scholarly journals Metabolic potential of uncultured Antarctic soil bacteria revealed through long-read metagenomic sequencing

2020 ◽  
Author(s):  
Valentin Waschulin ◽  
Chiara Borsetto ◽  
Robert James ◽  
Kevin K. Newsham ◽  
Stefano Donadio ◽  
...  
Keyword(s):  
Genome Mining ◽  
Biosynthetic Gene Cluster ◽  
Metagenomic Sequencing ◽  
Metabolic Potential ◽  
Uncultured Bacteria ◽  
Rich Diversity ◽  
Sequencing Studies ◽  
Long Read ◽  
The Rich ◽  
Uncultivated Bacteria

AbstractThe growing problem of antibiotic resistance has led to the exploration of uncultured bacteria as potential sources of new antimicrobials. PCR amplicon analyses and short-read sequencing studies of samples from different environments have reported evidence of high biosynthetic gene cluster (BGC) diversity in metagenomes. However, few complete BGCs from uncultivated bacteria have been recovered, making assessment of BGC diversity difficult. Here, long-read sequencing and genome mining were used to recover >1400 mostly complete BGCs that demonstrate the rich diversity of BGCs from uncultivated lineages present in soil from Mars Oasis, Antarctica. The phyla Acidobacteriota, Verrucomicrobiota and Gemmatimonadota, but also the actinobacterial classes Acidimicrobiia, Thermoleophilia, and the gammaproteobacterial order UBA7966, were found to encode a large number of highly divergent BGCs. Our findings underline the biosynthetic potential of underexplored phyla as well as unexplored lineages within seemingly well-studied producer phyla. They also showcase long-read metagenomic sequencing as a promising way to access the untapped reservoir of specialised metabolites of the uncultured majority of microbes.

scholarly journals Biosynthetic potential of uncultured Antarctic soil bacteria revealed through long-read metagenomic sequencing

2021 ◽  
Author(s):  
Valentin Waschulin ◽  
Chiara Borsetto ◽  
Robert James ◽  
Kevin K. Newsham ◽  
Stefano Donadio ◽  
...  
Keyword(s):  
Genome Mining ◽  
Gene Clusters ◽  
Biosynthetic Gene Cluster ◽  
Full Length ◽  
Metagenomic Sequencing ◽  
Short Read ◽  
Short Read Sequencing ◽  
Rich Diversity ◽  
Long Read ◽  
The Rich

AbstractThe growing problem of antibiotic resistance has led to the exploration of uncultured bacteria as potential sources of new antimicrobials. PCR amplicon analyses and short-read sequencing studies of samples from different environments have reported evidence of high biosynthetic gene cluster (BGC) diversity in metagenomes, indicating their potential for producing novel and useful compounds. However, recovering full-length BGC sequences from uncultivated bacteria remains a challenge due to the technological restraints of short-read sequencing, thus making assessment of BGC diversity difficult. Here, long-read sequencing and genome mining were used to recover >1400 mostly full-length BGCs that demonstrate the rich diversity of BGCs from uncultivated lineages present in soil from Mars Oasis, Antarctica. A large number of highly divergent BGCs were not only found in the phyla Acidobacteriota, Verrucomicrobiota and Gemmatimonadota but also in the actinobacterial classes Acidimicrobiia and Thermoleophilia and the gammaproteobacterial order UBA7966. The latter furthermore contained a potential novel family of RiPPs. Our findings underline the biosynthetic potential of underexplored phyla as well as unexplored lineages within seemingly well-studied producer phyla. They also showcase long-read metagenomic sequencing as a promising way to access the untapped genetic reservoir of specialised metabolite gene clusters of the uncultured majority of microbes.

Conclusion

2018 ◽  
Author(s):  
Stefan Winter
Keyword(s):  
Middle Eastern ◽  
Rich Diversity ◽  
The Social ◽  
Local Contexts ◽  
History Of ◽  
Religious Oppression ◽  
The Rich ◽  
To Come

This concluding chapter summarizes key themes and presents some final thoughts. The book has shown that the multiplicity of lived ʻAlawi experiences cannot be reduced to the sole question of religion or framed within a monolithic narrative of persecution; that the very attempt to outline a single coherent history of “the ʻAlawis” may indeed be misguided. The sources on which this study has drawn are considerably more accessible, and the social and administrative realities they reflect consistently more mundane and disjointed, than the discourse of the ʻAlawis' supposed exceptionalism would lead one to believe. Therefore, the challenge for historians of ʻAlawi society in Syria and elsewhere is not to use the specific events and structures these sources detail to merely add to the already existing metanarratives of religious oppression, Ottoman misrule, and national resistance but rather to come to a newer and more intricate understanding of that community, and its place in wider Middle Eastern society, by investigating the lives of individual ʻAlawi (and other) actors within the rich diversity of local contexts these sources reveal.

PSYCHOLOGICAL FEATURES OF EDUCATION AND TOLERANCE IN STUDENTS

2018 ◽  
Vol 16 (1) ◽  
pp. 112-119
Author(s):  
VLADIMIR GLEB NAYDONOV
Keyword(s):  
Statistical Analysis ◽  
Training Program ◽  
Rich Diversity ◽  
Interethnic Differences ◽  
The World ◽  
The Rich ◽  
Correct Understanding ◽  
Psychological Features ◽  
Different Levels

The article considers the students’ tolerance as a spectrum of personal manifestations of respect, acceptance and correct understanding of the rich diversity of cultures of the world, values of others’ personality. The purpose of the study is to investgate education and the formation of tolerance among the students. We have compiled a training program to improve the level of tolerance for interethnic differences. Based on the statistical analysis of the data obtained, the most important values that are significant for different levels of tolerance were identified.

scholarly journals Unraveling the Metabolic Potential of Asgardarchaeota in a Sediment from the Mediterranean Hydrocarbon-Contaminated Water Basin Mar Piccolo (Taranto, Italy)

2021 ◽  
Vol 9 (4) ◽  
pp. 859
Author(s):  
Andrea Firrincieli ◽  
Andrea Negroni ◽  
Giulio Zanaroli ◽  
Martina Cappelletti
Keyword(s):  
Archaeal Community ◽  
Hydrocarbon Biodegradation ◽  
Natural Ecosystems ◽  
Central Mediterranean ◽  
Metabolic Potential ◽  
Metabolic Role ◽  
Sequencing Studies ◽  
Terrestrial Environments ◽  
Metagenome Sequencing ◽  
Aliphatic And Aromatic Hydrocarbons

Increasing number of metagenome sequencing studies have proposed a central metabolic role of still understudied Archaeal members in natural and artificial ecosystems. However, their role in hydrocarbon cycling, particularly in the anaerobic biodegradation of aliphatic and aromatic hydrocarbons, is still mostly unknown in both marine and terrestrial environments. In this work, we focused our study on the metagenomic characterization of the archaeal community inhabiting the Mar Piccolo (Taranto, Italy, central Mediterranean) sediments heavily contaminated by petroleum hydrocarbons and polychlorinated biphenyls (PCB). Among metagenomic bins reconstructed from Mar Piccolo microbial community, we have identified members of the Asgardarchaeota superphylum that has been recently proposed to play a central role in hydrocarbon cycling in natural ecosystems under anoxic conditions. In particular, we found members affiliated with Thorarchaeota, Heimdallarchaeota, and Lokiarchaeota phyla and analyzed their genomic potential involved in central metabolism and hydrocarbon biodegradation. Metabolic prediction based on metagenomic analysis identified the malonyl-CoA and benzoyl-CoA routes as the pathways involved in aliphatic and aromatic biodegradation in these Asgardarchaeota members. This is the first study to give insight into the archaeal community functionality and connection to hydrocarbon degradation in marine sediment historically contaminated by hydrocarbons.

scholarly journals Microdiversity and phylogeographic diversification of bacterioplankton in pelagic freshwater systems revealed through long-read amplicon sequencing

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Yusuke Okazaki ◽  
Shohei Fujinaga ◽  
Michaela M. Salcher ◽  
Cristiana Callieri ◽  
Atsushi Tanaka ◽  
...  
Keyword(s):  
16S Rrna ◽  
Regional Scale ◽  
Scale Up ◽  
Amplicon Sequencing ◽  
Freshwater Ecosystems ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Long Read

Abstract Background Freshwater ecosystems are inhabited by members of cosmopolitan bacterioplankton lineages despite the disconnected nature of these habitats. The lineages are delineated based on > 97% 16S rRNA gene sequence similarity, but their intra-lineage microdiversity and phylogeography, which are key to understanding the eco-evolutional processes behind their ubiquity, remain unresolved. Here, we applied long-read amplicon sequencing targeting nearly full-length 16S rRNA genes and the adjacent ribosomal internal transcribed spacer sequences to reveal the intra-lineage diversities of pelagic bacterioplankton assemblages in 11 deep freshwater lakes in Japan and Europe. Results Our single nucleotide-resolved analysis, which was validated using shotgun metagenomic sequencing, uncovered 7–101 amplicon sequence variants for each of the 11 predominant bacterial lineages and demonstrated sympatric, allopatric, and temporal microdiversities that could not be resolved through conventional approaches. Clusters of samples with similar intra-lineage population compositions were identified, which consistently supported genetic isolation between Japan and Europe. At a regional scale (up to hundreds of kilometers), dispersal between lakes was unlikely to be a limiting factor, and environmental factors or genetic drift were potential determinants of population composition. The extent of microdiversification varied among lineages, suggesting that highly diversified lineages (e.g., Iluma-A2 and acI-A1) achieve their ubiquity by containing a consortium of genotypes specific to each habitat, while less diversified lineages (e.g., CL500-11) may be ubiquitous due to a small number of widespread genotypes. The lowest extent of intra-lineage diversification was observed among the dominant hypolimnion-specific lineage (CL500-11), suggesting that their dispersal among lakes is not limited despite the hypolimnion being a more isolated habitat than the epilimnion. Conclusions Our novel approach complemented the limited resolution of short-read amplicon sequencing and limited sensitivity of the metagenome assembly-based approach, and highlighted the complex ecological processes underlying the ubiquity of freshwater bacterioplankton lineages. To fully exploit the performance of the method, its relatively low read throughput is the major bottleneck to be overcome in the future.

scholarly journals Pivoting the Plant Immune System from Dissection to Deployment

Science ◽  
2013 ◽  
Vol 341 (6147) ◽  
pp. 746-751 ◽  
Author(s):  
Jeffery L. Dangl ◽  
Diana M. Horvath ◽  
Brian J. Staskawicz
Keyword(s):  
Immune System ◽  
Conceptual Understanding ◽  
Germ Plasm ◽  
Plant Diseases ◽  
Sequencing Technology ◽  
Plant Immune System ◽  
Rich Diversity ◽  
The World ◽  
The Rich ◽  
Molecular Components

Diverse and rapidly evolving pathogens cause plant diseases and epidemics that threaten crop yield and food security around the world. Research over the last 25 years has led to an increasingly clear conceptual understanding of the molecular components of the plant immune system. Combined with ever-cheaper DNA-sequencing technology and the rich diversity of germ plasm manipulated for over a century by plant breeders, we now have the means to begin development of durable (long-lasting) disease resistance beyond the limits imposed by conventional breeding and in a manner that will replace costly and unsustainable chemical controls.

The Oxford Handbook of Feminist Philosophy

2021 ◽  
Keyword(s):  
Critical Race Theory ◽  
Queer Theory ◽  
Postcolonial Theory ◽  
The Body ◽  
Feminist Philosophy ◽  
Comprehensive Overview ◽  
Rich Diversity ◽  
Trans Studies ◽  
Feminist Perspectives ◽  
The Rich

This exciting new Handbook offers a comprehensive overview of the contemporary state of the field. The editors’ introduction and forty-five essays cover feminist critical engagements with philosophy and adjacent scholarly fields, as well as feminist approaches to current debates and crises across the world. Authors cover topics ranging from the ways in which feminist philosophy attends to other systems of oppression, and the gendered, racialized, and classed assumptions embedded in philosophical concepts, to feminist perspectives on prominent subfields of philosophy. The first section contains chapters that explore feminist philosophical engagement with mainstream and marginalized histories and traditions, while the second section parses feminist philosophy’s contributions to with numerous philosophical subfields, for example metaphysics and bioethics. A third section explores what feminist philosophy can illuminate about crucial moral and political issues of identity, gender, the body, autonomy, prisons, among numerous others. The Handbook concludes with the field’s engagement with other theories and movements, including trans studies, queer theory, critical race, theory, postcolonial theory, and decolonial theory. The volume provides a rigorous but accessible resource for students and scholars who are interested in feminist philosophy, and how feminist philosophers situate their work in relation to the philosophical mainstream and other disciplines. Above all it aims to showcase the rich diversity of subject matter, approach, and method among feminist philosophers.

scholarly journals Tree Diversity and Their Regeneration in the Sacred Groves of Virajpet, Central Western Ghats, India

2016 ◽  
Vol 8 (3) ◽  
pp. 360-369
Author(s):  
Devi A.G. PRASAD ◽  
Shwetha BHARATHI
Keyword(s):  
Tree Species ◽  
Western Ghats ◽  
Basal Area ◽  
Sacred Groves ◽  
Forest Patches ◽  
Tree Species Composition ◽  
Rich Diversity ◽  
Central Western Ghats ◽  
Undisturbed Forest ◽  
The Rich

Sacred groves are one of the finest examples of informal way of conserving the forest wealth. Baseline data collection of their diversity, distribution and regeneration capacity becomes necessary for the management and conservation of these undisturbed forest patches. In this context, the present investigation was carried out using random quadrat method in the sacred groves of Virajpet, Karnataka, India. A total of 132 tree species belonging to 113 genera and 45 families were identified within five sacred groves. Higher basal area (51.73-85.65 m2/ha) and tree density (453.33-515.9 individuals/ha) were observed as compared to other forests of Western Ghats region. The present investigation has revealed a healthy regeneration of tree species. Seedling and sapling composition differed to some extent from the mature tree species composition which could be used in predicting the future possibilities. Protection and conservation of such sacred groves should be of interest, for better regeneration of the rich diversity they harbour.

scholarly journals Different Strokes for Different Folks: The Rich Diversity of Animal Models of Focal Cerebral Ischemia

2010 ◽  
Vol 30 (8) ◽  
pp. 1412-1431 ◽  
Author(s):  
David W Howells ◽  
Michelle J Porritt ◽  
Sarah SJ Rewell ◽  
Victoria O'Collins ◽  
Emily S Sena ◽  
...  
Keyword(s):  
Animal Model ◽  
Ischemic Stroke ◽  
Animal Models ◽  
Focal Cerebral Ischemia ◽  
Experimental Stroke ◽  
Stroke Outcome ◽  
Rich Diversity ◽  
Single Animal ◽  
The Rich ◽  
Use Of Models

No single animal model is able to encompass all of the variables known to affect human ischemic stroke. This review highlights the major strengths and weaknesses of the most commonly used animal models of acute ischemic stroke in the context of matching model and experimental aim. Particular emphasis is placed on the relationships between outcome and underlying vascular variability, physiologic control, and use of models of comorbidity. The aim is to provide, for novice and expert alike, an overview of the key controllable determinants of experimental stroke outcome to help ensure the most effective application of animal models to translational research.

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