scholarly journals Divergence in Gene Regulation Contributes to Sympatric Speciation of Shewanella baltica Strains

2017 ◽  
Vol 84 (4) ◽  
Author(s):  
Jie Deng ◽  
Jennifer M. Auchtung ◽  
Konstantinos T. Konstantinidis ◽  
Alejandro Caro-Quintero ◽  
Ingrid Brettar ◽  
...  
Keyword(s):  
Transition Zone ◽  
Sequence Divergence ◽  
Positive Association ◽  
Sulfur Compounds ◽  
Comparative Genomic ◽  
Sequence Evolution ◽  
Transcriptional Responses ◽  
Content Type ◽  
Redox Transition ◽  
Shewanella Baltica

ABSTRACT Niche partitioning and sequence evolution drive genomic and phenotypic divergence, which ultimately leads to bacterial diversification. This study investigated the genomic composition of two Shewanella baltica clades previously identified through multilocus sequencing typing and recovered from the redox transition zone in the central Baltic Sea. Comparative genomic analysis revealed significantly higher interclade than intraclade genomic dissimilarity and that a subset of genes present in clade A were associated with potential adaptation to respiration of sulfur compounds present in the redox transition zone. The transcriptomic divergence between two representative strains of clades A and D, OS185 and OS195, was also characterized and revealed marked regulatory differences. We found that both the transcriptional divergence of shared genes and expression of strain-specific genes led to differences in regulatory patterns between strains that correlate with environmental redox niches. For instance, under anoxic conditions of respiratory nitrate ammonification, OS185—the strain isolated from a nitrate-rich environment—upregulated nearly twice the number of shared genes upregulated by OS195—the strain isolated from an H 2 S-containing anoxic environment. Conversely, OS195 showed stronger induction of strain-specific genes, especially those associated with sulfur compound respiration, under thiosulfate-reducing conditions. A positive association between the level of transcriptional divergence and the level of sequence divergence for shared genes was also noted. Our results provide further support for the hypothesis that genomic changes impacting transcriptional regulation play an important role in the diversification of ecologically distinct populations. IMPORTANCE This study examined potential mechanisms through which co-occurring Shewanella baltica strains diversified to form ecologically distinct populations. At the time of isolation, the strains studied composed the major fraction of culturable nitrate-reducing communities in the Baltica Sea. Analysis of genomic content of 13 S. baltica strains from two clades representing different ecotypes demonstrated that one clade specifically possesses a number of genes that could favor successful adaptation to respire sulfur compounds in the portion of the water column from which these strains were isolated. In addition, transcriptional profiling of fully sequenced strains representative of these two clades, OS185 and OS195, under oxygen-, nitrate-, and thiosulfate-respiring conditions demonstrated that the strains exhibit relatively similar transcriptional responses during aerobic growth but more-distinct transcriptional responses under nitrate- and thiosulfate-respiring conditions. Results from this study provide insights into how genomic and gene regulatory diversification together impacted the redox specialization of the S. baltica strains.

scholarly journals Evolutionary Analysis of Plastid Genomes of Seven Lonicera L. Species: Implications for Sequence Divergence and Phylogenetic Relationships

2018 ◽  
Vol 19 (12) ◽  
pp. 4039 ◽  
Author(s):  
Mi-Li Liu ◽  
Wei-Bing Fan ◽  
Ning Wang ◽  
Peng-Bin Dong ◽  
Ting-Ting Zhang ◽  
...  
Keyword(s):  
Molecular Genetic ◽  
Phylogenetic Reconstruction ◽  
Sequence Divergence ◽  
Genomic Analysis ◽  
Repeat Sequence ◽  
Biological Research ◽  
Comparative Genomic ◽  
Sequence Evolution ◽  
Evolutionary Analysis ◽  
Plastid Genomes

Plant plastomes play crucial roles in species evolution and phylogenetic reconstruction studies due to being maternally inherited and due to the moderate evolutionary rate of genomes. However, patterns of sequence divergence and molecular evolution of the plastid genomes in the horticulturally- and economically-important Lonicera L. species are poorly understood. In this study, we collected the complete plastomes of seven Lonicera species and determined the various repeat sequence variations and protein sequence evolution by comparative genomic analysis. A total of 498 repeats were identified in plastid genomes, which included tandem (130), dispersed (277), and palindromic (91) types of repeat variations. Simple sequence repeat (SSR) elements analysis indicated the enriched SSRs in seven genomes to be mononucleotides, followed by tetra-nucleotides, dinucleotides, tri-nucleotides, hex-nucleotides, and penta-nucleotides. We identified 18 divergence hotspot regions (rps15, rps16, rps18, rpl23, psaJ, infA, ycf1, trnN-GUU-ndhF, rpoC2-rpoC1, rbcL-psaI, trnI-CAU-ycf2, psbZ-trnG-UCC, trnK-UUU-rps16, infA-rps8, rpl14-rpl16, trnV-GAC-rrn16, trnL-UAA intron, and rps12-clpP) that could be used as the potential molecular genetic markers for the further study of population genetics and phylogenetic evolution of Lonicera species. We found that a large number of repeat sequences were distributed in the divergence hotspots of plastid genomes. Interestingly, 16 genes were determined under positive selection, which included four genes for the subunits of ribosome proteins (rps7, rpl2, rpl16, and rpl22), three genes for the subunits of photosystem proteins (psaJ, psbC, and ycf4), three NADH oxidoreductase genes (ndhB, ndhH, and ndhK), two subunits of ATP genes (atpA and atpB), and four other genes (infA, rbcL, ycf1, and ycf2). Phylogenetic analysis based on the whole plastome demonstrated that the seven Lonicera species form a highly-supported monophyletic clade. The availability of these plastid genomes provides important genetic information for further species identification and biological research on Lonicera.

scholarly journals Genomic Variations Underlying Speciation and Niche Specialization of Shewanella baltica

mSystems ◽  
2019 ◽  
Vol 4 (5) ◽  
Author(s):  
Jie Deng ◽  
Jennifer M. Auchtung ◽  
Konstantinos T. Konstantinidis ◽  
Ingrid Brettar ◽  
Manfred G. Höfle ◽  
...  
Keyword(s):  
Baltic Sea ◽  
Water Column ◽  
Transition Zone ◽  
Anaerobic Respiration ◽  
Electron Acceptors ◽  
Gene Content ◽  
Content Type ◽  
Genomic Variations ◽  
Niche Specialization ◽  
Shewanella Baltica

ABSTRACT Shewanella baltica was the dominant culturable nitrate-reducing bacterium in the eutrophic and strongly stratified Baltic Sea in the 1980s, where it primarily inhabited the oxic-anoxic transition zone. The genomic structures of 46 of these isolates were investigated through comparative genomic hybridization (CGH), which revealed a gradient of genomic similarity, ranging from 65% to as high as 99%. The core genome of the S. baltica species was enriched in anaerobic respiration-associated genes. Auxiliary genes, most of which locate within a few genomic islands (GIs), were nonuniformly distributed among the isolates. Specifically, hypothetical and mobile genetic element (MGE)-associated genes dominated intraclade gene content differences, whereas gain/loss of functional genes drove gene content differences among less related strains. Among the major S. baltica clades, gene signatures related to specific redox-driven and spatial niches within the water column were identified. For instance, genes involved in anaerobic respiration of sulfur compounds may provide key adaptive advantages for clade A strains in anoxic waters where sulfur-containing electron acceptors are present. Genes involved in cell motility, in particular, a secondary flagellar biosynthesis system, may be associated with the free-living lifestyle by clade E strains. Collectively, this study revealed characteristics of genome variations present in the water column and active speciation of S. baltica strains, driven by niche partitioning and horizontal gene transfer (HGT). IMPORTANCE Speciation in nature is a fundamental process driving the formation of the vast microbial diversity on Earth. In the central Baltic Sea, the long-term stratification of water led to formation of a large-scale vertical redoxcline that provided a gradient of environmental niches with respect to the availability of electron acceptors and donors. The region was home to Shewanella baltica populations, which composed the dominant culturable nitrate-reducing bacteria, particularly in the oxic-anoxic transition zone. Using the collection of S. baltica isolates as a model system, genomic variations showed contrasting gene-sharing patterns within versus among S. baltica clades and revealed genomic signatures of S. baltica clades related to redox niche specialization as well as particle association. This study provides important insights into genomic mechanisms underlying bacterial speciation within this unique natural redoxcline.

scholarly journals Comparative Genomic and Transcriptomic Analyses Reveal Habitat Differentiation and Different Transcriptional Responses during Pectin Metabolism in Alishewanella Species

2013 ◽  
Vol 79 (20) ◽  
pp. 6351-6361 ◽  
Author(s):  
Jaejoon Jung ◽  
Woojun Park
Keyword(s):  
Oxidative Stress ◽  
Stress Responses ◽  
Expression Patterns ◽  
Genomic Islands ◽  
Comparative Genomic ◽  
Pectin Degradation ◽  
Transcriptional Responses ◽  
Natural Habitats ◽  
Content Type ◽  
Habitat Differentiation

ABSTRACTAlishewanellaspecies are expected to have high adaptability to diverse environments because they are isolated from different natural habitats. To investigate how the evolutionary history ofAlishewanellaspecies is reflected in their genomes, we performed comparative genomic and transcriptomic analyses ofA. jeotgali,A. aestuarii, andA. agri, which were isolated from fermented seafood, tidal flat sediment, and soil, respectively. Genomic islands with variable GC contents indicated that invasion of prophage and transposition events occurred inA. jeotgaliandA. agribut not inA. aestuarii. Habitat differentiation ofA. agrifrom a marine environment to a terrestrial environment was proposed because the species-specific genes ofA. agriwere similar to those of soil bacteria, whereas those ofA. jeotgaliandA. aestuariiwere more closely related to marine bacteria. Comparative transcriptomic analysis with pectin as a sole carbon source revealed different transcriptional responses inAlishewanellaspecies, especially in oxidative stress-, methylglyoxal detoxification-, membrane maintenance-, and protease/chaperone activity-related genes. Transcriptomic and experimental data demonstrated thatA. agrihad a higher pectin degradation rate and more resistance to oxidative stress under pectin-amended conditions than the other 2Alishewanellaspecies. However, expression patterns of genes in the pectin metabolic pathway and of glyoxylate bypass genes were similar among all 3Alishewanellaspecies. Our comparative genomic and transcriptomic data revealed thatAlishewanellaspecies have evolved through horizontal gene transfer and habitat differentiation and that pectin degradation pathways inAlishewanellaspecies are highly conserved, although stress responses of eachAlishewanellaspecies differed under pectin culture conditions.

Empirical analysis on corporate environmental performance and environmental disclosure in an emerging market context

2020 ◽  
Vol 15 (6) ◽  
pp. 1061-1082 ◽  
Author(s):  
Merve Acar ◽  
Hüseyin Temiz
Keyword(s):  
Environmental Performance ◽  
Emerging Market ◽  
Positive Association ◽  
Corporate Environmental Performance ◽  
Tobit Regression ◽  
Environmental Reporting ◽  
Environmental Disclosure ◽  
Significant Positive Association ◽  
Content Type ◽  
Environmental Disclosures

PurposeThe purpose of this study is to investigate the association between environmental performance of firms and the level of voluntary environmental disclosure in emerging markets.Design/methodology/approachWe used tobit regression OLS and t-test methods to reveal the association between environmental performance and the level of voluntary environmental disclosure.FindingsWe find a significant positive association between the level of discretionary environmental disclosures and corporate environmental performance. The result is in line with the arguments of economics disclosure theory that argues environmentally good performers disclose more.Practical implicationsMany of the environmentally good firms in Turkey are also listed in the “BIST Sustainability Index,” and this situation can be the result of the relative power of external regulations. Accordingly, it can be suggested to increase the community and governmental pressures for environmental reporting but also gives importance to increase intrinsic motivations for companies to engage in disclosure practices.Originality/valueThis study shed light on relation between environmental performance and environmental disclosure in an emerging market context. Also, it is revisited that the relation between environmental performance and the level of environmental disclosure by testing two different predictions on the level of environmental disclosures.

Social media engagement, service complexity, and experiential quality in US hospitals

2020 ◽  
Vol 34 (6) ◽  
pp. 833-845 ◽  
Author(s):  
Youngsu Lee ◽  
Joonhwan In ◽  
Seung Jun Lee
Keyword(s):  
Social Media ◽  
Demographic Data ◽  
Positive Association ◽  
Customer Engagement ◽  
Service Firms ◽  
Multiple Sources ◽  
Cross Sectional ◽  
Content Type ◽  
Social Media Engagement ◽  
Experiential Quality

Purpose As social media platforms become increasingly popular among service firms, many US hospitals have been using social media as a means to improve their patients’ experiences. However, little research has explored the implications of social media use within a hospital context. The purpose of this paper is to investigate a hospital’s customer engagement through social media and its association with customers’ experiential quality. Also, this study examines the role of a hospital’s service characteristics, which could shape the nature of the interactions between patients and the hospital. Design/methodology/approach Data from 669 hospitals with complete experiential quality and demographic data were collected from multiple sources of secondary data, including the rankings of social media friendly hospitals, the Hospital Compare database, the Center for Medicare and Medicaid (CMS) cost report, the CMS impact file, the Healthcare Information and Management Systems Society Analytics database and the Dartmouth Atlas of Health Care. Specifically, the authors designed the instrumental variable estimate to address the endogeneity issue. Findings The empirical results suggest a positive association between a hospital’s social media engagement and experiential quality. For hospitals with a high level of service sophistication, the association between online engagement and experiential quality becomes more salient. For hospitals offering various services, offline engagement is a critical predictor of experiential quality. Research limitations/implications A hospital with more complex services should make efforts to engage customers through social media for better patient experiences. The sample is selected from databases in the US, and the databases are cross-sectional in nature. Practical implications Not all hospitals may be better off improving the patient experience by engaging customers through social media. Therefore, practitioners should exercise caution in applying the study’s results to other contexts and in making causal inferences. Originality/value The current study delineates customer engagement through social media into online and offline customer engagement. This study is based on the theory of customer engagement and reflects the development of mobile technology. Moreover, this research may be considered as pioneering in that it considers the key characteristics of a hospital’s service operations (i.e., service complexity) when discovering the link between customers’ engagement through a hospital’s social media and experiential quality.

scholarly journals An Evolutionary Link between Natural Transformation and CRISPR Adaptive Immunity

mBio ◽  
2012 ◽  
Vol 3 (5) ◽  
Author(s):  
Peter Jorth ◽  
Marvin Whiteley
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Bacterial Diversity ◽  
Natural Transformation ◽  
Bacterial Species ◽  
Comparative Genomic ◽  
Content Type ◽  
Immune Systems ◽  
Adaptive Immune ◽  
Adaptive Immune Systems

ABSTRACTNatural transformation by competent bacteria is a primary means of horizontal gene transfer; however, evidence that competence drives bacterial diversity and evolution has remained elusive. To test this theory, we used a retrospective comparative genomic approach to analyze the evolutionary history ofAggregatibacter actinomycetemcomitans, a bacterial species with both competent and noncompetent sister strains. Through comparative genomic analyses, we reveal that competence is evolutionarily linked to genomic diversity and speciation. Competence loss occurs frequently during evolution and is followed by the loss of clustered regularly interspaced short palindromic repeats (CRISPRs), bacterial adaptive immune systems that protect against parasitic DNA. Relative to noncompetent strains, competent bacteria have larger genomes containing multiple rearrangements. In contrast, noncompetent bacterial genomes are extremely stable but paradoxically susceptible to infective DNA elements, which contribute to noncompetent strain genetic diversity. Moreover, incomplete noncompetent strain CRISPR immune systems are enriched for self-targeting elements, which suggests that the CRISPRs have been co-opted for bacterial gene regulation, similar to eukaryotic microRNAs derived from the antiviral RNA interference pathway.IMPORTANCEThe human microbiome is rich with thousands of diverse bacterial species. One mechanism driving this diversity is horizontal gene transfer by natural transformation, whereby naturally competent bacteria take up environmental DNA and incorporate new genes into their genomes. Competence is theorized to accelerate evolution; however, attempts to test this theory have proved difficult. Through genetic analyses of the human periodontal pathogenAggregatibacter actinomycetemcomitans, we have discovered an evolutionary connection between competence systems promoting gene acquisition and CRISPRs (clustered regularly interspaced short palindromic repeats), adaptive immune systems that protect bacteria against genetic parasites. We show that competentA. actinomycetemcomitansstrains have numerous redundant CRISPR immune systems, while noncompetent bacteria have lost their CRISPR immune systems because of inactivating mutations. Together, the evolutionary data linking the evolution of competence and CRISPRs reveals unique mechanisms promoting genetic heterogeneity and the rise of new bacterial species, providing insight into complex mechanisms underlying bacterial diversity in the human body.

scholarly journals Antibiotic Resistance Markers in Burkholderia pseudomallei Strain Bp1651 Identified by Genome Sequence Analysis

2017 ◽  
Vol 61 (6) ◽  
Author(s):  
Julia V. Bugrysheva ◽  
David Sue ◽  
Jay E. Gee ◽  
Mindy G. Elrod ◽  
Alex R. Hoffmaster ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Clavulanic Acid ◽  
Burkholderia Pseudomallei ◽  
Efflux Pump ◽  
Point Mutations ◽  
Comparative Genomic ◽  
Content Type ◽  
Reductase Gene ◽  
Amoxicillin Clavulanic Acid ◽  
Imipenem Resistance

ABSTRACT Burkholderia pseudomallei Bp1651 is resistant to several classes of antibiotics that are usually effective for treatment of melioidosis, including tetracyclines, sulfonamides, and β-lactams such as penicillins (amoxicillin-clavulanic acid), cephalosporins (ceftazidime), and carbapenems (imipenem and meropenem). We sequenced, assembled, and annotated the Bp1651 genome and analyzed the sequence using comparative genomic analyses with susceptible strains, keyword searches of the annotation, publicly available antimicrobial resistance prediction tools, and published reports. More than 100 genes in the Bp1651 sequence were identified as potentially contributing to antimicrobial resistance. Most notably, we identified three previously uncharacterized point mutations in penA, which codes for a class A β-lactamase and was previously implicated in resistance to β-lactam antibiotics. The mutations result in amino acid changes T147A, D240G, and V261I. When individually introduced into select agent-excluded B. pseudomallei strain Bp82, D240G was found to contribute to ceftazidime resistance and T147A contributed to amoxicillin-clavulanic acid and imipenem resistance. This study provides the first evidence that mutations in penA may alter susceptibility to carbapenems in B. pseudomallei. Another mutation of interest was a point mutation affecting the dihydrofolate reductase gene folA, which likely explains the trimethoprim resistance of this strain. Bp1651 was susceptible to aminoglycosides likely because of a frameshift in the amrB gene, the transporter subunit of the AmrAB-OprA efflux pump. These findings expand the role of penA to include resistance to carbapenems and may assist in the development of molecular diagnostics that predict antimicrobial resistance and provide guidance for treatment of melioidosis.

scholarly journals Microbial mineral colonization across a subsurface redox transition zone

2015 ◽  
Vol 6 ◽  
Author(s):  
Brandon J. Converse ◽  
James P. McKinley ◽  
Charles T. Resch ◽  
Eric E. Roden
Keyword(s):  
Transition Zone ◽  
Redox Transition

scholarly journals Naturally Occurring Motility-Defective Mutants of Salmonella enterica Serovar Enteritidis Isolated Preferentially from Nonhuman Rather than Human Sources

2011 ◽  
Vol 77 (21) ◽  
pp. 7740-7748 ◽  
Author(s):  
Lucía Yim ◽  
Laura Betancor ◽  
Arací Martínez ◽  
Clare Bryant ◽  
Duncan Maskell ◽  
...  
Keyword(s):  
Salmonella Enterica ◽  
Intestinal Epithelial ◽  
Salmonella Enterica Serovar Enteritidis ◽  
Transcriptional Responses ◽  
Content Type ◽  
Field Isolates ◽  
Specific Pcr ◽  
Human Intestinal Epithelial Cells ◽  
Natural Isolates ◽  
Cell Invasiveness

ABSTRACTSalmonellosis represents a worldwide health problem because it is one of the major causes of food-borne disease. Although motility is postulated as an importantSalmonellavirulence attribute, there is little information about variation in motility in natural isolates. Here we report the identification of a point mutation (T551 → G) inmotA, a gene essential for flagellar rotation, in severalSalmonella entericaserovar Enteritidis field isolates. This mutation results in bacteria that can biosynthesize structurally normal but paralyzed flagella and are impaired in their capacity to invade human intestinal epithelial cells. Introduction of a wild-type copy ofmotAinto one of these isolates restored both motility and cell invasiveness. ThemotAmutant triggered higher proinflammatory transcriptional responses than an aflagellate isolate in differentiated Caco-2 cells, suggesting that the paralyzed flagella are able to signal through pattern recognition receptors. A specific PCR was designed to screen for the T551 → G mutation in a collection of 266S. Enteritidis field isolates from a nationwide epidemic, comprising 194 from humans and 72 from other sources. We found that 72 of the 266 (27%) isolates were nonmotile, including 24.7% (48/194) of human and 33.3% (24/72) of food isolates. Among nonmotile isolates, 15 carried the T551 → G mutation and, significantly, 13 were recovered from food, including 7 from eggs, but only 2 were from human sources. These results suggest that the presence of paralyzed flagella may impair the ability ofS. Enteritidis to cause disease in the human host but does not prevent its ability to colonize chickens and infect eggs.

After-hours work-related technology use and individuals' deviance: the role of interruption overload, psychological transition and task closure

Kybernetes ◽  
2021 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Junaid Khalid ◽  
Qingxiong Derek Weng ◽  
Adeel Luqman ◽  
Muhammad Imran Rasheed ◽  
Maryam Hina
Keyword(s):  
Information And Communication Technologies ◽  
Technology Use ◽  
Deviant Behavior ◽  
Positive Association ◽  
Primary Data ◽  
Research Model ◽  
Content Type ◽  
Work Related ◽  
After Hours ◽  
And Task

PurposeThe information and communication technologies have made it progressively practical for employees to remain associated with work, even when they are not in the workplace. However, prior studies have provided very little understanding of the implications for the deviant behavior aspect. The current study aims to investigate the association between after-hours work-related technology usage and interpersonal, organizational and nonwork deviance through psychological transition, interruption overload and task closure. The authors draw upon the theory of conservation of resource (COR) to examine the research model.Design/methodology/approachThe primary data for the study has been collected in two waves from the sample of 318 employees who were working in diverse organizations in the Anhui province of the People's Republic of China for empirical testing of the authors’ research model.FindingsThis study's findings have revealed the positive association of after-hour work-related technology use with individuals' deviance in its entire three forms through psychological transition and interruption overload and have negative associations with all forms of deviance through task closure.Originality/valueThe significant contribution of this study is in the literature on technology use and employee outcomes, by identifying the consequences of technology use in both work (interpersonal deviance and organizational deviance) and outside work domain (nonwork deviance) and exploring the underlying mechanisms for these relationships in detail. To the best of the authors’ knowledge, this study is the first of its kind that investigates a relationship between after-hours technology use and all three kinds of deviance while exploring both the positive and negative perspectives in one study.

Sign in / Sign up

Export Citation Format

Share Document