scholarly journals Lytic archaeal viruses infect abundant primary producers in Earth’s crust

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Janina Rahlff ◽  
Victoria Turzynski ◽  
Sarah P. Esser ◽  
Indra Monsees ◽  
Till L. V. Bornemann ◽  
...  
Keyword(s):  
Fluorescence Microscopy ◽  
Carbon Cycling ◽  
Viral Genome ◽  
Major Portion ◽  
Primary Producers ◽  
Deep Subsurface ◽  
Archaeal Viruses ◽  
Abundance And Diversity ◽  
Genomic Relatedness ◽  
Over Time

AbstractThe continental subsurface houses a major portion of life’s abundance and diversity, yet little is known about viruses infecting microbes that reside there. Here, we use a combination of metagenomics and virus-targeted direct-geneFISH (virusFISH) to show that highly abundant carbon-fixing organisms of the uncultivated genus Candidatus Altiarchaeum are frequent targets of previously unrecognized viruses in the deep subsurface. Analysis of CRISPR spacer matches display resistances of Ca. Altiarchaea against eight predicted viral clades, which show genomic relatedness across continents but little similarity to previously identified viruses. Based on metagenomic information, we tag and image a putatively viral genome rich in protospacers using fluorescence microscopy. VirusFISH reveals a lytic lifestyle of the respective virus and challenges previous predictions that lysogeny prevails as the dominant viral lifestyle in the subsurface. CRISPR development over time and imaging of 18 samples from one subsurface ecosystem suggest a sophisticated interplay of viral diversification and adapting CRISPR-mediated resistances of Ca. Altiarchaeum. We conclude that infections of primary producers with lytic viruses followed by cell lysis potentially jump-start heterotrophic carbon cycling in these subsurface ecosystems.

scholarly journals Genome-informed microscopy reveals infections of uncultivated carbon-fixing archaea by lytic viruses in Earth’s crust

2020 ◽  
Author(s):  
Janina Rahlff ◽  
Victoria Turzynski ◽  
Sarah P. Esser ◽  
Indra Monsees ◽  
Till L.V. Bornemann ◽  
...  
Keyword(s):  
Fluorescence Microscopy ◽  
Carbon Cycling ◽  
Viral Genome ◽  
Cell Lysis ◽  
Major Portion ◽  
Primary Producers ◽  
Deep Subsurface ◽  
Abundance And Diversity ◽  
Genomic Relatedness ◽  
Over Time

ABSTRACTThe continental subsurface houses a major portion of life’s abundance and diversity, yet little is known about viruses infecting microbes that reside there. Here, we used a combination of metagenomics and genome-informed microscopy to show that highly abundant carbon-fixing organisms of the uncultivated genus Candidatus Altiarchaeum are frequent targets of previously unrecognized viruses in the deep subsurface. Analysis of CRISPR spacer matches displayed resistances of Ca. Altiarchaea against eight predicted viral clades, which showed genomic relatedness across continents but little similarity to previously identified viruses. Based on metagenomic information, we tagged and imaged a putatively viral genome rich in protospacers using fluorescence microscopy. Virus-targeted genomeFISH revealed a lytic lifestyle of the respective virus and challenges previous predictions that lysogeny prevails as the dominant viral lifestyle in the subsurface. CRISPR development over time and imaging of 18 samples from one subsurface ecosystem suggest a sophisticated interplay of viral diversification and adapting CRISPR-mediated resistances of Ca. Altiarchaeum. We conclude that infections of primary producers with lytic viruses followed by cell lysis potentially jump-start heterotrophic carbon cycling in these subsurface ecosystems.

scholarly journals Differential impacts of alternate primary producers on carbon cycling

Ecology ◽  
2021 ◽  
Author(s):  
Khashiff K. Miranda ◽  
Brooke L. Weigel ◽  
Sophie J. McCoy ◽  
Catherine A. Pfister
Keyword(s):  
Carbon Cycling ◽  
Primary Producers

scholarly journals 520. Longitudinal Analysis of SARS-CoV-2 Viruses in Hospitalized Adults

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S325-S326
Author(s):  
Lacy Simons ◽  
Ramon Lorenzo-Redondo ◽  
Hannah Nam ◽  
Scott C Roberts ◽  
Michael G Ison ◽  
...  
Keyword(s):  
Viral Load ◽  
Genome Sequencing ◽  
Viral Genome ◽  
Temporal Dynamics ◽  
Population Level ◽  
Hospital Staff ◽  
Therapeutic Interventions ◽  
Viral Loads ◽  
Qrt Pcr ◽  
Over Time

Abstract Background The rapid spread of SARS-CoV-2, the causative agent of Coronavirus disease 2019 (COVID-19), has been accompanied by the emergence of viral mutations, some of which may have distinct virological and clinical consequences. While whole genome sequencing efforts have worked to map this viral diversity at the population level, little is known about how SARS-CoV-2 may diversify within a host over time. This is particularly important for understanding the emergence of viral resistance to therapeutic interventions and immune pressure. The goal of this study was to assess the change in viral load and viral genome sequence within patients over time and determine if these changes correlate with clinical and/or demographic parameters. Methods Hospitalized patients admitted to Northwestern Memorial Hospital with a positive SARS-CoV-2 test were enrolled in a longitudinal study for the serial collection of nasopharyngeal specimens. Swabs were administered to patients by hospital staff every 4 ± 1 days for up to 32 days or until the patients were discharged. RNA was extracted from each specimen and viral loads were calculated by quantitative reverse transcriptase PCR (qRT-PCR). Specimens with qRT-PCR cycle threshold values less than or equal to 30 were subject to whole viral genome sequencing by reverse transcription, multiplex PCR, and deep sequencing. Variant populations sizes were estimated and subject to phylogenetic analysis relative to publicly available SARS-CoV-2 sequences. Sequence and viral load data were subsequently correlated to available demographic and clinical data. Results 60 patients were enrolled from March 26th to June 20th, 2020. We observed an overall decrease in nasopharyngeal viral load over time across all patients. However, the temporal dynamics of viral load differed on a patient-by-patient basis. Several mutations were also observed to have emerged within patients over time. Distribution of SARS-CoV-2 viral loads in serially collected nasopharyngeal swabs in hospitalized adults as determined by qRT-PCR. Samples were collected every 4 ± 1 days (T#1–8) and viral load is displayed by log(copy number). Conclusion These data indicate that SARS-CoV-2 viral loads in the nasopharynx decrease over time and that the virus can accumulate mutations during replication within individual patients. Future studies will examine if some of these mutations may provide fitness advantages in the presence of therapeutic and/or immune selective pressures. Disclosures Michael G. Ison, MD MS, AlloVir (Consultant)

scholarly journals Autochthonous faecal viral transfer (FVT) impacts the murine microbiome after antibiotic perturbation

BMC Biology ◽  
2020 ◽  
Vol 18 (1) ◽  
Author(s):  
Lorraine A. Draper ◽  
Feargal J. Ryan ◽  
Marion Dalmasso ◽  
Pat G. Casey ◽  
Angela McCann ◽  
...  
Keyword(s):  
Antibiotic Treatment ◽  
Healthy Donor ◽  
Metagenomic Sequencing ◽  
Faecal Microbiota ◽  
Gut Flora ◽  
Pre Treatment ◽  
Abundance And Diversity ◽  
Viral Transfer ◽  
And Control ◽  
Over Time

Abstract Background It has become increasingly accepted that establishing and maintaining a complex and diverse gut microbiota is fundamental to human health. There are growing efforts to identify means of modulating and influencing the microbiota, especially in individuals who have experienced a disruption in their native microbiota. Faecal microbiota transplantation (FMT) is one method that restores diversity to the microbiota of an individual by introducing microbes from a healthy donor. FMT introduces the total microbial load into the recipient, including the bacteria, archaea, yeasts, protists and viruses. In this study, we investigated whether an autochthonous faecal viral transfer (FVT), in the form of a sterile faecal filtrate, could impact the recovery of a bacteriome disrupted by antibiotic treatment. Results Following antibiotic disruption of the bacteriome, test mice received an FVT harvested prior to antibiotic treatment, while control mice received a heat- and nuclease-treated FVT. In both groups of mice, the perturbed microbiome reverted over time to one more similar to the pre-treatment one. However, the bacteriomes of mice that received an FVT, in which bacteriophages predominate, separated from those of the control mice as determined by principal co-ordinate analysis (PCoA). Moreover, analysis of the differentially abundant taxa indicated a closer resemblance to the pre-treatment bacteriome in the test mice that had received an FVT. Similarly, metagenomic sequencing of the virome confirmed that faecal bacteriophages of FVT and control mice differed over time in both abundance and diversity, with the phages constituting the FVT persisting in mice that received them. Conclusions An autochthonous virome transfer reshaped the bacteriomes of mice post-antibiotic treatment such that they more closely resembled the pre-antibiotic microbiota profile compared to mice that received non-viable phages. Thus, FVT may have a role in addressing antibiotic-associated microbiota alterations and potentially prevent the establishment of post-antibiotic infection. Given that bacteriophages are biologically inert in the absence of their host bacteria, they could form a safe and effective alternative to whole microbiota transplants that could be delivered during/following perturbation of the gut flora.

scholarly journals The <i>fortedata</i> R package: open-science datasets from a manipulative experiment testing forest resilience

2020 ◽  
Author(s):  
Jeff W. Atkins ◽  
Elizabeth Agee ◽  
Alexandra Barry ◽  
Kyla M. Dahlin ◽  
Kalyn Dorheim ◽  
...  
Keyword(s):  
Carbon Cycling ◽  
Error Propagation ◽  
Scientific Community ◽  
Temperate Forest ◽  
Open Data ◽  
R Package ◽  
Open Science ◽  
Manipulative Experiment ◽  
Forest Resilience ◽  
Over Time

Abstract. The fortedata R package is an open data notebook from the Forest Resilience Threshold Experiment (FoRTE) – a modeling and manipulative field experiment that tests the effects of disturbance severity and disturbance type on carbon cycling dynamics in a temperate forest. Package data consists of measurements of carbon pools and fluxes and ancillary measurements to help users analyse and interpret carbon cycling over time. Currently the package includes data and metadata from the first two years of FoRTE, and serves as a central, updatable resource for the FoRTE project team and is intended as a resource for external users over the course of the experiment and in perpetuity. Further, it supports all associated FoRTE publications, analyses, and modeling efforts. This increases efficiency, consistency, compatibility, and productivity, while minimizing duplicated effort and error propagation that can arise as a function of a large, distributed and collaborative effort. More broadly, fortedata represents an innovative, collaborative way of approaching science that unites and expedites the delivery of complementary datasets in near real time to the broader scientific community, increasing transparency and reproducibility of taxpayer-funded science. fortedata is available via GitHub: https://github.com/FoRTExperiment/fortedata and detailed documentation on the access, used, and applications of fortedata are available at: https://fortexperiment.github.io/fortedata/. The first public release, version 1.0.1 is also archived at: https://doi.org/10.5281/zenodo.3936146 (Atkins et al., 2020b). All level one data products are also available outside of the package as .csv files: https://doi.org/10.6084/m9.figshare.12292490.v3 (Atkins et al. 2020c).

Use of high-refractive index hydrogels and tissue clearing for large biological sample imaging (Preprint)

2021 ◽  
Author(s):  
Alexander Richardson ◽  
Sandra Fok ◽  
Victoria Lee ◽  
Kerry-Anne Rye ◽  
Nick Di Girolamo ◽  
...  
Keyword(s):  
Refractive Index ◽  
Fluorescence Microscopy ◽  
Water Content ◽  
Light Sheet ◽  
High Water ◽  
High Refractive Index ◽  
High Water Content ◽  
Tissue Clearing ◽  
Light Sheet Fluorescence Microscopy ◽  
Over Time

UNSTRUCTURED Recent advances in tissue clearing and light sheet fluorescence microscopy have improved insights into and understanding of tissue morphology and disease pathology by imaging large samples without the requirement of histological sectioning. However, sample handling and conservation of sample integrity during lengthy staining and acquisition protocols remains a challenge. This study overcomes these challenges with acrylamide hydrogels synthesised to match the refractive index of solutions typically utilised in aqueous tissue clearing protocols. These hydrogels have a high-water content (82.0+/-3.7% by weight). The gels are stable over time and FITC-IgG readily permeated into, and effluxed out of them. Whilst the gels deformed and/or swelled over time in some commonly used solutions, this was overcome by using a previously described custom refractive index matched solution. To validate their use, CUBIC cleared mouse tissues and whole embryos were embedded in hydrogels, stained using fluorescent small molecule dyes, labels and antibodies and successfully imaged using light sheet fluorescence microscopy. In conclusion, the high-water content, high refractive index hydrogels described in this study have a broad applicability to research that delves into pathophysiological processes by stabilising and protecting large and fragile samples.

PRE-HISPANIC-TO-COLONIAL DIETARY TRANSITIONS AT ETZATLAN, JALISCO, MEXICO

2012 ◽  
Vol 23 (2) ◽  
pp. 251-267 ◽  
Author(s):  
Judith F. Porcasi
Keyword(s):  
Dietary Patterns ◽  
Diversity Indices ◽  
Faunal Analysis ◽  
Large Mammals ◽  
Large Mammal ◽  
Dietary Breadth ◽  
Animal Remains ◽  
Early Colonial ◽  
Abundance And Diversity ◽  
Over Time

AbstractFaunal analysis of subsistence remains from four sites in the Etzatlan Basin in western central Mexico presents important contrasts between pre-Hispanic and colonial dietary patterns. Specific changes in animal remains are well correlated with the transition from pre-Hispanic to colonial occupations tracked along a statistically derived timeline in which ceramic evidence for the onset of colonization is found. Allometry is used to calculate faunal biomass, and abundance and diversity indices are used to define these dietary patterns relative to the timeline. There is a decrease in use of large mammals over time and an increased use of smaller mammals, birds, and reptiles/amphibians. In particular, a marked increase in exploitation of the most important native large mammal (for example, deer) is found during early colonial occupation. However, this bounty decreased appreciably during later periods, consistent with widening of dietary breadth by inclusion of less preferred resources.

scholarly journals Effect of Bt-maize on epigeic spiders (Araneae) and harvestmen (Opiliones)

2010 ◽  
Vol 42 (No. 1) ◽  
pp. 1-8 ◽  
Author(s):  
M. Řezáč ◽  
S. Pekár ◽  
F. Kocourek
Keyword(s):  
Pitfall Traps ◽  
Conventional System ◽  
The Czech Republic ◽  
Maize Hybrid ◽  
System A ◽  
The Family ◽  
Weed Cover ◽  
Abundance And Diversity ◽  
Over Time ◽  
Insect Resistant

The effect of two strategies, used to control <i>Ostrinia nubialis</i>, on the abundance and diversity of epigeic spiders and harvestmen in maize was monitored. The two strategies were (1) transgenic insect-resistant maize, and (2) biological control by <i>Trichogramma</i> wasps on an isogenic maize hybrid. They were compared with a conventional system (isogenic maize hybrid), which was taken as the control. The investigation was performed at two localities (Ivanovice na Hané and Prague) in the Czech Republic from 2002 to 2004. Spiders (Araneae) and harvestmen (Opiliones) were collected by means of pitfall traps. We found that the annual abundance and diversity of arachnids on plots with the two strategies were not significantly different from a conventional system. The overall abundance of spiders decreased over three years in all systems. There was no difference in the family and guild (hunters versus web-builders) composition between strategies and the conventional system. A displacement of linyphiid spiders with lycosids on all plots over time was observed. This change is attributed to the existence of a sparse weed cover of maize fields as a result of consecutive monocultural planting.

Light sheet fluorescence microscopy (LSFM): past, present and future

The Analyst ◽  
2014 ◽  
Vol 139 (19) ◽  
pp. 4758-4768 ◽  
Author(s):  
John Lim ◽  
Hwee Kuan Lee ◽  
Weimiao Yu ◽  
Sohail Ahmed
Keyword(s):  
Fluorescence Microscopy ◽  
Imaging Modality ◽  
Light Sheet ◽  
Light Sheet Fluorescence Microscopy ◽  
Over Time

Light sheet fluorescence microscopy (LSFM) has emerged as an important imaging modality to follow biology in live 3D samples over time with reduced phototoxicity and photobleaching.

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