scholarly journals Re-Thinking the Roles of Pathogens and Mutualists: Exploring the Continuum of Symbiosis in the Context of Microbial Ecology and Evolution

2022 ◽  
Author(s):  
Ashley Stengel ◽  
Rhae Drijber ◽  
Erin Carr ◽  
Thais Egreja ◽  
Edward Hillman ◽  
...  
Keyword(s):  
Ecological Factors ◽  
Plant Host ◽  
Holistic View ◽  
Microbial Life ◽  
Evolutionary Forces ◽  
Dynamic Relationship ◽  
Research Activities ◽  
Host Microbe Interactions ◽  
Static Conditions ◽  
The Continuum

Systems of classification are important for guiding research activities and providing a common platform for discussion and investigation. One such system is assigning microbial taxa to the roles of mutualists and pathogens. Yet, there are often challenges and even inconsistencies in reports of research findings when microbial taxa display behaviors outside of these two static conditions (e.g. commensal). Over the last two decades, there has been some effort to highlight a continuum of symbiosis, wherein certain microbial taxa may exhibit mutualistic or pathogenic traits depending on environmental contexts, life stages, and plant host associations. However, gaps remain in understanding how to apply the continuum approach to host-microbe pairs across a range of environmental and ecological factors. This commentary presents an alternative framework for evaluating the continuum of symbiosis using dominant archetypes that define symbiotic ranges. We focus particularly on fungi and bacteria, though we recognize that archaea and other microeukaryotes play important roles in host-microbe interactions that may be described by this approach. This framework is centered in eco-evolutionary theory and aims to enhance communication among researchers, as well as prioritize holistic consideration of the factors shaping microbial life strategies. We discuss the influence of plant-mediated factors, habitat constraints, co-evolutionary forces, and the genetic contributions which shape different microbial lifestyles. Looking to the future, using a continuum of symbiosis paradigm will enable greater flexibility in defining the roles of target microbes and facilitate a more holistic view of the complex and dynamic relationship between microbes and plants.

scholarly journals Evidence of gene nucleotide composition favoring replication and growth in a fastidious plant pathogen

2021 ◽  
Author(s):  
Andreina I Castillo ◽  
Rodrigo P P Almeida
Keyword(s):  
Plant Pathogen ◽  
Geographic Origin ◽  
Gc Content ◽  
Nucleotide Composition ◽  
Plant Host ◽  
Mixed Effect ◽  
Genomic Changes ◽  
Evolutionary Forces ◽  
Multiple Variables ◽  
Vector Borne

Abstract Nucleotide composition (GC content) varies across bacteria species, genome regions, and specific genes. In Xylella fastidiosa, a vector-borne fastidious plant pathogen infecting multiple crops, GC content ranges between ∼51-52%; however, these values were gathered using limited genomic data. We evaluated GC content variations across X. fastidiosa subspecies fastidiosa (N = 194), subsp. pauca (N = 107), and subsp. multiplex (N = 39). Genomes were classified based on plant host and geographic origin; individual genes within each genome were classified based on gene function, strand, length, ortholog group, Core vs. Accessory, and Recombinant vs. Non-recombinant. GC content was calculated for each gene within each evaluated genome. The effects of genome and gene level variables were evaluated with a mixed effect ANOVA, and the marginal-GC content was calculated for each gene. Also, the correlation between gene-specific GC content vs. natural selection (dN/dS) and recombination/mutation (r/m) was estimated. Our analyses show that intra-genomic changes in nucleotide composition in X. fastidiosa are small and influenced by multiple variables. Higher AT-richness is observed in genes involved in replication and translation, and genes in the leading strand. In addition, we observed a negative correlation between high-AT and dN/dS in subsp. pauca. The relationship between recombination and GC content varied between core and accessory genes. We hypothesize that distinct evolutionary forces and energetic constraints both drive and limit these small variations in nucleotide composition.

How far have we come with the study of knowledge risks?

2019 ◽  
Vol 49 (1) ◽  
pp. 21-34 ◽  
Author(s):  
Susanne Durst
Keyword(s):  
Design Methodology ◽  
Review Process ◽  
Future Research ◽  
Large Share ◽  
Complete Coverage ◽  
Holistic View ◽  
Content Type ◽  
Body Of Knowledge ◽  
Research Activities ◽  
Research Questions

Purpose This paper aims to review research on the topic of knowledge risks to establish the current body of knowledge and, on this basis, to suggest some promising avenues for future research. Design/methodology/approach This study consists of a systematic review of 52 refereed articles on knowledge risks. Findings The findings contribute to a more holistic view of the topic and related aspects and, thus, complement the study of knowledge management. Additionally, a number of research questions are proposed, aimed at guiding and informing future research activities. Research limitations/implications This study may not have enabled a complete coverage of all articles in the field of knowledge risks. Yet, based on the chosen research methodology, it seems reasonable to assume that the review process covered a large share of studies available. Originality/value To the best of the author’s knowledge, no systematic literature review on knowledge risks and related issues has previously been published in academic journals.

Pipe material and water quality in a holistic view

2001 ◽  
Vol 1 (3) ◽  
pp. 1-10
Author(s):  
T. Hedberg
Keyword(s):  
Water Quality ◽  
Drinking Water ◽  
Water Treatment ◽  
Distribution Networks ◽  
Pipe Material ◽  
Treatment Technology ◽  
Water And Wastewater Treatment ◽  
Holistic View ◽  
General Terms ◽  
Research Activities

The new trends in societies towards sustainable development have necessitated a new way of thinking regarding water treatment, the distribution of drinking water and wastewater treatment. A process of implementing new European water directives is ongoing and the consequences and need for coordination of these changes are discussed. Raw water qualities, water treatment technology and drinking water quality have impacts on water quality deterioration in the distribution networks that negatively affect the possibilities for recycling sewage sludge containing valuable nutrients. Measures for coping with these issues are discussed in general terms and suggestions for future strategies and research activities are given.

scholarly journals Working Towards a Framework for Governing Health Research in Nepal

2020 ◽  
Vol 18 (2) ◽  
pp. 342-344
Author(s):  
Ashok Bhurtyal ◽  
Suman Pant ◽  
Ganesh Dangal ◽  
Pradip Gyanwali
Keyword(s):  
Health Research ◽  
Information Needs ◽  
Management Research ◽  
The Past ◽  
Research Systems ◽  
Research Activities ◽  
Health Research Council ◽  
Health Research Systems ◽  
Support Research ◽  
The Continuum

Health research activities have advanced considerably in Nepal over the past several years. However, stakeholders’ confidence on scientific community is shaken as the latter failed occasionally in adhering to ethical principles. Nepal Health Research Council has exercised regulatory authority to control and support research works. However, much more is needed given the scale at which studies are being carried out. It is high time to conduct an analysis of the current situation followed by the development of an overarching framework to strengthen health research that facilitates a range of actions along the continuum of identifying information needs to translation of knowledge into policies and practices for ultimately improving people’s health. Keywords: Ethics; health research systems; knowledge management; research regulation

scholarly journals Monitoring and Modeling the Terrestrial System from Pores to Catchments: The Transregional Collaborative Research Center on Patterns in the Soil–Vegetation–Atmosphere System

2015 ◽  
Vol 96 (10) ◽  
pp. 1765-1787 ◽  
Author(s):  
Clemens Simmer ◽  
Insa Thiele-Eich ◽  
Matthieu Masbou ◽  
Wulf Amelung ◽  
Heye Bogena ◽  
...  
Keyword(s):  
Collaborative Research ◽  
Weather Prediction ◽  
Research Centre ◽  
Climate Projections ◽  
Catchment Scale ◽  
Water Quality Control ◽  
Holistic View ◽  
Terrestrial System ◽  
Societal Relevance ◽  
Research Activities

Abstract Most activities of humankind take place in the transition zone between four compartments of the terrestrial system: the unconfined aquifer, including the unsaturated zone; surface water; vegetation; and atmosphere. The mass, momentum, and heat energy fluxes between these compartments drive their mutual state evolution. Improved understanding of the processes that drive these fluxes is important for climate projections, weather prediction, flood forecasting, water and soil resources management, agriculture, and water quality control. The different transport mechanisms and flow rates within the compartments result in complex patterns on different temporal and spatial scales that make predictions of the terrestrial system challenging for scientists and policy makers. The Transregional Collaborative Research Centre 32 (TR32) was formed in 2007 to integrate monitoring with modeling and data assimilation in order to develop a holistic view of the terrestrial system. TR32 is a long-term research program funded by the German national science foundation Deutsche Forschungsgemeinschaft (DFG), in order to focus and integrate research activities of several universities on an emerging scientific topic of high societal relevance. Aiming to bridge the gap between microscale soil pores and catchment-scale atmospheric variables, TR32 unites research groups from the German universities of Aachen, Bonn, and Cologne, and from the environmental and geoscience departments of Forschungszentrum Jülich GmbH. Here, we report about recent achievements in monitoring and modeling of the terrestrial system, including the development of new observation techniques for the subsurface, the establishment of cross-scale, multicompartment modeling platforms from the pore to the catchment scale, and their use to investigate the propagation of patterns in the state and structure of the subsurface to the atmospheric boundary layer.

scholarly journals Challenge of investigating biologically relevant functions of virulence factors in bacterial pathogens

2000 ◽  
Vol 355 (1397) ◽  
pp. 643-656 ◽  
Author(s):  
Richard Moxon ◽  
Christoph Tang
Keyword(s):  
Virulence Factors ◽  
Molecular Basis ◽  
Evolutionary Dynamics ◽  
Bacterial Pathogens ◽  
Ecological Factors ◽  
Personal Perspective ◽  
Biologically Relevant ◽  
Microbe Interactions ◽  
Host Microbe Interactions

Recent innovations have increased enormously the opportunities for investigating the molecular basis of bacterial pathogenicity, including the availability of whole–genome sequences, techniques for identifying key virulence genes, and the use of microarrays and proteomics. These methods should provide powerful tools for analysing the patterns of gene expression and function required for investigating host–microbe interactions in vivo. But, the challenge is exacting. Pathogenicity is a complex phenotype and the reductionist approach does not adequately address the eclectic and variable outcomes of host–microbe interactions, including evolutionary dynamics and ecological factors. There are difficulties in distinguishing bacterial ‘virulence’ factors from the many determinants that are permissive for pathogenicity, for example those promoting general fitness. A further practical problem for some of the major bacterial pathogens is that there are no satisfactory animal models or experimental assays that adequately reflect the infection under investigation. In this review, we give a personal perspective on the challenge of characterizing how bacterial pathogens behave in vivo and discuss some of the methods that might be most relevant for understanding the molecular basis of the diseases for which they are responsible. Despite the powerful genomic, molecular, cellular and structural technologies available to us, we are still struggling to come to grips with the question of ‘What is a pathogen?’

scholarly journals Multi-level modelling of time-series cross-sectional data reveals the dynamic interaction between ecological threats and democratic development

2020 ◽  
Vol 7 (3) ◽  
pp. 191804
Author(s):  
Kodai Kusano ◽  
Markus Kemmelmeier
Keyword(s):  
Time Series ◽  
Ecological Factors ◽  
Cross Sectional ◽  
Economic Wealth ◽  
Poor Countries ◽  
Democratic Development ◽  
Dynamic Relationship ◽  
Pathogen Prevalence ◽  
Multi Level ◽  
The Relationship

What is the relationship between environment and democracy? The framework of cultural evolution suggests that societal development is an adaptation to ecological threats. Pertinent theories assume that democracy emerges as societies adapt to ecological factors such as higher economic wealth, lower pathogen threats, less demanding climates and fewer natural disasters. However, previous research confused within-country processes with between-country processes and erroneously interpreted between-country findings as if they generalize to within-country mechanisms. We analyse a time-series cross-sectional dataset to study the dynamic relationship between environment and democracy (1949–2016), accounting for previous misconceptions in levels of analysis. By separating within-country processes from between-country processes, we find that the relationship between environment and democracy not only differs by country but also depends on the level of analysis. Economic wealth predicts increasing levels of democracy in between-country comparisons, but within-country comparisons show that democracy declines in years when countries become wealthier. This relationship is only prevalent among historically wealthy countries but not among historically poor countries, whose wealth also increased over time. By contrast, pathogen prevalence predicts lower levels of democracy in both between-country and within-country comparisons. Multi-level modelling also confirms that the within-country effect of pathogen prevalence remains robust even after considering a region-level analysis. Longitudinal analyses identifying temporal precedence reveal that not only reductions in pathogen prevalence drive future democracy, but also democracy reduces future pathogen prevalence and increases future wealth. These nuanced results contrast with previous analyses using narrow, cross-sectional data. Overall, our findings illuminate the dynamic process by which environment and democracy shape each other.

Understanding knowledge leakage: a review of previous studies

VINE ◽  
2015 ◽  
Vol 45 (4) ◽  
pp. 568-586 ◽  
Author(s):  
Susanne Durst ◽  
Lena Aggestam ◽  
Helio Aisenberg Ferenhof
Keyword(s):  
Design Methodology ◽  
Review Process ◽  
Future Research ◽  
Large Share ◽  
Complete Coverage ◽  
Holistic View ◽  
Content Type ◽  
Body Of Knowledge ◽  
Research Activities ◽  
Knowledge Leakage

Purpose – This paper aims to review research on the topic of knowledge leakage to establish the current body of knowledge and, on this basis, to suggest some promising avenues for future research. Design/methodology/approach – The study consists of a systematic review of 57 refereed empirical articles on knowledge leakage. Findings – The findings contribute to a more holistic view of the topic and complement the study of knowledge management. Additionally, a conceptual framework is proposed that aims at guiding and informing future research activities. Research limitations/implications – This study may not have enabled a complete coverage of all empirical articles in the field of knowledge leakage. Yet, based on the chosen research methodology, it seems reasonable to assume that the review process covered a large share of studies available. Originality/value – To the best of the authors’ knowledge, no systematic literature review on knowledge leakage has previously been published in academic journals.

‘ISeeYou’: A woman-centred care education and research project in Dutch bachelor midwifery education

2018 ◽  
Vol 77 (8) ◽  
pp. 899-914 ◽  
Author(s):  
Yvonne Fontein-Kuipers ◽  
Enja Romeijn ◽  
Arwen Zwijnenberg ◽  
Willemijn Eekhof ◽  
AnneLoes van Staa
Keyword(s):  
Higher Education ◽  
Reflective Practice ◽  
Participant Observation ◽  
Structured Interview ◽  
Observation Study ◽  
Research Activities ◽  
The Individual ◽  
The Impact ◽  
Insight Into ◽  
The Continuum

Objective: To examine how student midwives in higher education learn to become competent and confident woman-centred practitioners. Design: Participant observation study using a ‘buddy’ approach. Setting: Bachelor of Midwifery students in one higher education institution in the Netherlands Methods: First-year student midwives followed one woman throughout the continuum of childbirth. The students attended a minimum of five of the woman’s antenatal care encounters and a minimum of one postnatal care encounter. In addition, students explored the woman’s professional care network. Student midwives used participant observation, structured interview techniques and reflective practice to focus on (1) the woman and to gain insight into her wishes and experiences of care throughout the continuum of pregnancy, birth and postpartum period; (2) the impact of the caregiver on the woman; and (3) the woman’s experience of the partnership. Lectures, peer-debriefing, competency assessments, research activities and a logbook supported students’ learning. Results: Learning was achieved through the student’s relational continuity and active engagement with the individual woman. Students gained insight into the experiences of individual pregnant and postpartum women, the individual practice of healthcare practitioners and the interaction between the woman and the healthcare practitioner. Students’ development of critical thinking and reflective practice was enhanced to begin to form a vision of woman-centred care. Conclusion: The project was successful in equipping Bachelor of Midwifery students with competencies to support them in their learning of providing woman-centred care and offered them unique and in-depth experiences supporting and augmenting their personal, professional and academic development.

scholarly journals Parallel Evolution of Genome Streamlining and Cellular Bioenergetics across the Marine Radiation of a Bacterial Phylum

mBio ◽  
2018 ◽  
Vol 9 (5) ◽  
Author(s):  
Eric W. Getz ◽  
Saima Sultana Tithi ◽  
Liqing Zhang ◽  
Frank O. Aylward
Keyword(s):  
Nutrient Dynamics ◽  
Parallel Evolution ◽  
Biogeochemical Cycles ◽  
Microbial Evolution ◽  
Global Ocean ◽  
Microbial Life ◽  
Respiratory Complex ◽  
Evolutionary Forces ◽  
Cellular Bioenergetics ◽  
Key Features

ABSTRACTDiverse bacterial and archaeal lineages drive biogeochemical cycles in the global ocean, but the evolutionary processes that have shaped their genomic properties and physiological capabilities remain obscure. Here we track the genome evolution of the globally abundant marine bacterial phylumMarinimicrobiaacross its diversification into modern marine environments and demonstrate that extant lineages are partitioned between epipelagic and mesopelagic habitats. Moreover, we show that these habitat preferences are associated with fundamental differences in genomic organization, cellular bioenergetics, and metabolic modalities. Multiple lineages present in epipelagic niches independently acquired genes necessary for phototrophy and environmental stress mitigation, and their genomes convergently evolved key features associated with genome streamlining. In contrast, lineages residing in mesopelagic waters independently acquired nitrate respiratory machinery and a variety of cytochromes, consistent with the use of alternative terminal electron acceptors in oxygen minimum zones (OMZs). Further, while epipelagic clades have retained an ancestral Na+-pumping respiratory complex, mesopelagic lineages have largely replaced this complex with canonical H+-pumping respiratory complex I, potentially due to the increased efficiency of the latter together with the presence of the more energy-limiting environments deep in the ocean’s interior. These parallel evolutionary trends indicate that key features of genomic streamlining and cellular bioenergetics have occurred repeatedly and congruently in disparate clades and underscore the importance of environmental conditions and nutrient dynamics in driving the evolution of diverse bacterioplankton lineages in similar ways throughout the global ocean.IMPORTANCEUnderstanding long-term patterns of microbial evolution is critical to advancing our knowledge of past and present role microbial life in driving global biogeochemical cycles. Historically, it has been challenging to study the evolution of environmental microbes due to difficulties in obtaining genome sequences from lineages that could not be cultivated, but recent advances in metagenomics and single-cell genomics have begun to obviate many of these hurdles. Here we present an evolutionary genomic analysis of theMarinimicrobia, a diverse bacterial group that is abundant in the global ocean. We demonstrate that distantly relatedMarinimicrobiaspecies that reside in similar habitats have converged to assume similar genome architectures and cellular bioenergetics, suggesting that common factors shape the evolution of a broad array of marine lineages. These findings broaden our understanding of the evolutionary forces that have given rise to microbial life in the contemporary ocean.

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