genetic but not the phenotypic level. Understanding how these influences drive evolution will allow us to better predict how bacteria will adapt to various ecological constraints.

scholarly journals Genetic Basis of Chromate Adaptation and the Role of the Pre-existing Genetic Divergence during an Experimental Evolution Study with Desulfovibrio vulgaris Populations

mSystems ◽  
2021 ◽  
Author(s):  
Weiling Shi ◽  
Qiao Ma ◽  
Feiyan Pan ◽  
Yupeng Fan ◽  
Megan L. Kempher ◽  
...  
Keyword(s):  
Heavy Metal ◽  
Experimental Evolution ◽  
Genetic Basis ◽  
Functional Genes ◽  
Desulfovibrio Vulgaris ◽  
Content Type ◽  
Metal Pollutants ◽  
Evolution Study ◽  
Heavy Metal Pollutants

Chromium is one of the most common heavy metal pollutants of soil and groundwater. The potential of Desulfovibrio vulgaris Hildenborough in heavy metal bioremediation such as Cr(VI) reduction was reported previously; however, experimental evidence of key functional genes involved in Cr(VI) resistance are largely unknown.

The impact of urban façade quality on affective feelings

2020 ◽  
Vol 14 (2) ◽  
pp. 219-232 ◽  
Author(s):  
Justin B. Hollander ◽  
Eric C. Anderson
Keyword(s):  
Evolutionary Biology ◽  
Design Methodology ◽  
Emotional Reaction ◽  
Urban Environments ◽  
Content Type ◽  
Individual Trait ◽  
Edge Conditions ◽  
Trait Difference ◽  
The Impact ◽  
The Relationship

PurposeMuch of the current literature on streetscape design emphasizes a need for well-articulated edge conditions to enhance pedestrian-orientation and the reason appears to lie in evolutionary biology: humans have a psychological preference for wall-hugging due to a well-established trait in other species: thigmotaxis.Design/methodology/approachThis study seeks to explore the relationship between urban facades and affective feelings through an empirical study, which asks: how do people perceive edge conditions in urban environments? Through a study of affect relative to edge conditions, greater insight can be generated as to the human experience in the built environment. We conducted a laboratory experiment with 76 subjects who each viewed 40 images of urban facades and rated each based on their emotional reaction.FindingsEach subject also completed two validated individual trait difference measures. We found that those images depicting thigmotaxic facades were more highly rated than other facades.Originality/valueHigh quality edge environment resulted in people feeling more pleasant than low quality edges.

scholarly journals Identification and Characterization of the Major Porin of Desulfovibrio vulgaris Hildenborough

2017 ◽  
Vol 199 (23) ◽  
Author(s):  
Lucy Zeng ◽  
Etsuko Wooton ◽  
David A. Stahl ◽  
Peter J. Walian
Keyword(s):  
Electron Microscopy ◽  
Sequence Analysis ◽  
Model Organism ◽  
Desulfovibrio Vulgaris ◽  
Gram Negative Bacteria ◽  
Diverse Range ◽  
Gram Negative ◽  
Content Type ◽  
Sulfate Reducing

ABSTRACT Due in large part to their ability to facilitate the diffusion of a diverse range of solutes across the outer membrane (OM) of Gram-negative bacteria, the porins represent one of the most prominent and important bacterial membrane protein superfamilies. Notably, for the Gram-negative bacterium Desulfovibrio vulgaris Hildenborough, a model organism for studies of sulfate-reducing bacteria, no genes for porins have been identified or proposed in its annotated genome. Results from initial biochemical studies suggested that the product of the DVU0799 gene, which is one of the most abundant proteins of the D. vulgaris Hildenborough OM and purified as a homotrimeric complex, was a strong porin candidate. To investigate this possibility, this protein was further characterized biochemically and biophysically. Structural analyses via electron microscopy of negatively stained protein identified trimeric particles with stain-filled depressions and structural modeling suggested a β-barrel structure for the monomer, motifs common among the known porins. Functional studies were performed in which crude OM preparations or purified DVU0799 was reconstituted into proteoliposomes and the proteoliposomes were examined for permeability against a series of test solutes. The results obtained establish DVU0799 to be a pore-forming protein with permeability properties similar to those observed for classical bacterial porins, such as those of Escherichia coli. Taken together, these findings identify this highly abundant OM protein to be the major porin of D. vulgaris Hildenborough. Classification of DVU0799 in this model organism expands the database of functionally characterized porins and may also extend the range over which sequence analysis strategies can be used to identify porins in other bacterial genomes. IMPORTANCE Porins are membrane proteins that form transmembrane pores for the passive transport of small molecules across the outer membranes of Gram-negative bacteria. The present study identified and characterized the major porin of the model sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough, observing its preference for anionic sugars over neutral ones. Its predicted architecture appears to be novel for a classical porin, as its core β-barrel structure is of a type typically found in solute-specific channels. Broader use of the methods employed here, such as assays for channel permeability and electron microscopy of purified samples, is expected to help expand the database of confirmed porin sequences and improve the range over which sequence analysis-based strategies can be used to identify porins in other Gram-negative bacteria. Functional characterization of these critical gatekeeping proteins from divergent Desulfovibrio species should offer an improved understanding of the physiological features that determine their habitat range and supporting activities.

scholarly journals Regulation of Nitrite Stress Response in Desulfovibrio vulgaris Hildenborough, a Model Sulfate-Reducing Bacterium

2015 ◽  
Vol 197 (21) ◽  
pp. 3400-3408 ◽  
Author(s):  
Lara Rajeev ◽  
Amy Chen ◽  
Alexey E. Kazakov ◽  
Eric G. Luning ◽  
Grant M. Zane ◽  
...  
Keyword(s):  
Nitrite Reductase ◽  
Nitrite Reduction ◽  
System Response ◽  
Desulfovibrio Vulgaris ◽  
Two Component System ◽  
Component System ◽  
Content Type ◽  
Sulfate Reducing ◽  
Low Concentrations ◽  
Two Component

ABSTRACTSulfate-reducing bacteria (SRB) are sensitive to low concentrations of nitrite, and nitrite has been used to control SRB-related biofouling in oil fields.Desulfovibrio vulgarisHildenborough, a model SRB, carries a cytochromec-type nitrite reductase (nrfHA) that confers resistance to low concentrations of nitrite. The regulation of this nitrite reductase has not been directly examined to date. In this study, we show that DVU0621 (NrfR), a sigma54-dependent two-component system response regulator, is the positive regulator for this operon. NrfR activates the expression of thenrfHAoperon in response to nitrite stress. We also show thatnrfRis needed for fitness at low cell densities in the presence of nitrite because inactivation ofnrfRaffects the rate of nitrite reduction. We also predict and validate the binding sites for NrfR upstream of thenrfHAoperon using purified NrfR in gel shift assays. We discuss possible roles for NrfR in regulating nitrate reductase genes in nitrate-utilizingDesulfovibriospp.IMPORTANCEThe NrfA nitrite reductase is prevalent across several bacterial phyla and required for dissimilatory nitrite reduction. However, regulation of thenrfAgene has been studied in only a few nitrate-utilizing bacteria. Here, we show that inD. vulgaris, a bacterium that does not respire nitrate, the expression ofnrfHAis induced by NrfR upon nitrite stress. This is the first report of regulation ofnrfAby a sigma54-dependent two-component system. Our study increases our knowledge of nitrite stress responses and possibly of the regulation of nitrate reduction in SRB.

scholarly journals High standing genetic variation in an invasive plant allows immediate evolutionary response to climate warming

2020 ◽  
Author(s):  
Yan Sun ◽  
Oliver Bossdorf ◽  
Ramon Diaz Grados ◽  
ZhiYong Liao ◽  
Heinz Müller-Schärer
Keyword(s):  
Climate Change ◽  
Climate Warming ◽  
Experimental Evolution ◽  
Invasive Plant ◽  
Plant Traits ◽  
Common Environment ◽  
Pooled Dna ◽  
Evolutionary Response ◽  
Evolution Study ◽  
Simulated Climate

AbstractPredicting plant distributions under climate change is constrained by our limited understanding of potential rapid adaptive evolution. In an experimental evolution study with the invasive common ragweed, we subjected replicated populations of the same initial genetic composition to simulated climate warming. Pooled DNA sequencing of parental and offspring populations showed that warming populations experienced a greater loss of genetic diversity, and greater genetic divergence from their parents, than control populations. In a common environment, offspring from warming populations showed more convergent phenotypes in seven out of nine plant traits, with later flowering and larger biomass, than plants from control populations. For both traits, we also found a significant higher ratio of phenotypic to genetic differentiation across generations for warming than for control populations, indicating stronger selection under warming conditions. Our findings demonstrate that ragweed populations can rapidly evolve in response to climate change within a single generation.

scholarly journals Deletion Mutants, Archived Transposon Library, and Tagged Protein Constructs of the Model Sulfate-Reducing Bacterium Desulfovibrio vulgaris Hildenborough

2021 ◽  
Vol 10 (11) ◽  
Author(s):  
Judy D. Wall ◽  
Grant M. Zane ◽  
Thomas R. Juba ◽  
Jennifer V. Kuehl ◽  
Jayashree Ray ◽  
...  
Keyword(s):  
Research Collaboration ◽  
Research Community ◽  
Desulfovibrio Vulgaris ◽  
Deletion Mutants ◽  
Content Type ◽  
Sulfate Reducing ◽  
Desulfovibrio Vulgaris Hildenborough ◽  
Genetic Constructs ◽  
Protein Constructs

ABSTRACT The dissimilatory sulfate-reducing deltaproteobacterium Desulfovibrio vulgaris Hildenborough (ATCC 29579) was chosen by the research collaboration ENIGMA to explore tools and protocols for bringing this anaerobe to model status. Here, we describe a collection of genetic constructs generated by ENIGMA that are available to the research community.

scholarly journals Rex (Encoded by DVU_0916) in Desulfovibrio vulgaris Hildenborough Is a Repressor of Sulfate Adenylyl Transferase and Is Regulated by NADH

2014 ◽  
Vol 197 (1) ◽  
pp. 29-39 ◽  
Author(s):  
G. A. Christensen ◽  
G. M. Zane ◽  
A. E. Kazakov ◽  
X. Li ◽  
D. A. Rodionov ◽  
...  
Keyword(s):  
Binding Site ◽  
Sulfate Reduction ◽  
Transcriptional Start Site ◽  
Redox Status ◽  
Desulfovibrio Vulgaris ◽  
Dissimilatory Sulfate Reduction ◽  
Content Type ◽  
Sulfate Reducing ◽  
Genes Encoding

Although the enzymes for dissimilatory sulfate reduction by microbes have been studied, the mechanisms for transcriptional regulation of the encoding genes remain unknown. In a number of bacteria the transcriptional regulator Rex has been shown to play a key role as a repressor of genes producing proteins involved in energy conversion. In the model sulfate-reducing microbeDesulfovibrio vulgarisHildenborough, the gene DVU_0916 was observed to resemble other known Rex proteins. Therefore, the DVU_0916 protein has been predicted to be a transcriptional repressor of genes encoding proteins that function in the process of sulfate reduction inD. vulgarisHildenborough. Examination of the deduced DVU_0916 protein identified two domains, one a winged helix DNA-binding domain common for transcription factors, and the other a Rossman fold that could potentially interact with pyridine nucleotides. A deletion of the putativerexgene was made inD. vulgarisHildenborough, and transcript expression studies ofsat, encoding sulfate adenylyl transferase, showed increased levels in theD. vulgarisHildenborough Rex (RexDvH) mutant relative to the parental strain. The RexDvH-binding site upstream ofsatwas identified, confirming RexDvHto be a repressor ofsat. We establishedin vitrothat the presence of elevated NADH disrupted the interaction between RexDvHand DNA. Examination of the 5′ transcriptional start site for thesatmRNA revealed two unique start sites, one for respiring cells that correlated with the RexDvH-binding site and a second for fermenting cells. Collectively, these data support the role of RexDvHas a transcription repressor forsatthat senses the redox status of the cell.

scholarly journals Effect of Quorum Sensing on the Ability of Desulfovibrio vulgaris To Form Biofilms and To Biocorrode Carbon Steel in Saline Conditions

2019 ◽  
Vol 86 (1) ◽  
Author(s):  
Giantommaso Scarascia ◽  
Robert Lehmann ◽  
Laura L. Machuca ◽  
Christina Morris ◽  
Ka Yu Cheng ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Carbon Steel ◽  
Quorum Sensing ◽  
Biofilm Formation ◽  
Sulfate Reducing Bacteria ◽  
Desulfovibrio Vulgaris ◽  
Content Type ◽  
Sulfate Reducing ◽  
Alternative Approach ◽  
Reducing Bacteria

ABSTRACT Sulfate-reducing bacteria (SRB) are key contributors to microbe-induced corrosion (MIC), which can lead to serious economic and environmental impact. The presence of a biofilm significantly increases the MIC rate. Inhibition of the quorum-sensing (QS) system is a promising alternative approach to prevent biofilm formation in various industrial settings, especially considering the significant ecological impact of conventional chemical-based mitigation strategies. In this study, the effect of the QS stimulation and inhibition on Desulfovibrio vulgaris is described in terms of anaerobic respiration, cell activity, biofilm formation, and biocorrosion of carbon steel. All these traits were repressed when bacteria were in contact with QS inhibitors but enhanced upon exposure to QS signal molecules compared to the control. The difference in the treatments was confirmed by transcriptomic analysis performed at different time points after treatment application. Genes related to lactate and pyruvate metabolism, sulfate reduction, electron transfer, and biofilm formation were downregulated upon QS inhibition. In contrast, QS stimulation led to an upregulation of the above-mentioned genes compared to the control. In summary, these results reveal the impact of QS on the activity of D. vulgaris, paving the way toward the prevention of corrosive SRB biofilm formation via QS inhibition. IMPORTANCE Sulfate-reducing bacteria (SRB) are considered key contributors to biocorrosion, particularly in saline environments. Biocorrosion imposes tremendous economic costs, and common approaches to mitigate this problem involve the use of toxic and hazardous chemicals (e.g., chlorine), which raise health and environmental safety concerns. Quorum-sensing inhibitors (QSIs) can be used as an alternative approach to inhibit biofilm formation and biocorrosion. However, this approach would only be effective if SRB rely on QS for the pathways associated with biocorrosion. These pathways would include biofilm formation, electron transfer, and metabolism. This study demonstrates the role of QS in Desulfovibrio vulgaris on the above-mentioned pathways through both phenotypic measurements and transcriptomic approach. The results of this study suggest that QSIs can be used to mitigate SRB-induced corrosion problems in ecologically sensitive areas.

scholarly journals Key Metabolites and Mechanistic Changes for Salt Tolerance in an Experimentally Evolved Sulfate-Reducing Bacterium, Desulfovibrio vulgaris

mBio ◽  
2017 ◽  
Vol 8 (6) ◽  
Author(s):  
Aifen Zhou ◽  
Rebecca Lau ◽  
Richard Baran ◽  
Jincai Ma ◽  
Frederick von Netzer ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Experimental Evolution ◽  
High Salinity ◽  
Desulfovibrio Vulgaris ◽  
Salt Adaptation ◽  
Toxic Heavy Metals ◽  
Natural Habitats ◽  
Adaptation Mechanism ◽  
Sulfate Reducing

ABSTRACT Rapid genetic and phenotypic adaptation of the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough to salt stress was observed during experimental evolution. In order to identify key metabolites important for salt tolerance, a clone, ES10-5, which was isolated from population ES10 and allowed to experimentally evolve under salt stress for 5,000 generations, was analyzed and compared to clone ES9-11, which was isolated from population ES9 and had evolved under the same conditions for 1,200 generations. These two clones were chosen because they represented the best-adapted clones among six independently evolved populations. ES10-5 acquired new mutations in genes potentially involved in salt tolerance, in addition to the preexisting mutations and different mutations in the same genes as in ES9-11. Most basal abundance changes of metabolites and phospholipid fatty acids (PLFAs) were lower in ES10-5 than ES9-11, but an increase of glutamate and branched PLFA i17:1ω9c under high-salinity conditions was persistent. ES9-11 had decreased cell motility compared to the ancestor; in contrast, ES10-5 showed higher cell motility under both nonstress and high-salinity conditions. Both genotypes displayed better growth energy efficiencies than the ancestor under nonstress or high-salinity conditions. Consistently, ES10-5 did not display most of the basal transcriptional changes observed in ES9-11, but it showed increased expression of genes involved in glutamate biosynthesis, cation efflux, and energy metabolism under high salinity. These results demonstrated the role of glutamate as a key osmolyte and i17:1ω9c as the major PLFA for salt tolerance in D. vulgaris. The mechanistic changes in evolved genotypes suggested that growth energy efficiency might be a key factor for selection. IMPORTANCE High salinity (e.g., elevated NaCl) is a stressor that affects many organisms. Salt tolerance, a complex trait involving multiple cellular pathways, is attractive for experimental evolutionary studies. Desulfovibrio vulgaris Hildenborough is a model sulfate-reducing bacterium (SRB) that is important in biogeochemical cycling of sulfur, carbon, and nitrogen, potentially for bio-corrosion, and for bioremediation of toxic heavy metals and radionuclides. The coexistence of SRB and high salinity in natural habitats and heavy metal-contaminated field sites laid the foundation for the study of salt adaptation of D. vulgaris Hildenborough with experimental evolution. Here, we analyzed a clone that evolved under salt stress for 5,000 generations and compared it to a clone evolved under the same condition for 1,200 generations. The results indicated the key roles of glutamate for osmoprotection and of i17:1ω9c for increasing membrane fluidity during salt adaptation. The findings provide valuable insights about the salt adaptation mechanism changes during long-term experimental evolution. IMPORTANCE High salinity (e.g., elevated NaCl) is a stressor that affects many organisms. Salt tolerance, a complex trait involving multiple cellular pathways, is attractive for experimental evolutionary studies. Desulfovibrio vulgaris Hildenborough is a model sulfate-reducing bacterium (SRB) that is important in biogeochemical cycling of sulfur, carbon, and nitrogen, potentially for bio-corrosion, and for bioremediation of toxic heavy metals and radionuclides. The coexistence of SRB and high salinity in natural habitats and heavy metal-contaminated field sites laid the foundation for the study of salt adaptation of D. vulgaris Hildenborough with experimental evolution. Here, we analyzed a clone that evolved under salt stress for 5,000 generations and compared it to a clone evolved under the same condition for 1,200 generations. The results indicated the key roles of glutamate for osmoprotection and of i17:1ω9c for increasing membrane fluidity during salt adaptation. The findings provide valuable insights about the salt adaptation mechanism changes during long-term experimental evolution.

The More Control, the Better?

2014 ◽  
Vol 26 (2) ◽  
pp. 81-91 ◽  
Author(s):  
Jeeyun Oh ◽  
Mun-Young Chung ◽  
Sangyong Han
Keyword(s):  
Mixed Design ◽  
Negative Effects ◽  
Story Structure ◽  
Content Type ◽  
High User ◽  
User Control ◽  
Rigorous Research ◽  
Control Versus ◽  
The Media ◽  
The Impact

Despite of the popularity of interactive movie trailers, rigorous research on one of the most apparent features of these interfaces – the level of user control – has been scarce. This study explored the effects of user control on users’ immersion and enjoyment of the movie trailers, moderated by the content type. We conducted a 2 (high user control versus low user control) × 2 (drama film trailer versus documentary film trailer) mixed-design factorial experiment. The results showed that the level of user control over movie trailer interfaces decreased users’ immersion when the trailer had an element of traditional story structure, such as a drama film trailer. Participants in the high user control condition answered that they were less fascinated with, absorbed in, focused on, mentally involved with, and emotionally affected by the movie trailer than participants in the low user control condition only with the drama movie trailer. The negative effects of user control on the level of immersion for the drama trailer translated into users’ enjoyment. The impact of user control over interfaces on immersion and enjoyment varies depending on the nature of the media content, which suggests a possible trade-off between the level of user control and entertainment outcomes.

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