scholarly journals Soil Candidate Phyla Radiation Bacteria Encode Components of Aerobic Metabolism and Co-occur with Nanoarchaea in the Rare Biosphere of Rhizosphere Grassland Communities

mSystems ◽  
2021 ◽  
Vol 6 (4) ◽  
Author(s):  
Alexa M. Nicolas ◽  
Alexander L. Jaffe ◽  
Erin E. Nuccio ◽  
Michiko E. Taga ◽  
Mary K. Firestone ◽  
...  
Keyword(s):  
Aerobic Metabolism ◽  
Small Cells ◽  
Small Particles ◽  
Rare Biosphere ◽  
Grassland Communities ◽  
Candidate Phyla Radiation

Here, we investigated overlooked microbes in soil, candidate phyla radiation (CPR) bacteria and Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) archaea, by size fractionating small particles from soil, an approach typically used for the recovery of viral metagenomes. Concentration of these small cells (<0.2 μm) allowed us to identify these organisms as part of the rare soil biosphere and to sample genomes that were absent from non-size-fractionated metagenomes.

scholarly journals Unexpected diversity of CPR bacteria and nanoarchaea in the rare biosphere of rhizosphere-associated grassland soil

2020 ◽  
Author(s):  
Alexa M. Nicolas ◽  
Alexander L. Jaffe ◽  
Erin E. Nuccio ◽  
Michiko E. Taga ◽  
Mary K. Firestone ◽  
...  
Keyword(s):  
Microbial Community ◽  
Soil Microbial Community ◽  
Host Organism ◽  
Grassland Soil ◽  
Soil Microbial ◽  
Community Function ◽  
Ubiquinol Oxidase ◽  
Rare Biosphere ◽  
Aerobic Soil ◽  
Candidate Phyla Radiation

AbstractCandidate Phyla Radiation (CPR) bacteria and nanoarchaea populate most ecosystems, but are rarely detected in soil. We concentrated particles less than 0.2 μm from grassland soil, enabling targeted metagenomic analysis of these organisms, which are almost totally unexplored in soil. We recovered a diversity of CPR bacteria and some nanoarchaea sequences, but no sequences from other cellular organisms. The sampled sequences include Doudnabacteria (SM2F11) and Pacearchaeota, organisms not previously reported in soil, as well as Saccharibacteria, Parcubacteria and Microgenomates. CPR and DPANN (an acronym of the names of the first included archaea phyla) enrichments of 100-1000-fold were achieved compared to bulk soil, in which we estimate these organisms comprise about 1 to 100 cells per gram of soil. Like most CPR and DPANN sequenced to date, we predict these microorganisms live symbiotic, anaerobic lifestyles. However, Saccharibacteria, Parcubacteria, and Doudnabacteria genomes sampled here also encode ubiquinol oxidase operons that may have been acquired from other bacteria, likely during adaptation to aerobic soil environments. We posit that although present at low abundance, CPR bacteria and DPANN archaea could impact overall soil microbial community function by modulating host organism abundances and activity.

scholarly journals Features of smaller ribosomes in Candidate Phyla Radiation (CPR) bacteria revealed with a molecular evolutionary analysis

2022 ◽  
Author(s):  
Megumi Tsurumaki ◽  
Motofumi Saito ◽  
Masaru Tomita ◽  
Akio Kanai
Keyword(s):  
Amino Acids ◽  
Ribosomal Proteins ◽  
Surface Structures ◽  
Small Cells ◽  
Evolutionary Analysis ◽  
Genomic Information ◽  
Free Living ◽  
Specific Manner ◽  
Molecular Evolutionary Analysis ◽  
Candidate Phyla Radiation

The Candidate Phyla Radiation (CPR) is a large bacterial group consisting mainly of uncultured lineages. They have small cells and small genomes, and often lack ribosomal proteins L1, L9, and/or L30, which are basically ubiquitous in ordinary (non-CPR) bacteria. Here, we comprehensively analyzed the genomic information of CPR bacteria and identified their unique properties. In the distribution of protein lengths in CPR bacteria, the peak was at around 100–150 amino acids, whereas the position of the peak varies in the range of 100–300 amino acids in free-living non-CPR bacteria, and at around 100–200 amino acids in most symbiotic non-CPR bacteria. These results show that CPR bacteria have smaller proteins on average, like symbiotic non-CPR bacteria. We found that ribosomal proteins L28, L29, L32, and L33 are also deleted in CPR bacteria, in a lineage-specific manner. Moreover, the sequences of approximately half of all ribosomal proteins in CPR differ, in part, from those of non-CPR bacteria, with missing regions or specific added region. We also found that several regions of the 16S, 23S, and 5S rRNAs are lacking in CPR bacteria and that the total predicted length of the three rRNAs in CPR bacteria is smaller than that in non-CPR bacteria. The regions missing in the CPR ribosomal proteins and rRNAs are located near the surface of the ribosome, and some are close to one another. These observations suggest that ribosomes are smaller in CPR bacteria than in free-living non-CPR bacteria, with simplified surface structures.

Comparison of Choriocarcinoma and Normal Placenta

1971 ◽  
Vol 29 ◽  
pp. 324-325
Author(s):  
John C. Garancis ◽  
Roland A. Pattillo ◽  
Robert O. Hussa ◽  
Jon V. Straumfjord
Keyword(s):  
Cell Lines ◽  
Small Cells ◽  
Tissue Cultures ◽  
Glycogen Depletion ◽  
Cell Surfaces ◽  
Intercellular Spaces ◽  
Concomitant Increase ◽  
Gestational Choriocarcinoma ◽  
Cytoplasmic Glycogen ◽  
Normal Placenta

Two different cell lines (Be-Wo and Jar) of human gestational choriocarcinoma have been maintained in continuous tissue culture for a period of four and two years respectively without losing the ability to elaborate human chorionic gonadotropin (HCG). Tissue cultures, as revealed by electron microscopy, consisted of small cells with single nuclei. In some instances cell surfaces were provided with microvilli but more often the intercellular spaces were narrow and bridged by desmosomes. However, syncytium was not formed. Endoplasmic reticulum (ER) was poorly developed in both cell lines, except in some Be-Wo cells it was prominent. Golgi complex, lysosomes and numerous free ribosomes, as well as excessive cytoplasmic glycogen, were present in all cells (Fig. 1). Glycogen depletion and concomitant increase of ER were observed in many cells following a single dose of 10 ugm/ml of adrenalin added to medium (Fig. 2).

Stereo Electron Microscopy Applied to High Resolution Freeze-Etch Replicas

1970 ◽  
Vol 28 ◽  
pp. 306-307
Author(s):  
L. Andrew Staehelin
Keyword(s):  
Electron Microscopy ◽  
Plastic Deformation ◽  
High Resolution ◽  
Smooth Surfaces ◽  
Small Particles ◽  
Membrane Surfaces ◽  
Wide Acceptance ◽  
New Information ◽  
Number Of Particles ◽  
Small Holes

Freeze-etched membranes usually appear as relatively smooth surfaces covered with numerous small particles and a few small holes (Fig. 1). In 1966 Branton (1“) suggested that these surfaces represent split inner mem¬brane faces and not true external membrane surfaces. His theory has now gained wide acceptance partly due to new information obtained from double replicas of freeze-cleaved specimens (2,3) and from freeze-etch experi¬ments with surface labeled membranes (4). While theses studies have fur¬ther substantiated the basic idea of membrane splitting and have shown clearly which membrane faces are complementary to each other, they have left the question open, why the replicated membrane faces usually exhibit con¬siderably fewer holes than particles. According to Branton's theory the number of holes should on the average equal the number of particles. The absence of these holes can be explained in either of two ways: a) it is possible that no holes are formed during the cleaving process e.g. due to plastic deformation (5); b) holes may arise during the cleaving process but remain undetected because of inadequate replication and microscope techniques.

Dynamic Scanning Electron Microscopy of Small Particles

1975 ◽  
Vol 33 ◽  
pp. 280-281
Author(s):  
W. Krakow ◽  
W. C. Nixon
Keyword(s):  
Electron Microscopy ◽  
Low Noise ◽  
Time Sequence ◽  
Field Of View ◽  
Video Tape ◽  
Small Particles ◽  
Polystyrene Spheres ◽  
Field Distributions ◽  
Dynamic Scanning ◽  
Scanning Electron

The scanning electron microscope (SEM) can be run at television scanning rates and used with a video tape recorder to observe dynamic specimen changes. With a conventional tungsten source, a low noise TV image is obtained with a field of view sufficient to cover the area of the specimen to be recorded. Contrast and resolution considerations have been elucidated and many changing specimens have been studied at TV rates.To extend the work on measuring the magnitude of charge and field distributions of small particles in the SEM, we have investigated their motion and electrostatic interaction at TV rates. Fig. 1 shows a time sequence of polystyrene spheres on a conducting grating surface inclined to the microscope axis. In (la) there are four particles present in the field of view, while in (lb) a fifth particle has moved into view.

The Shadow Widths of Very Small Particles are Formed Independently of the Metal Cap Build Up on the Particle

1981 ◽  
Vol 39 ◽  
pp. 568-569
Author(s):  
George C. Ruben
Keyword(s):  
Gold Particle ◽  
Film Surface ◽  
Small Particles ◽  
Geometric Process ◽  
Metal Free ◽  
Shadow Area

The formation of shadows behind small particles has been thought to be a geometric process (GP) where the metal cap build up on the particle creates a shadow width the same size as or larger than the particle. This GP cannot explain why gold particle shadow widths are generally larger than the gold particle and may have no appreciable metal cap build up (fig. 1). Ruben and Telford have suggested that particle shadow widths are formed by the width dependent deflection of shadow metal (SM) lateral to and infront of the particle. The trajectory of the deflected SM is determined by the incoming shadow angle (45°). Since there can be up to 1.4 times (at 45°) more SM directly striking the particle than the film surface, a ridge of metal nuclei lateral to and infront of the particle can be formed. This ridge in turn can prevent some SM from directly landing in the metal free shadow area. However, the SM that does land in the shadow area (not blocked by the particle or its ridge) does not stick and apparently surface migrates into the SM film behind the particle.

STEM Study of Surface Plasmon Excitation in Small Spherical Particles

1990 ◽  
Vol 48 (2) ◽  
pp. 42-43
Author(s):  
Daniel UGARTE
Keyword(s):  
Energy Loss ◽  
Spherical Particles ◽  
Small Particles ◽  
Bulk Materials ◽  
Low Loss ◽  
Plasmon Excitation ◽  
Surface Modes ◽  
Surface Plasmon Excitation ◽  
Analytical Electron ◽  
Analytical Electron Microscope

Small particles exhibit chemical and physical behaviors substantially different from bulk materials. This is due to the fact that boundary conditions can induce specific constraints on the observed properties. As an example, energy loss experiments carried out in an analytical electron microscope, constitute a powerful technique to investigate the excitation of collective surface modes (plasmons), which are modified in a limited size medium. In this work a STEM VG HB501 has been used to study the low energy loss spectrum (1-40 eV) of silicon spherical particles [1], and the spatial localization of the different modes has been analyzed through digitally acquired energy filtered images. This material and its oxides have been extensively studied and are very well characterized, because of their applications in microelectronics. These particles are thus ideal objects to test the validity of theories developed up to now.Typical EELS spectra in the low loss region are shown in fig. 2 and energy filtered images for the main spectral features in fig. 3.

SREM observation of the interaction between the in-situ deposited Pd small particles and MgO cleavage surface

1986 ◽  
Vol 44 ◽  
pp. 382-383
Author(s):  
H.-J. Ou
Keyword(s):  
Electron Microscopy ◽  
Small Particle ◽  
Small Particles ◽  
Cleavage Surface ◽  
Metallic Particles ◽  
Microscopy Technique ◽  
Ceramic Surfaces ◽  
Reflection Electron Microscopy ◽  
New Perspective

The understanding of the interactions between the small metallic particles and ceramic surfaces has been studied by many catalyst scientists. We had developed Scanning Reflection Electron Microscopy technique to study surface structure of MgO hulk cleaved surface and the interaction with the small particle of metals. Resolutions of 10Å has shown the periodic array of surface atomic steps on MgO. The SREM observation of the interaction between the metallic particles and the surface may provide a new perspective on such processes.

Scanning electron microscopy of composite hydroxylapatite/plaster implants for bone reconstruction

1986 ◽  
Vol 44 ◽  
pp. 326-327
Author(s):  
J. S. Hanker ◽  
B. L. Giammara
Keyword(s):  
Tooth Extraction ◽  
Alveolar Ridge ◽  
Small Particles ◽  
Alveolar Ridge Augmentation ◽  
Sintered Ceramic ◽  
Ridge Augmentation ◽  
Fibrovascular Tissue ◽  
Infrabony Defects ◽  
Edentulous Patients ◽  
Scanning Electron

Nonresorbable sintered ceramic hydroxylapatite (HA) is widely employed for filling defects in jaw bone. The small particles used for alveolar ridge augmentation in edentulous patients or for infrabony defects due to periodontal disease tend to scatter when implanted using water or saline as the vehicle. Larger blocks of this material used for filling sockets after tooth extraction don't fit well. Studies in our laboratory where we compared bovine serum albumin, collagen and plaster of Paris as binders to prevent particle scatter during implantation suggested that plaster was most useful for this purpose. In addition to preventing scatter of the particles, plaster enables the formation of implants of any size and.shape either prior to or during surgery. Studies with the PATS reaction have indicated that plaster acts as a scaffold for the incorporation of HA particles into bone in areas where the implant contacts either host bone or periosteum. The shape and integrity of the implant is maintained by the plaster component until it is replaced over a period of days by fibrovascular tissue.

Convergent Beam Electron Diffraction Zone Axis Pattern Map of Zirconium

1990 ◽  
Vol 48 (2) ◽  
pp. 496-497
Author(s):  
E. Silva ◽  
R. Scozia
Keyword(s):  
Electron Diffraction ◽  
Convergent Beam Electron Diffraction ◽  
Zone Axis ◽  
Pole Piece ◽  
Small Particles ◽  
Present Communication ◽  
Beam Electron ◽  
Zero Layer ◽  
Set Up ◽  
Convergent Beam

The purpose in obtaining zone axis pattern map (zap map) from a given material is to provide a quick and reliable tool to identify cristaline phases, and crystallographic directions, even in small particles. Bend contours patterns and Kossel lines patterns maps from Zr single crystal in the [0001] direction have been presented previously. In the present communication convergent beam electron diffraction (CBED) zap map of Zr will be shown. CBED patterns were obtained using a Philips microscope model EM300, which was set up to carry out this technique. Convergent objective upper pole piece for STEM and some electronic modifications in the lens circuits were required, furthermore the microscope was carefully cleaned and it was operated at a vacuum eminently good.CBED patterns in the Zr zap map consist of zero layer disks, showing fine details within them which correspond to intersecting set of higher order Laue zone (HOLZ) deficiency lines.

Sign in / Sign up

Export Citation Format

Share Document