Genome-centric metagenomics reveals insights into the evolution and metabolism of a new free-living group in Rhizobiales

Abstract Background The Rhizobiales (Proteobacteria) order is an abundant and diverse group of microorganisms, being extensively studied for its lifestyle based on the association with plants, animals, and humans. New studies have demonstrated that the last common ancestor (LCA) of Rhizobiales had a free-living lifestyle, but the phylogenetic and metabolism characterization of basal lineages remains unclear. Here, we used a high-resolution phylogenomic approach to test the monophyly of the Aestuariivirgaceae family, a new taxonomic group of Rhizobiales. Furthermore, a deep metabolic investigation provided an overview of the main functional traits that can be associated with its lifestyle. We hypothesized that the presence of pathways (e.g., Glycolysis/Gluconeogenesis) and the absence of pathogenic genes would be associated with a free-living lifestyle in Aestuariivirgaceae. Results Using high-resolution phylogenomics approaches, our results revealed a clear separation of Aestuariivirgaceae into a distinct clade of other Rhizobiales family, suggesting a basal split early group and corroborate the monophyly of this group. A deep functional annotation indicated a metabolic versatility, which includes putative genes related to sugar degradation and aerobic respiration. Furthermore, many of these traits could reflect a basal metabolism and adaptations of Rhizobiales, as such the presence of Glycolysis/Gluconeogenesis pathway and the absence of pathogenicity genes, suggesting a free-living lifestyle in the Aestuariivirgaceae members. Conclusions Aestuariivirgaceae (Rhizobiales) family is a monophyletic taxon of the Rhizobiales with a free-living lifestyle and a versatile metabolism that allows these microorganisms to survive in the most diverse microbiomes, demonstrating their adaptability to living in systems with different conditions, such as extremely cold environments to tropical rivers.

Download Full-text

Localization and Functional Characterization of the Alternative Oxidase in Naegleria

10.1101/2020.09.26.314807 ◽

2020 ◽

Author(s):

Diego Cantoni ◽

Ashley Osborne ◽

Najwa Taib ◽

Gary Thompson ◽

Eleanna Kazana ◽

...

Keyword(s):

Cell Biology ◽

Structure Prediction ◽

Alternative Oxidase ◽

Functional Characterization ◽

Krebs Cycle ◽

Last Common Ancestor ◽

Free Living ◽

And Function ◽

Potential Pathogenicity

ABSTRACTThe Alternative oxidase (AOX) is a protein involved in maintaining the Krebs cycle in instances where the respiratory chain has been inhibited, while allowing for the maintenance of cell growth and necessary metabolic processes for survival. Among eukaryotes, alternative oxidases have disperse distribution and are found in plants, fungi and a few protists, including Naegleria ssp. Naegleria species are free-living unicellular amoeboflagellates, and include the pathogenic species of N. fowleri, the so-called brain eating amoeba. Using a multidisciplinary approach, we aimed to understand the evolution, localization and function of AOX and the role that plays in Naegleria’s biology. Our analyses suggest that the protein was present in last common ancestor of the genus and structure prediction showed that all functional residues are also present in Naegleria species. Using a combination of cellular and biochemical techniques, we also functionally characterize N. gruberi’s AOX in its mitochondria and we demonstrate that its inactivation affects its proliferation. Consequently, we discuss the benefits of the presence of this protein in Naegleria species, along with its potential pathogenicity role in N. fowleri. We predict that our findings will spearhead new explorations to understand the cell biology, metabolism and evolution of Naegleria and other free-living relatives.

Download Full-text

DOZ047.17: Characterization of esophageal motility in children with operated esophageal atresia using high-resolution impedance manometry and pressure flow analysis

Diseases of the Esophagus ◽

10.1093/dote/doz047.17 ◽

2019 ◽

Vol 32 (Supplement_1) ◽

Author(s):

O Courbette ◽

T Omari ◽

A Aspirot ◽

C Faure

Keyword(s):

High Resolution ◽

Esophageal Atresia ◽

Esophageal Motility ◽

Flow Analysis ◽

Esophageal Pressure ◽

Pressure Flow ◽

Impedance Ratio ◽

Group A ◽

Group B

Abstract Background Esophageal dysmotility is common in patients with esophageal atresia (EA). High-resolution impedance manometry (HRIM) and pressure flow analysis (PFA) allow characterization of biomechanical bolus flow and swallow properties. The aim of this study was to characterize esophageal motility and bolus flow propulsion in children who underwent surgical EA repair. Patients and Methods HRIM was used in 14 children with EA (type C, n = 13; type A, n = 1). Study was performed at a median (range) age of 11 years (5–17). The HRIM recordings were analyzed using conventional esophageal pressure topography and PFA (AIMplot software deployed via the open access Swallow Gateway application) and were compared with 13 patient controls (median age 14 years, range 5.75–17; P = NS vs patients) who underwent HRIM considered as normal according to Chicago classification and for whom the manometry results did not lead to treatment changes. Medical charts were reviewed for medical/surgical history and symptoms were assessed by standardized questionnaires. Results Esophageal peristaltic motor patterns were abnormal in all EA patients and were subdivided in two groups: Group A with presence of distal contraction in ≥ 50% of the swallows (n = 6) and Group B with presence of distal contractions in < 50% of the swallows (n = 8). IRP4s was similar in EA and controls. Bolus transport was impaired as shown by the higher impedance ratio (IR) in EA than in controls (0.47 vs 0.22, P < 0.001). In Group A, proximal and distal contractile integrals were lower than in controls (P < 0.001) and distal contractile velocity was shorter in EA (P < 0.01). IR was lower in Group A than in Group B (P < 0.01). In this sample, symptoms of dysphagia and presence of gastric metaplasia or esophagitis were not correlated with any of the measures determined. Conclusions Bolus transport as measured by impedance ratio is severely altered in EA patients but is not predictive of symptoms. The presence of residual distal contractions is associated with a more efficient bolus propulsion. Whether this is associated with a better outcome warrants further studies.

Download Full-text

Skeletal elements of crinoid echinoderms: High-resolution structural and microanalytical results

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100074768 ◽

1983 ◽

Vol 41 ◽

pp. 194-195

Author(s):

D. F. Blake ◽

L. F. Allard ◽

D. R. Peacor

Keyword(s):

High Resolution ◽

Marine Invertebrates ◽

Sea Urchins ◽

Structural Features ◽

Sea Stars ◽

High Resolution Tem ◽

Relationship Of ◽

The Relationship ◽

Insight Into

Echinodermata is a phylum of marine invertebrates which has been extant since Cambrian time (c.a. 500 m.y. before the present). Modern examples of echinoderms include sea urchins, sea stars, and sea lilies (crinoids). The endoskeletons of echinoderms are composed of plates or ossicles (Fig. 1) which are with few exceptions, porous, single crystals of high-magnesian calcite. Despite their single crystal nature, fracture surfaces do not exhibit the near-perfect {10.4} cleavage characteristic of inorganic calcite. This paradoxical mix of biogenic and inorganic features has prompted much recent work on echinoderm skeletal crystallography. Furthermore, fossil echinoderm hard parts comprise a volumetrically significant portion of some marine limestones sequences. The ultrastructural and microchemical characterization of modern skeletal material should lend insight into: 1). The nature of the biogenic processes involved, for example, the relationship of Mg heterogeneity to morphological and structural features in modern echinoderm material, and 2). The nature of the diagenetic changes undergone by their ancient, fossilized counterparts. In this study, high resolution TEM (HRTEM), high voltage TEM (HVTEM), and STEM microanalysis are used to characterize tha ultrastructural and microchemical composition of skeletal elements of the modern crinoid Neocrinus blakei.

Download Full-text

High-resolution electron microscopy of nanostructured materials

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100137239 ◽

1995 ◽

Vol 53 ◽

pp. 172-173

Author(s):

M. José-Yacamán

Keyword(s):

Electron Microscopy ◽

High Resolution ◽

Grain Boundaries ◽

Nanostructured Materials ◽

High Resolution Electron Microscopy ◽

Hrem Image ◽

Small Particles ◽

Resolution Electron ◽

Nanophase Materials

Electron microscopy is a fundamental tool in materials characterization. In the case of nanostructured materials we are looking for features with a size in the nanometer range. Therefore often the conventional TEM techniques are not enough for characterization of nanophases. High Resolution Electron Microscopy (HREM), is a key technique in order to characterize those materials with a resolution of ~ 1.7A. High resolution studies of metallic nanostructured materials has been also reported in the literature. It is concluded that boundaries in nanophase materials are similar in structure to the regular grain boundaries. That work therefore did not confirm the early hipothesis on the field that grain boundaries in nanostructured materials have a special behavior. We will show in this paper that by a combination of HREM image processing, and image calculations, it is possible to prove that small particles and coalesced grains have a significant surface roughness, as well as large internal strain.

Download Full-text

High-resolution transmission electron microscopic study of highly oxygen doped silicon layer

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100155438 ◽

1989 ◽

Vol 47 ◽

pp. 692-693

Author(s):

H. Takaoka ◽

M. Tomita ◽

T. Hayashi

Keyword(s):

High Resolution ◽

Oxygen Concentration ◽

Silicon Layer ◽

Detailed Structure ◽

Electron Microscopic ◽

Cross Sectional ◽

Transmission Electron ◽

Doped Silicon ◽

Argon Ion

High resolution transmission electron microscopy (HRTEM) is the effective technique for characterization of detailed structure of semiconductor materials. Oxygen is one of the important impurities in semiconductors. Detailed structure of highly oxygen doped silicon has not clearly investigated yet. This report describes detailed structure of highly oxygen doped silicon observed by HRTEM. Both samples prepared by Molecular beam epitaxy (MBE) and ion implantation were observed to investigate effects of oxygen concentration and doping methods to the crystal structure.The observed oxygen doped samples were prepared by MBE method in oxygen environment on (111) substrates. Oxygen concentration was about 1021 atoms/cm3. Another sample was silicon of (100) orientation implanted with oxygen ions at an energy of 180 keV. Oxygen concentration of this sample was about 1020 atoms/cm3 Cross-sectional specimens of (011) orientation were prepared by argon ion thinning and were observed by TEM at an accelerating voltage of 400 kV.

Download Full-text

HRTEM simulation of interfacial structure in amorphous multilayers

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100154305 ◽

1989 ◽

Vol 47 ◽

pp. 466-467

Author(s):

Margaret L. Sattler ◽

Michael A. O'Keefe

Keyword(s):

Electron Microscopy ◽

High Resolution ◽

Cross Section ◽

High Resolution Electron Microscopy ◽

Interfacial Structure ◽

Multilayer Sample ◽

Resolution Electron ◽

Multilayered Materials ◽

Simulated Images

Multilayered materials have been fabricated with such high perfection that individual layers having two atoms deep are possible. Characterization of the interfaces between these multilayers is achieved by high resolution electron microscopy and Figure 1a shows the cross-section of one type of multilayer. The production of such an image with atomically smooth interfaces depends upon certain factors which are not always reliable. For example, diffusion at the interface may produce complex interlayers which are important to the properties of the multilayers but which are difficult to observe. Similarly, anomalous conditions of imaging or of fabrication may occur which produce images having similar traits as the diffusion case above, e.g., imaging on a tilted/bent multilayer sample (Figure 1b) or deposition upon an unaligned substrate (Figure 1c). It is the purpose of this study to simulate the image of the perfect multilayer interface and to compare with simulated images having these anomalies.

Download Full-text