scholarly journals Denitrification byAnaeromyxobacter dehalogenans, a Common Soil Bacterium Lacking the Nitrite Reductase GenesnirSandnirK

2017 ◽  
Vol 84 (4) ◽  
Author(s):  
Jenny R. Onley ◽  
Samiha Ahsan ◽  
Robert A. Sanford ◽  
Frank E. Löffler
Keyword(s):  
Soil Bacterium ◽  
Reference Sequence ◽  
Bacterial Genomes ◽  
N Loss ◽  
Content Type ◽  
Denitrification Potential ◽  
Soil Ecosystems ◽  
New Findings ◽  
Soils And Sediments ◽  
Denitrification Genes

ABSTRACTThe versatile soil bacteriumAnaeromyxobacter dehalogenanslacks the hallmark denitrification genesnirSandnirK(encoding NO2−→NO reductases) and couples growth to NO3−reduction to NH4+(respiratory ammonification) and to N2O reduction to N2.A. dehalogenansalso grows by reducing Fe(III) to Fe(II), which chemically reacts with NO2−to form N2O (i.e., chemodenitrification). Following the addition of 100 μmol of NO3−or NO2−to Fe(III)-grown axenic cultures ofA. dehalogenans, 54 (±7) μmol and 113 (±2) μmol N2O-N, respectively, were produced and subsequently consumed. The conversion of NO3−to N2in the presence of Fe(II) through linked biotic-abiotic reactions represents an unrecognized ecophysiology ofA. dehalogenans. The new findings demonstrate that the assessment of gene content alone is insufficient to predict microbial denitrification potential and N loss (i.e., the formation of gaseous N products). A survey of complete bacterial genomes in the NCBI Reference Sequence database coupled with available physiological information revealed that organisms lackingnirSornirKbut with Fe(III) reduction potential and genes for NO3−and N2O reduction are not rare, indicating that NO3−reduction to N2through linked biotic-abiotic reactions is not limited toA. dehalogenans. Considering the ubiquity of iron in soils and sediments and the broad distribution of dissimilatory Fe(III) and NO3−reducers, denitrification independent of NO-forming NO2−reductases (through combined biotic-abiotic reactions) may have substantial contributions to N loss and N2O flux.IMPORTANCECurrent attempts to gauge N loss from soils rely on the quantitative measurement ofnirKandnirSgenes and/or transcripts. In the presence of iron, the common soil bacteriumAnaeromyxobacter dehalogenansis capable of denitrification and the production of N2without the key denitrification genesnirKandnirS. Such chemodenitrifiers denitrify through combined biotic and abiotic reactions and have potentially large contributions to N loss to the atmosphere and fill a heretofore unrecognized ecological niche in soil ecosystems. The findings emphasize that the comprehensive understanding of N flux and the accurate assessment of denitrification potential can be achieved only when integrated studies of interlinked biogeochemical cycles are performed.

scholarly journals Detection and Diversity of Fungal Nitric Oxide Reductase Genes (p450nor) in Agricultural Soils

2016 ◽  
Vol 82 (10) ◽  
pp. 2919-2928 ◽  
Author(s):  
Steven A. Higgins ◽  
Allana Welsh ◽  
Luis H. Orellana ◽  
Konstantinos T. Konstantinidis ◽  
Joanne C. Chee-Sanford ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Agricultural Soils ◽  
Agricultural Practices ◽  
Environmental Dna ◽  
Pcr Primers ◽  
Amino Acid Identity ◽  
N Loss ◽  
Content Type ◽  
Denitrification Potential ◽  
Fungal Isolates

ABSTRACTMembers of the Fungi convert nitrate (NO3−) and nitrite (NO2−) to gaseous nitrous oxide (N2O) (denitrification), but the fungal contributions to N loss from soil remain uncertain. Cultivation-based methodologies that include antibiotics to selectively assess fungal activities have limitations, and complementary molecular approaches to assign denitrification potential to fungi are desirable. Microcosms established with soils from two representative U.S. Midwest agricultural regions produced N2O from added NO3−or NO2−in the presence of antibiotics to inhibit bacteria. Cultivation efforts yielded 214 fungal isolates belonging to at least 15 distinct morphological groups, 151 of which produced N2O from NO2−. Novel PCR primers targeting thep450norgene, which encodes the nitric oxide (NO) reductase responsible for N2O production in fungi, yielded 26 novelp450noramplicons from DNA of 37 isolates and 23 amplicons from environmental DNA obtained from two agricultural soils. The sequences shared 54 to 98% amino acid identity with reference P450nor sequences within the phylumAscomycotaand expand the known fungal P450nor sequence diversity.p450norwas detected in all fungal isolates that produced N2O from NO2−, whereasnirK(encoding the NO-forming NO2−reductase) was amplified in only 13 to 74% of the N2O-forming isolates using two separatenirKprimer sets. Collectively, our findings demonstrate the value ofp450nor-targeted PCR to complement existing approaches to assess the fungal contributions to denitrification and N2O formation.IMPORTANCEA comprehensive understanding of the microbiota controlling soil N loss and greenhouse gas (N2O) emissions is crucial for sustainable agricultural practices and addressing climate change concerns. We report the design and application of a novel PCR primer set targeting fungalp450nor, a biomarker for fungal N2O production, and demonstrate the utility of the new approach to assess fungal denitrification potential in fungal isolates and agricultural soils. These new PCR primers may find application in a variety of biomes to assess the fungal contributions to N loss and N2O emissions.

scholarly journals NovelP450norGene Detection Assay Used To Characterize the Prevalence and Diversity of Soil Fungal Denitrifiers

2016 ◽  
Vol 82 (15) ◽  
pp. 4560-4569 ◽  
Author(s):  
Amy Novinscak ◽  
Claudia Goyer ◽  
Bernie J. Zebarth ◽  
David L. Burton ◽  
Martin H. Chantigny ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Agricultural Soils ◽  
Pcr Primers ◽  
Soil Samples ◽  
Pcr Assay ◽  
Gene Encoding ◽  
Content Type ◽  
Soil Ecosystems ◽  
Detection Assay ◽  
Denitrification Genes

ABSTRACTDenitrifying fungi produce nitrous oxide (N2O), a potent greenhouse gas, as they generally lack the ability to convert N2O to dinitrogen. Contrary to the case for bacterial denitrifiers, the prevalence and diversity of denitrifying fungi found in the environment are not well characterized. In this study, denitrifying fungi were isolated from various soil ecosystems, and novel PCR primers targeting theP450norgene, encoding the enzyme responsible for the conversion of nitric oxide to N2O, were developed, validated, and used to study the diversity of cultivable fungal denitrifiers. This PCR assay was also used to detectP450norgenes directly from environmental soil samples. Fungal denitrification capabilities were further validated using an N2O gas detection assay and a PCR assay targeting thenirKgene. A collection of 492 facultative anaerobic fungi was isolated from 15 soil ecosystems and taxonomically identified by sequencing the internal transcribed spacer sequence. Twenty-seven fungal denitrifiers belonging to 10 genera had theP450norand thenirKgenes and produced N2O from nitrite. N2O production is reported in strains not commonly known as denitrifiers, such asByssochlamys nivea,Volutella ciliata,Chloridiumspp., andTrichocladiumspp. The prevalence of fungal denitrifiers did not follow a soil ecosystem distribution; however, a higher diversity was observed in compost and agricultural soils. The phylogenetic trees constructed using partialP450norandnirKgene sequences revealed that both genes clustered taxonomically closely related strains together.IMPORTANCEA PCR assay targeting theP450norgene involved in fungal denitrification was developed and validated. The newly developedP450norprimers were used on fungal DNA extracted from a collection of fungi isolated from various soil environments and on DNA directly extracted from soil. The results indicated that approximatively 25% of all isolated fungi possessed this gene and were able to convert nitrite to N2O. All soil samples from which denitrifying fungi were isolated also tested positive for the presence ofP450nor. TheP450norgene detection assay was reliable in detecting a large diversity of fungal denitrifiers. Due to the lack of homology existing betweenP450norand bacterial denitrification genes, it is expected that this assay will become a tool of choice for studying fungal denitrifiers.

scholarly journals Complete Sequences of Two Plasmids Found in a Brazilian Bacillus thuringiensis Serovar israelensis Strain

2019 ◽  
Vol 8 (9) ◽  
Author(s):  
Fabrício S. Campos ◽  
Fernando B. Cerqueira ◽  
Gil R. Santos ◽  
Eliseu J. G. Pereira ◽  
Roberto F. T. Corrêia ◽  
...  
Keyword(s):  
Bacillus Thuringiensis ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Crucial Role ◽  
Bacterial Genomes ◽  
Content Type ◽  
Complete Sequences

Plasmids play a crucial role in the evolution of bacterial genomes by mediating horizontal gene transfer. In this work, we sequenced two plasmids found in a Brazilian Bacillus thuringiensis serovar israelensis strain which showed 100% nucleotide identities with Bacillus thuringiensis serovar kurstaki plasmids.

A (2 + 1)-dimensional extension of the Benjamin-Ono equation

2018 ◽  
Vol 28 (11) ◽  
pp. 2681-2687 ◽  
Author(s):  
Abdul-Majid Wazwaz
Keyword(s):  
Soliton Solutions ◽  
Traveling Wave Solutions ◽  
Content Type ◽  
Multiple Soliton Solutions ◽  
Proposed Model ◽  
New Findings ◽  
Propagation Of Waves ◽  
Model Features ◽  
Multiple Complex Soliton Solutions ◽  
Practical Implications

Purpose The purpose of this paper is concerned with developing a (2 + 1)-dimensional Benjamin–Ono equation. The study shows that multiple soliton solutions exist and multiple complex soliton solutions exist for this equation. Design/methodology/approach The proposed model has been handled by using the Hirota’s method. Other techniques were used to obtain traveling wave solutions. Findings The examined extension of the Benjamin–Ono model features interesting results in propagation of waves and fluid flow. Research limitations/implications The paper presents a new efficient algorithm for constructing extended models which give a variety of multiple soliton solutions. Practical implications This work is entirely new and provides new findings, where although the new model gives multiple soliton solutions, it is nonintegrable. Originality/value The work develops two complete sets of multiple soliton solutions, the first set is real solitons, whereas the second set is complex solitons.

Big Five personality traits in simulated negotiation settings

2018 ◽  
Vol 13 (2) ◽  
pp. 201-213 ◽  
Author(s):  
Pedro Fontes Falcão ◽  
Manuel Saraiva ◽  
Eduardo Santos ◽  
Miguel Pina e Cunha
Keyword(s):  
Personality Traits ◽  
Factor Model ◽  
Five Factor Model ◽  
Big Five Personality ◽  
Content Type ◽  
Situational Variables ◽  
Integrative Negotiation ◽  
Negotiation Behavior ◽  
New Findings ◽  
And Behavior

Purpose After a hiatus in the research on individual differences in negotiation, there has been a surge of renewed interest in recent years followed by several new findings. The purpose of this paper is to explore the effects that personality, as structured by the five-factor model, have over negotiation behavior and decision making in order to create new knowledge and prescribe advice to negotiators. Design/methodology/approach This study replicates observations from earlier studies but with the innovation of using a different methodology, as data from a sample of volunteer participants were collected in regard to their personality and behavior during two computerized negotiation simulations, one with the potential for joint gains and the other following a more traditional bargaining scenario. Findings Significant results for both settings were found, with the personality dimensions of agreeableness, conscientiousness, and extraversion systematically reoccurring as the most statistically relevant, although expressing different roles according to the type of negotiation and measure being registered. The findings thus suggest a multidimensional relationship between personality and situational variables in which specific traits can either become liabilities or assets depending upon whether the potential for value creation is present or not. Originality/value The new findings on the impacts of personality traits on both distributive and integrative negotiations allow negotiators to improve their performance and to adapt to specific distributive or integrative negotiation situations.

scholarly journals Modulating Pathogenesis with Mobile-CRISPRi

2019 ◽  
Vol 201 (22) ◽  
Author(s):  
Jiuxin Qu ◽  
Neha K. Prasad ◽  
Michelle A. Yu ◽  
Shuyan Chen ◽  
Amy Lyden ◽  
...  
Keyword(s):  
Gene Expression ◽  
Pathogenic Bacteria ◽  
Bacterial Species ◽  
Effector Proteins ◽  
Infection Model ◽  
Secretion Systems ◽  
Bacterial Genomes ◽  
Gene Encoding ◽  
Content Type ◽  
Animal Infection

ABSTRACT Conditionally essential (CE) genes are required by pathogenic bacteria to establish and maintain infections. CE genes encode virulence factors, such as secretion systems and effector proteins, as well as biosynthetic enzymes that produce metabolites not found in the host environment. Due to their outsized importance in pathogenesis, CE gene products are attractive targets for the next generation of antimicrobials. However, the precise manipulation of CE gene expression in the context of infection is technically challenging, limiting our ability to understand the roles of CE genes in pathogenesis and accordingly design effective inhibitors. We previously developed a suite of CRISPR interference-based gene knockdown tools that are transferred by conjugation and stably integrate into bacterial genomes that we call Mobile-CRISPRi. Here, we show the efficacy of Mobile-CRISPRi in controlling CE gene expression in an animal infection model. We optimize Mobile-CRISPRi in Pseudomonas aeruginosa for use in a murine model of pneumonia by tuning the expression of CRISPRi components to avoid nonspecific toxicity. As a proof of principle, we demonstrate that knock down of a CE gene encoding the type III secretion system (T3SS) activator ExsA blocks effector protein secretion in culture and attenuates virulence in mice. We anticipate that Mobile-CRISPRi will be a valuable tool to probe the function of CE genes across many bacterial species and pathogenesis models. IMPORTANCE Antibiotic resistance is a growing threat to global health. To optimize the use of our existing antibiotics and identify new targets for future inhibitors, understanding the fundamental drivers of bacterial growth in the context of the host immune response is paramount. Historically, these genetic drivers have been difficult to manipulate precisely, as they are requisite for pathogen survival. Here, we provide the first application of Mobile-CRISPRi to study conditionally essential virulence genes in mouse models of lung infection through partial gene perturbation. We envision the use of Mobile-CRISPRi in future pathogenesis models and antibiotic target discovery efforts.

scholarly journals Knowledge is power – conceptualizing collaborative financial risk assessment

2019 ◽  
Vol 20 (3) ◽  
pp. 226-248 ◽  
Author(s):  
Thomas Michael Brunner-Kirchmair ◽  
Melanie Wiener
Keyword(s):  
Risk Assessment ◽  
Risk Management ◽  
Financial Risk ◽  
Risk Identification ◽  
Modern World ◽  
Risk Governance ◽  
Financial Risks ◽  
Financial Risk Management ◽  
Content Type ◽  
New Findings

Purpose Inspired by new findings on and perceptions of risk governance, such as the necessity of taking a broader perspective in coping with risks in companies and working together in interactive groups with various stakeholders to deal with complex risks in the modern world, the purpose of this paper is looking for new ways to deal with financial risks. Current methods dealing with those risks are confronted with the problems of being primarily based on past data and experience, neglecting the need for objectivity, focusing on the short-term future and disregarding the interconnectedness of different financial risk categories. Design/methodology/approach A literature review of risk governance, financial risk management and open foresight was executed to conceptualize solutions to the mentioned-above problems. Findings Collaborative financial risk assessment (CFRA) is a promising approach in financial risk governance with respect to overcoming said problems. It is a method of risk identification and assessment, which combines aspects of “open foresight” and the financial risk management and governance literature. CFRA is characterized as bringing together members of different companies in trying to detect weak signals and trends to gain knowledge about the future, which helps companies to reduce financial risks and increase the chance of gaining economic value. By overcoming organizational boundaries, individual companies may gain the knowledge they would probably not have without CFRA and achieve a competitive advantage. Research limitations/implications A conceptual paper like the one at hand wants empirical proof. Therefore, the authors developed a research agenda in the form of five propositions for further research. Originality/value This paper discusses the existing problems of financial risk identification and assessment methods. It contributes to the existing literature by proposing CFRA as a solution to those problems and adding a new perspective to financial risk governance.

scholarly journals Draft Genome Sequence of Rhizobium tropici SARCC-755, a Free-Living Rhizobium That Nodulated and Promoted Growth in Pigeonpea [Cajanus cajan (L.) Millsp.]

2020 ◽  
Vol 9 (2) ◽  
Author(s):  
Francina Lebogang Bopape ◽  
Ahmed Idris Hassen ◽  
Zacharias H. Swanevelder ◽  
Eastonce T. Gwata
Keyword(s):  
Genome Sequence ◽  
Cajanus Cajan ◽  
Draft Genome ◽  
Soil Bacterium ◽  
Draft Genome Sequence ◽  
Rhizobium Tropici ◽  
Free Living ◽  
Content Type ◽  
Legume Plant ◽  
The Common

Rhizobium tropici SARCC-755 is a free-living soil bacterium that formed nodules on pigeonpea roots in the present study. However, the draft genome sequence reveals that this Rhizobium species contains the nolR gene but lacks the common nodulation (nodABC) genes and probably uses other pathways to induce nodules on the legume plant.

scholarly journals MITEAba12, a Novel Mobile Miniature Inverted-Repeat Transposable Element Identified inAcinetobacter baumanniiATCC 17978 and Its Prevalence across theMoraxellaceaeFamily

mSphere ◽  
2019 ◽  
Vol 4 (1) ◽  
Author(s):  
Felise G. Adams ◽  
Melissa H. Brown
Keyword(s):  
Inverted Repeat ◽  
Bacterial Species ◽  
Consensus Sequence ◽  
Target Site ◽  
The Novel ◽  
Bacterial Genomes ◽  
Content Type ◽  
Promoter Sequences ◽  
Moraxella Osloensis ◽  
Genome Level

ABSTRACTInsertion sequences (IS) are fundamental mediators of genome plasticity with the potential to generate phenotypic variation with significant evolutionary outcomes. Here, a recently active miniature inverted-repeat transposon element (MITE) was identified in a derivative ofAcinetobacter baumanniiATCC 17978 after being subjected to stress conditions. Transposition of the novel element led to the disruption of thehnsgene, resulting in a characteristic hypermotile phenotype. DNA identity shared between the terminal inverted repeats of this MITE and coresident ISAba12elements, together with the generation of 9-bp target site duplications, provides strong evidence that ISAba12elements were responsible for mobilization of the MITE (designated MITEAba12) within this strain. A wider genome-level survey identified MITEAba12in 30 additionalAcinetobactergenomes at various frequencies and oneMoraxella osloensisgenome. Ninety MITEAba12copies could be identified, of which 40% had target site duplications, indicating recent transposition events. Elements ranged between 111 and 114 bp; 90% were 113 bp in length. Using the MITEAba12consensus sequence, putative outward-facingEscherichia coliσ70 promoter sequences in both orientations were identified. The identification of transcripts originating from the promoter in one direction supports the proposal that the element can influence neighboring host gene transcription. The location of MITEAba12varied significantly between and within genomes, preferentially integrating into AT-rich regions. Additionally, a copy of MITEAba12was identified in a novel 8.5-kb composite transposon, Tn6645, in theM. osloensisCCUG 350 chromosome. Overall, this study shows that MITEAba12is the most abundant nonautonomous element currently found inAcinetobacter.IMPORTANCEOne of the most important weapons in the armory ofAcinetobacteris its impressive genetic plasticity, facilitating rapid genetic mutations and rearrangements as well as integration of foreign determinants carried by mobile genetic elements. Of these, IS are considered one of the key forces shaping bacterial genomes and ultimately evolution. We report the identification of a novel nonautonomous IS-derived element present in multiple bacterial species from theMoraxellaceaefamily and its recent translocation into thehnslocus in theA. baumanniiATCC 17978 genome. The latter finding adds new knowledge to only a limited number of documented examples of MITEs in the literature and underscores the plastic nature of thehnslocus inA. baumannii. MITEAba12, and its predicted parent(s), may be a source of substantial adaptive evolution within environmental and clinically relevant bacterial pathogens and, thus, have broad implications for niche-specific adaptation.

scholarly journals Draft Genome Sequence of Gordonia lacunae BS2T

2017 ◽  
Vol 5 (40) ◽  
Author(s):  
Kim Durrell ◽  
Alaric Prins ◽  
Marilize Le Roes-Hill
Keyword(s):  
South Africa ◽  
Secondary Metabolite ◽  
Genome Sequence ◽  
Draft Genome ◽  
Soil Bacterium ◽  
Draft Genome Sequence ◽  
Biosynthetic Genes ◽  
Content Type ◽  
New Compounds

ABSTRACT We report here the draft genome sequence of the soil bacterium Gordonia lacunae BS2T (= DSM 45085T = JCM 14873T = NRRL B-24551T), isolated from an estuary in Plettenberg Bay, South Africa. Analysis of the draft genome revealed that more than 40% of the secondary metabolite biosynthetic genes encode new compounds.

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