scholarly journals Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems

2021 ◽  
Vol 6 (3) ◽  
pp. 354-365 ◽  
Author(s):  
Christine He ◽  
Ray Keren ◽  
Michael L. Whittaker ◽  
Ibrahim F. Farag ◽  
Jennifer A. Doudna ◽  
...  
Keyword(s):  
Drinking Water ◽  
Taxonomic Diversity ◽  
Host Cells ◽  
Microscopy Imaging ◽  
Site Specific ◽  
Groundwater Aquifers ◽  
Transmission Electron ◽  
Groundwater Ecosystems ◽  
Genomic Analyses ◽  
Candidate Phyla Radiation

AbstractCandidate phyla radiation (CPR) bacteria and DPANN archaea are unisolated, small-celled symbionts that are often detected in groundwater. The effects of groundwater geochemistry on the abundance, distribution, taxonomic diversity and host association of CPR bacteria and DPANN archaea has not been studied. Here, we performed genome-resolved metagenomic analysis of one agricultural and seven pristine groundwater microbial communities and recovered 746 CPR and DPANN genomes in total. The pristine sites, which serve as local sources of drinking water, contained up to 31% CPR bacteria and 4% DPANN archaea. We observed little species-level overlap of metagenome-assembled genomes (MAGs) across the groundwater sites, indicating that CPR and DPANN communities may be differentiated according to physicochemical conditions and host populations. Cryogenic transmission electron microscopy imaging and genomic analyses enabled us to identify CPR and DPANN lineages that reproducibly attach to host cells and showed that the growth of CPR bacteria seems to be stimulated by attachment to host-cell surfaces. Our analysis reveals site-specific diversity of CPR bacteria and DPANN archaea that coexist with diverse hosts in groundwater aquifers. Given that CPR and DPANN organisms have been identified in human microbiomes and their presence is correlated with diseases such as periodontitis, our findings are relevant to considerations of drinking water quality and human health.

scholarly journals Huge and variable diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems

2020 ◽  
Author(s):  
Christine He ◽  
Ray Keren ◽  
Michael Whittaker ◽  
Ibrahim F. Farag ◽  
Jennifer Doudna ◽  
...  
Keyword(s):  
Cell Attachment ◽  
Taxonomic Diversity ◽  
Host Cells ◽  
Groundwater Aquifers ◽  
Groundwater Ecosystems ◽  
Genomic Analyses ◽  
Host Cell Attachment ◽  
Health Relevance ◽  
Candidate Phyla Radiation

AbstractCandidate Phyla Radiation (CPR) bacteria and DPANN archaea are uncultivated, small-celled symbionts often detected in groundwater. However, variations in CPR/DPANN organism abundance, distribution, taxonomic diversity, and degree/nature of host association with groundwater chemistry remain understudied. Here, we performed genome-resolved metagenomic characterization of one agriculturally-impacted and seven pristine groundwater microbial communities in California, recovering 746 dereplicated CPR and DPANN genomes. Our finding of up to 31% CPR bacteria and 4% DPANN archaea in the pristine sites, which serve as local sources of drinking water, may hold health relevance, given growing awareness of the presence of CPR/DPANN organisms in human microbiomes and their association with disease. There is little species-level genome overlap across groundwater sites, indicating that CPR and DPANN communities are highly differentiated according to host populations and physicochemical conditions. Cryo-TEM imaging and genomic analyses indicate that CPR growth may be stimulated by attachment to the surface of host cells, and identified CPR and DPANN lineages with particularly prevalent and/or resilient host cell attachment. These results establish the huge but site-specific diversity of CPR bacteria and DPANN archaea coexisting with diverse hosts in groundwater aquifers, and raise important questions about potential impacts on human health.

To Eliminate Curtain Effect of FIB TEM Samples by a Combination of Sample Dicing and Backside Milling

2014 ◽  
Author(s):  
Jian-Shing Luo ◽  
Hsiu Ting Lee
Keyword(s):  
Sample Preparation ◽  
Focused Ion Beam ◽  
Preparation Method ◽  
Low Cost ◽  
Ion Beam ◽  
Sample Preparation Method ◽  
Site Specific ◽  
Dual Beam ◽  
Transmission Electron

Abstract Several methods are used to invert samples 180 deg in a dual beam focused ion beam (FIB) system for backside milling by a specific in-situ lift out system or stages. However, most of those methods occupied too much time on FIB systems or requires a specific in-situ lift out system. This paper provides a novel transmission electron microscopy (TEM) sample preparation method to eliminate the curtain effect completely by a combination of backside milling and sample dicing with low cost and less FIB time. The procedures of the TEM pre-thinned sample preparation method using a combination of sample dicing and backside milling are described step by step. From the analysis results, the method has applied successfully to eliminate the curtain effect of dual beam FIB TEM samples for both random and site specific addresses.

scholarly journals Fabrication of a liquid cell for in situ transmission electron microscopy

Microscopy ◽  
2020 ◽  
Author(s):  
Xiaoguang Li ◽  
Kazutaka Mitsuishi ◽  
Masaki Takeguchi
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Cost Effective ◽  
Production Method ◽  
Microscopy Imaging ◽  
Transmission Electron ◽  
In Situ Electron Microscopy ◽  
Liquid Cell ◽  
Si Wafer

Abstract Liquid cell transmission electron microscopy (LCTEM) enables imaging of dynamic processes in liquid with high spatial and temporal resolution. The widely used liquid cell (LC) consists of two stacking microchips with a thin wet sample sandwiched between them. The vertically overlapped electron-transparent membrane windows on the microchips provide passage for the electron beam. However, microchips with imprecise dimensions usually cause poor alignment of the windows and difficulty in acquiring high-quality images. In this study, we developed a new and efficient microchip fabrication process for LCTEM with a large viewing area (180 µm × 40 µm) and evaluated the resultant LC. The new positioning reference marks on the surface of the Si wafer dramatically improve the precision of dicing the wafer, making it possible to accurately align the windows on two stacking microchips. The precise alignment led to a liquid thickness of 125.6 nm close to the edge of the viewing area. The performance of our LC was demonstrated by in situ transmission electron microscopy imaging of the dynamic motions of 2-nm Pt particles. This versatile and cost-effective microchip production method can be used to fabricate other types of microchips for in situ electron microscopy.

scholarly journals Annular Bright Field Scanning Transmission Electron Microscopy Imaging Dynamics

2010 ◽  
Vol 16 (S2) ◽  
pp. 80-81 ◽  
Author(s):  
SD Findlay ◽  
N Shibata ◽  
H Sawada ◽  
E Okunishi ◽  
Y Kondo ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Scanning Transmission Electron Microscopy ◽  
Bright Field ◽  
Microscopy Imaging ◽  
Scanning Transmission Electron ◽  
Transmission Electron ◽  
Scanning Transmission

Extended abstract of a paper presented at Microscopy and Microanalysis 2010 in Portland, Oregon, USA, August 1 – August 5, 2010.

scholarly journals Rapid evolution of decreased host susceptibility drives a stable relationship between ultrasmall parasite TM7x and its bacterial host

2018 ◽  
Vol 115 (48) ◽  
pp. 12277-12282 ◽  
Author(s):  
Batbileg Bor ◽  
Jeffrey S. McLean ◽  
Kevin R. Foster ◽  
Lujia Cen ◽  
Thao T. To ◽  
...  
Keyword(s):  
Host Cell ◽  
Rapid Evolution ◽  
Host Population ◽  
Host Cells ◽  
Host Susceptibility ◽  
Bacterial Host ◽  
Narrow Host Range ◽  
Stable Relationship ◽  
Candidate Phyla Radiation

Around one-quarter of bacterial diversity comprises a single radiation with reduced genomes, known collectively as the Candidate Phyla Radiation. Recently, we coisolated TM7x, an ultrasmall strain of the Candidate Phyla Radiation phylum Saccharibacteria, with its bacterial host Actinomyces odontolyticus strain XH001 from human oral cavity and stably maintained as a coculture. Our current work demonstrates that within the coculture, TM7x cells establish a long-term parasitic association with host cells by infecting only a subset of the population, which stay viable yet exhibit severely inhibited cell division. In contrast, exposure of a naïve A. odontolyticus isolate, XH001n, to TM7x cells leads to high numbers of TM7x cells binding to each host cell, massive host cell death, and a host population crash. However, further passaging reveals that XH001n becomes less susceptible to TM7x over time and enters a long-term stable relationship similar to that of XH001. We show that this reduced susceptibility is driven by rapid host evolution that, in contrast to many forms of phage resistance, offers only partial protection. The result is a stalemate where infected hosts cannot shed their parasites; nevertheless, parasite load is sufficiently low that the host population persists. Finally, we show that TM7x can infect and form stable long-term relationships with other species in a single clade of Actinomyces, displaying a narrow host range. This system serves as a model to understand how parasitic bacteria with reduced genomes such as those of the Candidate Phyla Radiation have persisted with their hosts and ultimately expanded in their diversity.

scholarly journals Potential Decontamination of Drinking Water Pathogens through k-Carrageenan Integrated Green Bottle Fly Bio-Synthesized Silver Nanoparticles

Molecules ◽  
2020 ◽  
Vol 25 (8) ◽  
pp. 1936 ◽  
Author(s):  
M. A. Abu-Saied ◽  
Mohamed Elnouby ◽  
Tarek Taha ◽  
Muhammad El-shafeey ◽  
Ali G. Alshehri ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Antimicrobial Activity ◽  
Silver Nanoparticles ◽  
Drinking Water ◽  
Pathogenic Bacteria ◽  
Polymeric Nanoparticles ◽  
Wide Distribution ◽  
Spectrophotometric Analysis ◽  
Transmission Electron ◽  
Green Bottle

The wide distribution of infections-related pathogenic microbes is almost related to the contamination of food and/or drinking water. The current applied treatments face some limitations. In the current study, k-carrageenan polymer was used as supporting material for the proper/unreleased silver nanoparticles that showed strong antimicrobial activity against six pathogenic bacteria and yeast. The bio-extract of the pupa of green bottle fly was used as the main agent for the synthesis of silver nanoparticles. The qualitative investigation of biologically synthesized silver nanoparticles was determined using UV-Vis spectrophotometric analysis; however, the size of nanoparticles was in range of 30–100 nm, as confirmed by scanning electron microscopy (SEM), transmission electron microscopy (TEM), and particle size analyzer. The proper integration of silver nanoparticles into the polymeric substrate was also characterized through fourier transform infrared (FT-IR), thermogravimetric analysis (TGA), SEM, and tensile strength. The antimicrobial activity of k-carrageenan/silver nanoparticles against Gram positive, Gram negative, and yeast pathogens was highly effective. These results indicate the probable exploitation of the polymeric/nanoparticles composite as an extra stage in water purification systems in homes or even at water treatment plants.

scholarly journals Monitoring and risk assessment for groundwater sources in rural communities of Romania (GROUNDWATERISK)

2019 ◽  
Vol 5 ◽  
Author(s):  
Oana Teodora Moldovan ◽  
Rannveig Øvrevik Skoglund ◽  
Horia Leonard Banciu ◽  
Alexandra Dinu Cucoș ◽  
Erika Andrea Levei ◽  
...  
Keyword(s):  
Risk Assessment ◽  
Drinking Water ◽  
Rural Communities ◽  
Groundwater Resources ◽  
Molecular Techniques ◽  
The Past ◽  
Physico Chemical ◽  
Groundwater Ecosystems ◽  
Alternative Sources ◽  
Agricultural Areas

In the past 100 years, a decreasing rainfall trend has been recorded on Romanian territory, a trend that continues today. Therefore, realistic estimation of the groundwater resources is crucial, especially for the rural communities lacking the economic power to use alternative sources of drinking water. The groundwater sources used by rural communities in Romania generally originate directly from caves, wells or springs with no proper evaluation of the water quality. Groundwater is exposed to different pollutants, as bats' guano in caves, fertilizers in agricultural areas or livestock (cattle, sheep, goats, etc.) farms on the surface. On the other hand, the water extracted directly from inside the caves is affecting groundwater ecosystems, highly vulnerable to any human impact and neglected by European legislation so far. The project aims to monitor, during two consecutive years, groundwater sources with different degrees of above- and underground pollution, from different regions of Romania. To achieve the goals of the project, a multidisciplinary monitoring strategy that will include measurements of hydrological, physico-chemical and biological (microbiology and aquatic invertebrates’ assessment) parameters alongside the quantification of radon and stable isotopes, rainfall or possible inflows of water. The specific outcomes of this project are: i) to test, develop and validate a new, more rapid and efficient method for monitoring and risk assessment of groundwater sources – and not only – by using molecular techniques, and propose this method to the water agencies in Romania; ii) to propose for Romanian authorities to implement a harmonized coherent methodology to measure radon concentration in water, as a consequence of EURATOM Directive; and iii) to educate local communities that are using groundwater as source for drinking water and raise young people’s awareness on the benefits of ecosystem services provided by the groundwater.

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