scholarly journals Approaches to understanding the ecology and evolution of understudied terrestrial archaeal ammonia-oxidisers

2018 ◽  
Vol 2 (4) ◽  
pp. 619-628 ◽  
Author(s):  
Cécile Gubry-Rangin ◽  
William Williams ◽  
James I. Prosser
Keyword(s):  
Evolutionary History ◽  
Phylogenetic Group ◽  
Ecological Adaptation ◽  
Physiological Characteristics ◽  
Marker Genes ◽  
Ecological Significance ◽  
Biogeochemical Process ◽  
Environmental Distribution ◽  
Laboratory Cultures ◽  
Ammonia Oxidising Archaea

Ammonia-oxidising archaea (AOA) form a phylogenetic group within the phylum Thaumarchaeota and are of ecological significance due to their role in nitrification, an important biogeochemical process. Previous research has provided information on their ecosystem role and potential physiological characteristics, for example, through analyses of their environmental distribution, ecological adaptation and evolutionary history. However, most AOA diversity, assessed using several environmental marker genes, is not represented in laboratory cultures, with consequent gaps in knowledge of their physiology and evolution. The present study critically reviews existing and developing approaches for the assessment of AOA function and diversity and their potential to provide a deeper understanding of these ecologically important, but understudied microorganisms.

scholarly journals Comparative Genomics and Environmental Distribution of Large dsDNA viruses in the family Asfarviridae

2021 ◽  
Author(s):  
Sangita Karki ◽  
Mohammad Moniruzzaman ◽  
Frank O. Aylward
Keyword(s):  
Amino Acid ◽  
African Swine Fever Virus ◽  
Phylogenetic Analyses ◽  
African Swine Fever ◽  
Amino Acid Identity ◽  
Metagenomic Data ◽  
Genome Comparison ◽  
Marker Genes ◽  
Environmental Distribution ◽  
Acid Identity

AbstractThe Asfarviridae is a family of Nucleo-Cytoplasmic Large DNA Viruses (NCLDV) of which African swine fever virus (ASFV) is the most well-characterized. Recently the discovery of several Asfarviridae members other than ASFV has suggested that this family represents a diverse and cosmopolitan group of viruses, but the genomics and distribution of this family have not been studied in detail. To this end we analyzed five complete genomes and 35 metagenome-assembled genomes (MAGs) of viruses from this family to shed light on their evolutionary relationships and environmental distribution. The Asfarvirus MAGs derive from diverse marine, freshwater, and terrestrial habitats, underscoring the broad environmental distribution of this family. We present phylogenetic analyses using conserved marker genes and whole-genome comparison of pairwise average amino acid identity values, revealing a high level of genomic divergence across disparate Asfarviruses. Further, we found that Asfarviridae genomes encode genes with diverse predicted metabolic roles and detectable sequence homology to proteins in bacteria, archaea, and different eukaryotes, highlighting the genomic chimerism that is a salient feature of NCLDV. Our read mapping from Tara oceans metagenomic data also revealed that three Asfarviridae MAGs were present in multiple marine samples, indicating that they are widespread in the ocean. In one of these MAGs we identified four marker genes with >95% amino acid identity to genes sequenced from a virus that infects the dinoflagellate Heterocapsa circularisquama (HcDNAV). This suggests a potential host for this MAG, which would thereby represent a near-complete genome of a dinoflagellate-infecting giant virus. Together, these results show that Asfarviridae are ubiquitous, comprise similar sequence divergence as other NCLDV families, and include several members that are widespread in the ocean and potentially infect ecologically important protists.

scholarly journals Comparative Genomics and Environmental Distribution of Large dsDNA Viruses in the Family Asfarviridae

2021 ◽  
Vol 12 ◽  
Author(s):  
Sangita Karki ◽  
Mohammad Moniruzzaman ◽  
Frank O. Aylward
Keyword(s):  
African Swine Fever Virus ◽  
Phylogenetic Analyses ◽  
Sequence Divergence ◽  
African Swine Fever ◽  
Salient Feature ◽  
Metagenomic Data ◽  
Genome Comparison ◽  
Marker Genes ◽  
Environmental Distribution ◽  
The Family

The family Asfarviridae is a group of nucleo-cytoplasmic large DNA viruses (NCLDVs) of which African swine fever virus (ASFV) is well-characterized. Recently the discovery of several Asfarviridae members other than ASFV has suggested that this family represents a diverse and cosmopolitan group of viruses, but the genomics and distribution of this family have not been studied in detail. To this end we analyzed five complete genomes and 35 metagenome-assembled genomes (MAGs) of viruses from this family to shed light on their evolutionary relationships and environmental distribution. The Asfarvirus MAGs derive from diverse marine, freshwater, and terrestrial habitats, underscoring the broad environmental distribution of this family. We present phylogenetic analyses using conserved marker genes and whole-genome comparison of pairwise average amino acid identity (AAI) values, revealing a high level of genomic divergence across disparate Asfarviruses. Further, we found that Asfarviridae genomes encode genes with diverse predicted metabolic roles and detectable sequence homology to proteins in bacteria, archaea, and eukaryotes, highlighting the genomic chimerism that is a salient feature of NCLDV. Our read mapping from Tara oceans metagenomic data also revealed that three Asfarviridae MAGs were present in multiple marine samples, indicating that they are widespread in the ocean. In one of these MAGs we identified four marker genes with > 95% AAI to genes sequenced from a virus that infects the dinoflagellate Heterocapsa circularisquama (HcDNAV). This suggests a potential host for this MAG, which would thereby represent a reference genome of a dinoflagellate-infecting giant virus. Together, these results show that Asfarviridae are ubiquitous, comprise similar sequence divergence as other NCLDV families, and include several members that are widespread in the ocean and potentially infect ecologically important protists.

scholarly journals Linking pangenomes and metagenomes: the Prochlorococcus metapangenome

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4320 ◽  
Author(s):  
Tom O. Delmont ◽  
A. Murat Eren
Keyword(s):  
Sugar Metabolism ◽  
Gene Clusters ◽  
Genomic Islands ◽  
Metagenomic Data ◽  
Integrated Analysis ◽  
Marker Genes ◽  
Relative Distribution ◽  
Environmental Distribution ◽  
Microbial Genomes ◽  
Core Genes

Pangenomes offer detailed characterizations of core and accessory genes found in a set of closely related microbial genomes, generally by clustering genes based on sequence homology. In comparison, metagenomes facilitate highly resolved investigations of the relative distribution of microbial genomes and individual genes across environments through read recruitment analyses. Combining these complementary approaches can yield unique insights into the functional basis of microbial niche partitioning and fitness, however, advanced software solutions are lacking. Here we present an integrated analysis and visualization strategy that provides an interactive and reproducible framework to generate pangenomes and to study them in conjunction with metagenomes. To investigate its utility, we applied this strategy to a Prochlorococcus pangenome in the context of a large-scale marine metagenomic survey. The resulting Prochlorococcus metapangenome revealed remarkable differential abundance patterns between very closely related isolates that belonged to the same phylogenetic cluster and that differed by only a small number of gene clusters in the pangenome. While the relationships between these genomes based on gene clusters correlated with their environmental distribution patterns, phylogenetic analyses using marker genes or concatenated single-copy core genes did not recapitulate these patterns. The metapangenome also revealed a small set of core genes that mostly occurred in hypervariable genomic islands of the Prochlorococcus populations, which systematically lacked read recruitment from surface ocean metagenomes. Notably, these core gene clusters were all linked to sugar metabolism, suggesting potential benefits to Prochlorococcus from a high sequence diversity of sugar metabolism genes. The rapidly growing number of microbial genomes and increasing availability of environmental metagenomes provide new opportunities to investigate the functioning and the ecology of microbial populations, and metapangenomes can provide unique insights for any taxon and biome for which genomic and sufficiently deep metagenomic data are available.

scholarly journals Dramatic expansion of microbial groups that shape the global sulfur cycle

2017 ◽  
Author(s):  
Karthik Anantharaman ◽  
Sean P. Jungbluth ◽  
Rose S. Kantor ◽  
Adi Lavy ◽  
Lesley A. Warren ◽  
...  
Keyword(s):  
Sulfate Reduction ◽  
Microbial Community Composition ◽  
Sulfur Oxidation ◽  
Sulfur Cycle ◽  
Process Models ◽  
Marker Genes ◽  
Biogeochemical Process ◽  
Sulfate Reducing ◽  
Microbial Sulfate Reduction ◽  
Microbial Groups

AbstractThe biogeochemical cycle of sulfur on Earth is driven by microbial sulfate reduction, yet organisms from relatively few lineages have been implicated in this process. Recent studies using functional marker genes have detected abundant, novel dissimilatory sulfite reductases that confer the capacity for microbial sulfate reduction and could do not be affiliated with known organisms. Thus, the identity of a significant fraction of sulfate reducing microbes has remained elusive. Here we report the discovery of the capacity for sulfate reduction in the genomes of organisms from twelve bacterial and archaeal phyla, thereby doubling the number of microbial phyla associated with this process. Eight of the twelve newly identified groups are candidate phyla that lack isolated representatives, a finding only possible given genomes from metagenomes. Two candidate phyla, Candidatus Rokubacteria and Candidatus Hydrothermarchaeota contain the earliest evolved genes. The capacity for sulfate reduction has been laterally transferred in multiple events within some phyla, and a key gene potentially capable of switching sulfur oxidation to sulfate reduction in associated cells has been acquired by putatively symbiotic bacteria. We conclude that functional predictions based on phylogeny will significantly underestimate the extent of sulfate reduction across Earth’s ecosystems. Understanding the prevalence of this capacity is integral to interpreting the carbon cycle because sulfate reduction is often coupled to turnover of buried organic carbon. Our findings expand the diversity of microbial groups associated with sulfur transformations in the environment and motivate revision of biogeochemical process models based on microbial community composition.

scholarly journals Unifying the global phylogeny and environmental distribution of ammonia-oxidising archaea based on amoA genes

2018 ◽  
Vol 9 (1) ◽  
Author(s):  
Ricardo J. Eloy Alves ◽  
Bui Quang Minh ◽  
Tim Urich ◽  
Arndt von Haeseler ◽  
Christa Schleper
Keyword(s):  
Environmental Distribution ◽  
Ammonia Oxidising Archaea

scholarly journals Panoramic Insights into the Microevolution and Macroevolution of Prevotella copri-containing Lineage in Primate Guts

2020 ◽  
Author(s):  
Hao Li ◽  
Jan P. Meier-Kolthoff ◽  
Can-Xin Hu ◽  
Zhong-Jie Wang ◽  
Jun Zhu ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Horizontal Transmission ◽  
Marker Genes ◽  
Rrna Gene ◽  
Biogeographical Distribution ◽  
Bacterial Lineage ◽  
Genomic Divergence

AbstractPrevotella copri and related taxa are widely detected in mammalian gut microbiomes and have been linked with one human enterotype. However, their microevolution and macroevolution among hosts are poorly characterized. In this study, extensively collected marker genes and genomes were analyzed to trace their evolutionary history, host specificity, and biogeographic distribution. Investigations based on 16S rRNA gene, gyrB, and genomes suggested that a multi-specific P. copri-containing lineage (PCL) harbors diverse species in higher primates. Firstly, P. copri is the dominant species of PCL in the human gut and consists of multiple groups exhibiting high genomic divergence and conspicuous but non-strict biogeographic pattern. Most African strains with high genomic divergence from other strains were phylogenetically placed near the species root, indicating the co-evolutionary history of P. copri and Homo sapiens. Secondly, although long-term co-evolution between PCL and higher primates was revealed, sporadic signals of co-speciation and extensive host jumping of PCL members were observed among higher primates. Metagenomic and phylogenetic analyses indicated that P. copri and other PCL species found in captive mammals have been recently transmitted from humans. Thirdly, strong evidence was found on the extensively horizontal transfer of genes (e.g., carbohydrate-active enzyme encoding genes) among sympatric P. copri groups and PCL species in the same primate host. Our study provides panoramic insights into the complex effects of vertical and horizontal transmission, and potential niche adaption on speciation, host, and biogeographical distribution spanning microevolutionary and macroevolutionary history for a certain gut bacterial lineage.ImportancePrevotella copri and its related taxa, which we designated as Prevotella copri-containing lineage (PCL) in the present study, are widely detected in guts of human, non-human primates and many captive mammals, showing positive or negative correlation to some human diseases. However, a comprehensive understanding on its microevolutionary (within P. copri) and macroevolutionary (among PCL members) history across host species and host biogeography is still lacking. According to our analysis based on 16S rRNA gene, gyrB and genomes, we provided the panoramic insights into the putative effects of vertical transfer, horizontal transmission and potential niche selection on host and biogeographical distribution of this gut bacterial lineage and P. copri. To our knowledge, it is the first time that a gut bacterial lineage was studied at both micro- and macroevolutionary levels, which can aid our systematic understanding on the host-microbe co-evolutionary interactions.

Elaborating the role of reflection and individual differences in the study of folk-economic beliefs

2018 ◽  
Vol 41 ◽  
Author(s):  
Kevin Arceneaux
Keyword(s):  
Decision Making ◽  
Individual Differences ◽  
Cognitive Processes ◽  
Evolutionary History ◽  
Behavioral Responses ◽  
History Of ◽  
Economic Beliefs

AbstractIntuitions guide decision-making, and looking to the evolutionary history of humans illuminates why some behavioral responses are more intuitive than others. Yet a place remains for cognitive processes to second-guess intuitive responses – that is, to be reflective – and individual differences abound in automatic, intuitive processing as well.

Ultrastructural Localization of Phycocyanin in the Acidophilic, Thermophilic Alga, Cyanidium Caldarium

1973 ◽  
Vol 31 ◽  
pp. 462-463
Author(s):  
M. R. Edwards ◽  
J. D. Mainwaring
Keyword(s):  
Yellowstone National Park ◽  
National Park ◽  
Ultrastructural Localization ◽  
Review Of Literature ◽  
Cyanidium Caldarium ◽  
Taxonomic Rank ◽  
Thin Sections ◽  
Standard Methods ◽  
Laboratory Cultures

Although the general ultrastructure of Cyanidium caldarium, an acidophilic, thermophilic alga of questionable taxonomic rank, has been extensively studied (see review of literature in reference 1), some peculiar ultrastructural features of the chloroplast of this alga have not been noted by other investigators.Cells were collected and prepared for thin sections at the Yellowstone National Park and were also grown in laboratory cultures (45-52°C; pH 2-5). Fixation (glutaraldehyde-osmium), dehydration (ethanol), and embedding (Epon 812) were accomplished by standard methods. Replicas of frozenfracture d- etched cells were obtained in a Balzers apparatus. In addition, cells were examined after disruption in a French Press.

Interrelationship of the cellular distribution and secretion of regular structure (RS) protein in Bacillus licheniformis nm 105

1992 ◽  
Vol 50 (1) ◽  
pp. 712-713
Author(s):  
Xiaorong Zhu ◽  
Richard McVeigh ◽  
Bijan K. Ghosh
Keyword(s):  
Alkaline Phosphatase ◽  
Bacillus Licheniformis ◽  
Self Assembly ◽  
Gel Electrophoresis ◽  
Culture Supernatant ◽  
Regular Structure ◽  
The Self ◽  
Cellular Distribution ◽  
Structural Protein ◽  
Laboratory Cultures

A mutant of Bacillus licheniformis 749/C, NM 105 exhibits some notable properties, e.g., arrest of alkaline phosphatase secretion and overexpression and hypersecretion of RS protein. Although RS is known to be widely distributed in many microbes, it is rarely found, with a few exceptions, in laboratory cultures of microorganisms. RS protein is a structural protein and has the unusual properties to form aggregate. This characteristic may have been responsible for the self assembly of RS into regular tetragonal structures. Another uncommon characteristic of RS is that enhanced synthesis and secretion which occurs when the cells cease to grow. Assembled RS protein with a tetragonal structure is not seen inside cells at any stage of cell growth including cells in the stationary phase of growth. Gel electrophoresis of the culture supernatant shows a very large amount of RS protein in the stationary culture of the B. licheniformis. It seems, Therefore, that the RS protein is cotranslationally secreted and self assembled on the envelope surface.

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