scholarly journals Physiology, Biochemistry, and Applications of F420- and Fo-Dependent Redox Reactions

2016 ◽  
Vol 80 (2) ◽  
pp. 451-493 ◽  
Author(s):  
Chris Greening ◽  
F. Hafna Ahmed ◽  
A. Elaaf Mohamed ◽  
Brendon M. Lee ◽  
Gunjan Pandey ◽  
...  
Keyword(s):  
Redox Reactions ◽  
Methanogenic Archaea ◽  
Content Type ◽  
Sulfate Reducing ◽  
Single Function ◽  
Wide Range ◽  
Domains Of Life ◽  
Photochemical Properties ◽  
Endogenous Metabolites ◽  
Dependent Processes

SUMMARY5-Deazaflavin cofactors enhance the metabolic flexibility of microorganisms by catalyzing a wide range of challenging enzymatic redox reactions. While structurally similar to riboflavin, 5-deazaflavins have distinctive and biologically useful electrochemical and photochemical properties as a result of the substitution of N-5 of the isoalloxazine ring for a carbon. 8-Hydroxy-5-deazaflavin (Fo) appears to be used for a single function: as a light-harvesting chromophore for DNA photolyases across the three domains of life. In contrast, its oligoglutamyl derivative F420is a taxonomically restricted but functionally versatile cofactor that facilitates many low-potential two-electron redox reactions. It serves as an essential catabolic cofactor in methanogenic, sulfate-reducing, and likely methanotrophic archaea. It also transforms a wide range of exogenous substrates and endogenous metabolites in aerobic actinobacteria, for example mycobacteria and streptomycetes. In this review, we discuss the physiological roles of F420in microorganisms and the biochemistry of the various oxidoreductases that mediate these roles. Particular focus is placed on the central roles of F420in methanogenic archaea in processes such as substrate oxidation, C1pathways, respiration, and oxygen detoxification. We also describe how two F420-dependent oxidoreductase superfamilies mediate many environmentally and medically important reactions in bacteria, including biosynthesis of tetracycline and pyrrolobenzodiazepine antibiotics by streptomycetes, activation of the prodrugs pretomanid and delamanid byMycobacterium tuberculosis, and degradation of environmental contaminants such as picrate, aflatoxin, and malachite green. The biosynthesis pathways of Foand F420are also detailed. We conclude by considering opportunities to exploit deazaflavin-dependent processes in tuberculosis treatment, methane mitigation, bioremediation, and industrial biocatalysis.

scholarly journals Abundance and Genetic Diversity ofnifHGene Sequences in Anthropogenically Affected Brazilian Mangrove Sediments

2012 ◽  
Vol 78 (22) ◽  
pp. 7960-7967 ◽  
Author(s):  
Armando Cavalcante Franco Dias ◽  
Michele de Cassia Pereira e Silva ◽  
Simone Raposo Cotta ◽  
Francisco Dini-Andreote ◽  
Fábio Lino Soares ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Gene Diversity ◽  
Conservation Strategies ◽  
Mangrove Sediment ◽  
Nitrogen Fixing ◽  
Content Type ◽  
Sulfate Reducing ◽  
Wide Range ◽  
Gradient Gel Electrophoresis

ABSTRACTAlthough mangroves represent ecosystems of global importance, the genetic diversity and abundance of functional genes that are key to their functioning scarcely have been explored. Here, we present a survey based on thenifHgene across transects of sediments of two mangrove systems located along the coast line of São Paulo state (Brazil) which differed by degree of disturbance, i.e., an oil-spill-affected and an unaffected mangrove. The diazotrophic communities were assessed by denaturing gradient gel electrophoresis (DGGE), quantitative PCR (qPCR), and clone libraries. ThenifHgene abundance was similar across the two mangrove sediment systems, as evidenced by qPCR. However, thenifH-based PCR-DGGE profiles revealed clear differences between the mangroves. Moreover, shifts in thenifHgene diversities were noted along the land-sea transect within the previously oiled mangrove. ThenifHgene diversity depicted the presence of nitrogen-fixing bacteria affiliated with a wide range of taxa, encompassing members of theAlphaproteobacteria,Betaproteobacteria,Gammaproteobacteria,Firmicutes, and also a group of anaerobic sulfate-reducing bacteria. We also detected a unique mangrove-specific cluster of sequences denoted Mgv-nifH. Our results indicate that nitrogen-fixing bacterial guilds can be partially endemic to mangroves, and these communities are modulated by oil contamination, which has important implications for conservation strategies.

scholarly journals Biomineralization of Cu2S Nanoparticles by Geobacter sulfurreducens

2020 ◽  
Vol 86 (18) ◽  
Author(s):  
Richard L. Kimber ◽  
Heath Bagshaw ◽  
Kurt Smith ◽  
Dawn M. Buchanan ◽  
Victoria S. Coker ◽  
...  
Keyword(s):  
Biogeochemical Cycling ◽  
Geobacter Sulfurreducens ◽  
Edge Structure ◽  
Colloidal Transport ◽  
Content Type ◽  
Anoxic Conditions ◽  
X Ray ◽  
Sulfate Reducing ◽  
Wide Range ◽  
X Ray Absorption

ABSTRACT Biomineralization of Cu has been shown to control contaminant dynamics and transport in soils. However, very little is known about the role that subsurface microorganisms may play in the biogeochemical cycling of Cu. In this study, we investigate the bioreduction of Cu(II) by the subsurface metal-reducing bacterium Geobacter sulfurreducens. Rapid removal of Cu from solution was observed in cell suspensions of G. sulfurreducens when Cu(II) was supplied, while transmission electron microscopy (TEM) analyses showed the formation of electron-dense nanoparticles associated with the cell surface. Energy-dispersive X-ray spectroscopy (EDX) point analysis and EDX spectrum image maps revealed that the nanoparticles are rich in both Cu and S. This finding was confirmed by X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) analyses, which identified the nanoparticles as Cu2S. Biomineralization of CuxS nanoparticles in soils has been reported to enhance the colloidal transport of a number of contaminants, including Pb, Cd, and Hg. However, formation of these CuxS nanoparticles has only been observed under sulfate-reducing conditions and could not be repeated using isolates of implicated organisms. As G. sulfurreducens is unable to respire sulfate, and no reducible sulfur was supplied to the cells, these data suggest a novel mechanism for the biomineralization of Cu2S under anoxic conditions. The implications of these findings for the biogeochemical cycling of Cu and other metals as well as the green production of Cu catalysts are discussed. IMPORTANCE Dissimilatory metal-reducing bacteria are ubiquitous in soils and aquifers and are known to utilize a wide range of metals as terminal electron acceptors. These transformations play an important role in the biogeochemical cycling of metals in pristine and contaminated environments and can be harnessed for bioremediation and metal bioprocessing purposes. However, relatively little is known about their interactions with Cu. As a trace element that becomes toxic in excess, Cu can adversely affect soil biota and fertility. In addition, biomineralization of Cu nanoparticles has been reported to enhance the mobilization of other toxic metals. Here, we demonstrate that when supplied with acetate under anoxic conditions, the model metal-reducing bacterium Geobacter sulfurreducens can transform soluble Cu(II) to Cu2S nanoparticles. This study provides new insights into Cu biomineralization by microorganisms and suggests that contaminant mobilization enhanced by Cu biomineralization could be facilitated by Geobacter species and related organisms.

scholarly journals Draft Genome Sequence of Desulfobacter hydrogenophilus DSM 3380, a Psychrotolerant Sulfate-Reducing Bacterium

2020 ◽  
Vol 9 (14) ◽  
Author(s):  
Emma Bertran ◽  
Lewis M. Ward ◽  
David T. Johnston
Keyword(s):  
Sulfate Reduction ◽  
Genome Sequence ◽  
Environmental Conditions ◽  
Anaerobic Bacterium ◽  
Draft Genome ◽  
Strictly Anaerobic ◽  
Content Type ◽  
Sulfate Reducing ◽  
Microbial Sulfate Reduction ◽  
Wide Range

Here, we describe the genome of Desulfobacter hydrogenophilus DSM 3380, a bacterium that belongs to the Desulfobacterales. The genome of this strictly anaerobic bacterium capable of sulfate reduction expands our understanding of microbial sulfate reduction in a wide range of environmental conditions.

scholarly journals A Limited Microbial Consortium Is Responsible for Extended Bioreduction of Uranium in a Contaminated Aquifer

2011 ◽  
Vol 77 (17) ◽  
pp. 5955-5965 ◽  
Author(s):  
Thomas M. Gihring ◽  
Gengxin Zhang ◽  
Craig C. Brandt ◽  
Scott C. Brooks ◽  
James H. Campbell ◽  
...  
Keyword(s):  
16S Rrna ◽  
Temporal Dynamics ◽  
Methanogenic Archaea ◽  
Acid Oxidation ◽  
Rapid Decline ◽  
Effective Electron ◽  
Content Type ◽  
Sulfate Reducing ◽  
Spatial And Temporal Dynamics ◽  
Groundwater Systems

ABSTRACTSubsurface amendments of slow-release substrates (e.g., emulsified vegetable oil [EVO]) are thought to be a pragmatic alternative to using short-lived, labile substrates for sustained uranium bioimmobilization within contaminated groundwater systems. Spatial and temporal dynamics of subsurface microbial communities during EVO amendment are unknown and likely differ significantly from those of populations stimulated by soluble substrates, such as ethanol and acetate. In this study, a one-time EVO injection resulted in decreased groundwater U concentrations that remained below initial levels for approximately 4 months. Pyrosequencing and quantitative PCR of 16S rRNA from monitoring well samples revealed a rapid decline in groundwater bacterial community richness and diversity after EVO injection, concurrent with increased 16S rRNA copy levels, indicating the selection of a narrow group of taxa rather than a broad community stimulation. Members of theFirmicutesfamilyVeillonellaceaedominated after injection and most likely catalyzed the initial oil decomposition. Sulfate-reducing bacteria from the genusDesulforegula, known for long-chain fatty acid oxidation to acetate, also dominated after EVO amendment. Acetate and H2production during EVO degradation appeared to stimulate NO3−, Fe(III), U(VI), and SO42−reduction by members of theComamonadaceae,Geobacteriaceae, andDesulfobacterales. Methanogenic archaea flourished late to comprise over 25% of the total microbial community. Bacterial diversity rebounded after 9 months, although community compositions remained distinct from the preamendment conditions. These results demonstrated that a one-time EVO amendment served as an effective electron donor source forin situU(VI) bioreduction and that subsurface EVO degradation and metal reduction were likely mediated by successive identifiable guilds of organisms.

scholarly journals Stratified Microbial Structure and Activity in Sulfide- and Methane-Producing Anaerobic Sewer Biofilms

2014 ◽  
Vol 80 (22) ◽  
pp. 7042-7052 ◽  
Author(s):  
Jing Sun ◽  
Shihu Hu ◽  
Keshab Raj Sharma ◽  
Bing-Jie Ni ◽  
Zhiguo Yuan
Keyword(s):  
Surface Layer ◽  
Methanogenic Archaea ◽  
Molecular Techniques ◽  
Content Type ◽  
Sulfate Reducing ◽  
Biofilm Model ◽  
Reducing Bacteria ◽  
Microelectrode Measurements ◽  
Good Agreement

ABSTRACTSimultaneous production of sulfide and methane by anaerobic sewer biofilms has recently been observed, suggesting that sulfate-reducing bacteria (SRB) and methanogenic archaea (MA), microorganisms known to compete for the same substrates, can coexist in this environment. This study investigated the community structures and activities of SRB and MA in anaerobic sewer biofilms (average thickness of 800 μm) using a combination of microelectrode measurements, molecular techniques, and mathematical modeling. It was seen that sulfide was mainly produced in the outer layer of the biofilm, between the depths of 0 and 300 μm, which is in good agreement with the distribution of SRB population as revealed by cryosection-fluorescencein situhybridization (FISH). SRB had a higher relative abundance of 20% on the surface layer, which decreased gradually to below 3% at a depth of 400 μm. In contrast, MA mainly inhabited the inner layer of the biofilm. Their relative abundances increased from 10% to 75% at depths of 200 μm and 700 μm, respectively, from the biofilm surface layer. High-throughput pyrosequencing of 16S rRNA amplicons showed that SRB in the biofilm were mainly affiliated with five genera,Desulfobulbus,Desulfomicrobium,Desulfovibrio,Desulfatiferula, andDesulforegula, while about 90% of the MA population belonged to the genusMethanosaeta. The spatial organizations of SRB and MA revealed by pyrosequencing were consistent with the FISH results. A biofilm model was constructed to simulate the SRB and MA distributions in the anaerobic sewer biofilm. The good fit between model predictions and the experimental data indicate that the coexistence and spatial structure of SRB and MA in the biofilm resulted from the microbial types and their metabolic transformations and interactions with substrates.

scholarly journals Transfer of Plasmid DNA to Clinical Coagulase-Negative Staphylococcal Pathogens by Using a Unique Bacteriophage

2015 ◽  
Vol 81 (7) ◽  
pp. 2481-2488 ◽  
Author(s):  
Volker Winstel ◽  
Petra Kühner ◽  
Bernhard Krismer ◽  
Andreas Peschel ◽  
Holger Rohde
Keyword(s):  
Plasmid Dna ◽  
Genetic Manipulation ◽  
Current Knowledge ◽  
Virulence Determinants ◽  
Coagulase Negative Staphylococci ◽  
Reliable Technique ◽  
Content Type ◽  
Research Activities ◽  
Wide Range ◽  
Genetic Barriers

ABSTRACTGenetic manipulation of emerging bacterial pathogens, such as coagulase-negative staphylococci (CoNS), is a major hurdle in clinical and basic microbiological research. Strong genetic barriers, such as restriction modification systems or clustered regularly interspaced short palindromic repeats (CRISPR), usually interfere with available techniques for DNA transformation and therefore complicate manipulation of CoNS or render it impossible. Thus, current knowledge of pathogenicity and virulence determinants of CoNS is very limited. Here, a rapid, efficient, and highly reliable technique is presented to transfer plasmid DNA essential for genetic engineering to important CoNS pathogens from a uniqueStaphylococcus aureusstrain via a specificS. aureusbacteriophage, Φ187. Even strains refractory to electroporation can be transduced by this technique once donor and recipient strains share similar Φ187 receptor properties. As a proof of principle, this technique was used to delete the alternative transcription factor sigma B (SigB) via allelic replacement in nasal and clinicalStaphylococcus epidermidisisolates at high efficiencies. The described approach will allow the genetic manipulation of a wide range of CoNS pathogens and might inspire research activities to manipulate other important pathogens in a similar fashion.

scholarly journals Use of Proteins Identified through a Functional Genomic Screen To Develop a Protein Subunit Vaccine That Provides Significant Protection against Virulent Streptococcus suis in Pigs

2017 ◽  
Vol 86 (3) ◽  
Author(s):  
Susan L. Brockmeier ◽  
Crystal L. Loving ◽  
Tracy L. Nicholson ◽  
Jinhong Wang ◽  
Sarah E. Peters ◽  
...  
Keyword(s):  
Immune Response ◽  
Vaccine Trial ◽  
Streptococcus Suis ◽  
Protein Subunit ◽  
Content Type ◽  
Degree Of Protection ◽  
Wide Range ◽  
Associated Proteins ◽  
Clinical Protection ◽  
Cellular Immune

ABSTRACT Streptococcus suis is a bacterium that is commonly carried in the respiratory tract and that is also one of the most important invasive pathogens of swine, commonly causing meningitis, arthritis, and septicemia. Due to the existence of many serotypes and a wide range of immune evasion capabilities, efficacious vaccines are not readily available. The selection of S. suis protein candidates for inclusion in a vaccine was accomplished by identifying fitness genes through a functional genomics screen and selecting conserved predicted surface-associated proteins. Five candidate proteins were selected for evaluation in a vaccine trial and administered both intranasally and intramuscularly with one of two different adjuvant formulations. Clinical protection was evaluated by subsequent intranasal challenge with virulent S. suis . While subunit vaccination with the S. suis proteins induced IgG antibodies to each individual protein and a cellular immune response to the pool of proteins and provided substantial protection from challenge with virulent S. suis , the immune response elicited and the degree of protection were dependent on the parenteral adjuvant given. Subunit vaccination induced IgG reactive against different S. suis serotypes, indicating a potential for cross protection.

scholarly journals The Fennoscandian Shield deep terrestrial virosphere suggests slow motion ‘boom and burst’ cycles

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Karin Holmfeldt ◽  
Emelie Nilsson ◽  
Domenico Simone ◽  
Margarita Lopez-Fernandez ◽  
Xiaofen Wu ◽  
...  
Keyword(s):  
Antibiotic Production ◽  
Nutrient Recycling ◽  
Slow Motion ◽  
Deep Biosphere ◽  
Wide Range ◽  
Domains Of Life ◽  
Microbial Turnover ◽  
Rna Transcript ◽  
Viral Isolates ◽  
Antagonistic Interactions

AbstractThe deep biosphere contains members from all three domains of life along with viruses. Here we investigate the deep terrestrial virosphere by sequencing community nucleic acids from three groundwaters of contrasting chemistries, origins, and ages. These viromes constitute a highly unique community compared to other environmental viromes and sequenced viral isolates. Viral host prediction suggests that many of the viruses are associated with Firmicutes and Patescibacteria, a superphylum lacking previously described active viruses. RNA transcript-based activity implies viral predation in the shallower marine water-fed groundwater, while the deeper and more oligotrophic waters appear to be in ‘metabolic standby’. Viral encoded antibiotic production and resistance systems suggest competition and antagonistic interactions. The data demonstrate a viral community with a wide range of predicted hosts that mediates nutrient recycling to support a higher microbial turnover than previously anticipated. This suggests the presence of ‘kill-the-winner’ oscillations creating slow motion ‘boom and burst’ cycles.

scholarly journals Microbial Diversity Dynamics in a Methanogenic-Sulfidogenic UASB Reactor

2021 ◽  
Vol 18 (3) ◽  
pp. 1305
Author(s):  
E. Fernández-Palacios ◽  
Xudong Zhou ◽  
Mabel Mora ◽  
David Gabriel
Keyword(s):  
Paper Industry ◽  
Chemical Species ◽  
Methanogenic Archaea ◽  
Granular Sludge ◽  
Upflow Anaerobic Sludge Blanket ◽  
Uasb Reactor ◽  
Anaerobic Sludge ◽  
Rrna Gene ◽  
Sulfate Reducing ◽  
Long Run

In this study, the long-term performance and microbial dynamics of an Upflow Anaerobic Sludge Blanket (UASB) reactor targeting sulfate reduction in a SOx emissions treatment system were assessed using crude glycerol as organic carbon source and electron donor under constant S and C loading rates. The reactor was inoculated with granular sludge obtained from a pulp and paper industry and fed at a constant inlet sulfate concentration of 250 mg S-SO42−L−1 and a constant C/S ratio of 1.5 ± 0.3 g Cg−1 S for over 500 days. Apart from the regular analysis of chemical species, Illumina analyses of the 16S rRNA gene were used to study the dynamics of the bacterial community along with the whole operation. The reactor was sampled along the operation to monitor its diversity and the changes in targeted species to gain insight into the performance of the sulfidogenic UASB. Moreover, studies on the stratification of the sludge bed were performed by sampling at different reactor heights. Shifts in the UASB performance correlated well with the main shifts in microbial communities of interest. A progressive loss of the methanogenic capacity towards a fully sulfidogenic UASB was explained by a progressive wash-out of methanogenic Archaea, which were outcompeted by sulfate-reducing bacteria. Desulfovibrio was found as the main sulfate-reducing genus in the reactor along time. A progressive reduction in the sulfidogenic capacity of the UASB was found in the long run due to the accumulation of a slime-like substance in the UASB.

The role of organizational culture in the knowledge management process

2015 ◽  
Vol 19 (3) ◽  
pp. 433-455 ◽  
Author(s):  
Christina Ling-hsing Chang ◽  
Tung-Ching Lin
Keyword(s):  
Organizational Culture ◽  
Knowledge Management ◽  
Customer Service ◽  
Survey Methodology ◽  
Cultural Dimensions ◽  
Content Type ◽  
Knowledge Resources ◽  
Positive Effects ◽  
Wide Range ◽  
The Individual

Purpose – The purpose of the study is to focus on the enhancement of knowledge management (KM) performance and the relationship between organizational culture and KM process intention of individuals because of the diversity of organizational cultures (which include results-oriented, tightly controlled, job-oriented, closed system and professional-oriented cultures). Knowledge is a primary resource in organizations. If firms are able to effectively manage their knowledge resources, then a wide range of benefits can be reaped such as improved corporate efficiency, effectiveness, innovation and customer service. Design/methodology/approach – The survey methodology, which has the ability to enhance generalization of results (Dooley, 2001), was used to collect the data utilized in the testing of the research hypotheses. Findings – Results- and job-oriented cultures have positive effects on employee intention in the KM process (creation, storage, transfer and application), whereas a tightly controlled culture has negative effects. Research limitations/implications – However, it would have been better to use a longitudinal study to collect useful long-term data to understand how the KM process would be influenced when organizational culture dimensions are changed through/by management. This is the first limitation of this study. According to Mason and Pauleen (2003), KM culture is a powerful predictor of individual knowledge-sharing behavior, which is not included in this study. Thus, this is the second limitation of this paper. Moreover, national culture could be an important issue in the KM process (Jacks et al., 2012), which is the third limitation of this paper for not comprising it. Practical implications – In researchers’ point of view, results- and job-oriented cultures have positive effects, whereas a tightly controlled culture has a negative effect on the KM process intention of the individual. These findings provide evidences that challenge the perspective of Kayworth and Leidner (2003) on this issue. As for practitioners, management has a direction to modify their organizational culture to improve the performance of KM process. Social implications – Both behavioral and value perspectives of the organizational cultural dimensions (results-oriented, tightly control, job-oriented, sociability, solidarity, need for achievement and democracy) should be examined to ascertain their effects firstly on KM culture and then on the KM process intention of the individual. It is hoped that the current study will spawn future investigations that lead to the development of an integrated model which includes organizational culture, KM culture and the KM process intention of the individual. Originality/value – The results-oriented, loosely controlled and job-oriented cultures will improve the effectiveness of the KM process and will also increase employees’ satisfaction and willingness to stay with the organization.

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