1
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Trubl G, Stedman KM, Bywaters KF, Matula EE, Sommers P, Roux S, Merino N, Yin J, Kaelber JT, Avila-Herrera A, Johnson PA, Johnson JC, Borges S, Weber PK, Pett-Ridge J, Boston PJ. Astrovirology: how viruses enhance our understanding of life in the Universe. INTERNATIONAL JOURNAL OF ASTROBIOLOGY 2023; 22:247-271. [PMID: 38046673 PMCID: PMC10691837 DOI: 10.1017/s1473550423000058] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Viruses are the most numerically abundant biological entities on Earth. As ubiquitous replicators of molecular information and agents of community change, viruses have potent effects on the life on Earth, and may play a critical role in human spaceflight, for life-detection missions to other planetary bodies and planetary protection. However, major knowledge gaps constrain our understanding of the Earth's virosphere: (1) the role viruses play in biogeochemical cycles, (2) the origin(s) of viruses and (3) the involvement of viruses in the evolution, distribution and persistence of life. As viruses are the only replicators that span all known types of nucleic acids, an expanded experimental and theoretical toolbox built for Earth's viruses will be pivotal for detecting and understanding life on Earth and beyond. Only by filling in these knowledge and technical gaps we will obtain an inclusive assessment of how to distinguish and detect life on other planetary surfaces. Meanwhile, space exploration requires life-support systems for the needs of humans, plants and their microbial inhabitants. Viral effects on microbes and plants are essential for Earth's biosphere and human health, but virus-host interactions in spaceflight are poorly understood. Viral relationships with their hosts respond to environmental changes in complex ways which are difficult to predict by extrapolating from Earth-based proxies. These relationships should be studied in space to fully understand how spaceflight will modulate viral impacts on human health and life-support systems, including microbiomes. In this review, we address key questions that must be examined to incorporate viruses into Earth system models, life-support systems and life detection. Tackling these questions will benefit our efforts to develop planetary protection protocols and further our understanding of viruses in astrobiology.
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Affiliation(s)
- Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Kenneth M. Stedman
- Center for Life in Extreme Environments, Department of Biology, Portland State University, Portland, OR, USA
| | | | | | | | - Simon Roux
- DOE Joint Genome Institute, Berkeley, CA, USA
| | - Nancy Merino
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - John Yin
- Chemical and Biological Engineering, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
| | - Jason T. Kaelber
- Institute for Quantitative Biomedicine, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Aram Avila-Herrera
- Computing Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Peter Anto Johnson
- Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, Canada
| | | | | | - Peter K. Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Life & Environmental Sciences Department, University of California Merced, Merced, CA, USA
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2
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Abstract
High-resolution imaging with secondary ion mass spectrometry (nanoSIMS) has become a standard method in systems biology and environmental biogeochemistry and is broadly used to decipher ecophysiological traits of environmental microorganisms, metabolic processes in plant and animal tissues, and cross-kingdom symbioses. When combined with stable isotope-labeling-an approach we refer to as nanoSIP-nanoSIMS imaging offers a distinctive means to quantify net assimilation rates and stoichiometry of individual cell-sized particles in both low- and high-complexity environments. While the majority of nanoSIP studies in environmental and microbial biology have focused on nitrogen and carbon metabolism (using 15N and 13C tracers), multiple advances have pushed the capabilities of this approach in the past decade. The development of a high-brightness oxygen ion source has enabled high-resolution metal analyses that are easier to perform, allowing quantification of metal distribution in cells and environmental particles. New preparation methods, tools for automated data extraction from large data sets, and analytical approaches that push the limits of sensitivity and spatial resolution have allowed for more robust characterization of populations ranging from marine archaea to fungi and viruses. NanoSIMS studies continue to be enhanced by correlation with orthogonal imaging and 'omics approaches; when linked to molecular visualization methods, such as in situ hybridization and antibody labeling, these techniques enable in situ function to be linked to microbial identity and gene expression. Here we present an updated description of the primary materials, methods, and calculations used for nanoSIP, with an emphasis on recent advances in nanoSIMS applications, key methodological steps, and potential pitfalls.
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Affiliation(s)
- Jennifer Pett-Ridge
- Lawrence Livermore National Lab, Physical and Life Science Directorate, Livermore, CA, USA.
| | - Peter K Weber
- Lawrence Livermore National Lab, Physical and Life Science Directorate, Livermore, CA, USA.
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3
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Sommers P, Chatterjee A, Varsani A, Trubl G. Integrating Viral Metagenomics into an Ecological Framework. Annu Rev Virol 2021; 8:133-158. [PMID: 34033501 DOI: 10.1146/annurev-virology-010421-053015] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Viral metagenomics has expanded our knowledge of the ecology of uncultured viruses, within both environmental (e.g., terrestrial and aquatic) and host-associated (e.g., plants and animals, including humans) contexts. Here, we emphasize the implementation of an ecological framework in viral metagenomic studies to address questions in virology rarely considered ecological, which can change our perception of viruses and how they interact with their surroundings. An ecological framework explicitly considers diverse variants of viruses in populations that make up communities of interacting viruses, with ecosystem-level effects. It provides a structure for the study of the diversity, distributions, dynamics, and interactions of viruses with one another, hosts, and the ecosystem, including interactions with abiotic factors. An ecological framework in viral metagenomics stands poised to broadly expand our knowledge in basic and applied virology. We highlight specific fundamental research needs to capitalize on its potential and advance the field. Expected final online publication date for the Annual Review of Virology, Volume 8 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Pacifica Sommers
- Department of Ecology and Evolutionary Biology, University of Colorado at Boulder, Boulder, Colorado 80309, USA.,These authors contributed equally to this article
| | - Anushila Chatterjee
- Department of Ecology and Evolutionary Biology, University of Colorado at Boulder, Boulder, Colorado 80309, USA.,These authors contributed equally to this article
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, Arizona 85287, USA; .,Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Observatory 7925, South Africa
| | - Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
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4
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de Jesus JR, de Araújo Andrade T. Understanding the relationship between viral infections and trace elements from a metallomics perspective: implications for COVID-19. Metallomics 2020; 12:1912-1930. [PMID: 33295922 PMCID: PMC7928718 DOI: 10.1039/d0mt00220h] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 11/13/2020] [Indexed: 12/11/2022]
Abstract
Recently, the World Health Organization (WHO) declared a pandemic situation due to a new viral infection (COVID-19) caused by a novel virus (Sars-CoV-2). COVID-19 is today the leading cause of death from viral infections in the world. It is known that many elements play important roles in viral infections, both in virus survival, and in the activation of the host's immune system, which depends on the presence of micronutrients to maintain the integrity of its functions. In this sense, the metallome can be an important object of study for understanding viral infections. Therefore, this work presents an overview of the role of trace elements in the immune system and the state of the art in metallomics, highlighting the challenges found in studies focusing on viral infections.
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Affiliation(s)
- Jemmyson Romário de Jesus
- University of Campinas, Institute of Chemistry, Dept of Analytical Chemistry, Campinas, São Paulo, Brazil.
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5
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Thomen A, Najafinobar N, Penen F, Kay E, Upadhyay PP, Li X, Phan NTN, Malmberg P, Klarqvist M, Andersson S, Kurczy ME, Ewing AG. Subcellular Mass Spectrometry Imaging and Absolute Quantitative Analysis across Organelles. ACS NANO 2020; 14:4316-4325. [PMID: 32239916 PMCID: PMC7199216 DOI: 10.1021/acsnano.9b09804] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 04/02/2020] [Indexed: 05/22/2023]
Abstract
Mass spectrometry imaging is a field that promises to become a mainstream bioanalysis technology by allowing the combination of single-cell imaging and subcellular quantitative analysis. The frontier of single-cell imaging has advanced to the point where it is now possible to compare the chemical contents of individual organelles in terms of raw or normalized ion signal. However, to realize the full potential of this technology, it is necessary to move beyond this concept of relative quantification. Here we present a nanoSIMS imaging method that directly measures the absolute concentration of an organelle-associated, isotopically labeled, pro-drug directly from a mass spectrometry image. This is validated with a recently developed nanoelectrochemistry method for single organelles. We establish a limit of detection based on the number of isotopic labels used and the volume of the organelle of interest, also offering this calculation as a web application. This approach allows subcellular quantification of drugs and metabolites, an overarching and previously unmet goal in cell science and pharmaceutical development.
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Affiliation(s)
- Aurélien Thomen
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Gothenburg, 412 96, Sweden
| | - Neda Najafinobar
- Medicinal
Chemistry, Research and Early Development, Respiratory, Inflammation,
and Autoimmune, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, 430 51, Sweden
| | - Florent Penen
- Department
of Chemistry and Chemical Engineering, Chalmers
University of Technology, Gothenburg, 412 96, Sweden
| | - Emma Kay
- Bioscience,
Research and Early Development, Cardiovascular, Renal and Metabolism,
BioPharmaceuticals R&D, AstraZeneca, Gothenburg, 430 51, Sweden
| | - Pratik P. Upadhyay
- Pharmaceutical
Technolgy and Development, AstraZeneca R&D, Gothenburg, 430 52, Sweden
| | - Xianchan Li
- Center
for Imaging and Systems Biology, College of Life and Environmental
Sciences, Minzu University of China, Beijing, 100081, China
| | - Nhu T. N. Phan
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Gothenburg, 412 96, Sweden
| | - Per Malmberg
- Department
of Chemistry and Chemical Engineering, Chalmers
University of Technology, Gothenburg, 412 96, Sweden
| | - Magnus Klarqvist
- Early
Product Development, Pharmaceutical Science, R&D, AstraZeneca, Gothenburg, 431 50, Sweden
| | - Shalini Andersson
- New Modalities,
Discovery Sciences, R&D, AstraZeneca, Gothenburg, 430 51, Sweden
| | - Michael E. Kurczy
- DMPK,
Research and Early Development, Cardiovascular, Renal and Metabolism,
BioPharmaceuticals R&D, AstraZeneca, Gothenburg, 430 51, Sweden
| | - Andrew G. Ewing
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Gothenburg, 412 96, Sweden
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6
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Mayali X. NanoSIMS: Microscale Quantification of Biogeochemical Activity with Large-Scale Impacts. ANNUAL REVIEW OF MARINE SCIENCE 2020; 12:449-467. [PMID: 31299167 DOI: 10.1146/annurev-marine-010419-010714] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
One major objective of aquatic microbial ecology is to understand the distribution of microbial populations over space and time and in response to environmental factors. Perhaps more importantly, it is crucial to quantify how those microbial cells affect biogeochemical processes of interest, such as primary production, nitrogen cycling, or the breakdown of pollutants. One valuable approach to link microbial identity to activity is to carry out incubations with stable-isotope-labeled substrates and then quantify the isotope incorporation by individual microbial cells using nanoscale secondary ion mass spectrometry (NanoSIMS). This review summarizes recent efforts in this field, highlights novel methods, describes studies investigating rare metabolisms as well as widespread microbial activity, and hopes to provide a framework to increase the use and capabilities of NanoSIMS for microbial biogeochemical studies in the future.
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Affiliation(s)
- Xavier Mayali
- Lawrence Livermore National Laboratory, Livermore, California 94550, USA;
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7
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Trubl G, Roux S, Solonenko N, Li YF, Bolduc B, Rodríguez-Ramos J, Eloe-Fadrosh EA, Rich VI, Sullivan MB. Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils. PeerJ 2019; 7:e7265. [PMID: 31309007 PMCID: PMC6612421 DOI: 10.7717/peerj.7265] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 06/07/2019] [Indexed: 11/29/2022] Open
Abstract
Soils impact global carbon cycling and their resident microbes are critical to their biogeochemical processing and ecosystem outputs. Based on studies in marine systems, viruses infecting soil microbes likely modulate host activities via mortality, horizontal gene transfer, and metabolic control. However, their roles remain largely unexplored due to technical challenges with separating, isolating, and extracting DNA from viruses in soils. Some of these challenges have been overcome by using whole genome amplification methods and while these have allowed insights into the identities of soil viruses and their genomes, their inherit biases have prevented meaningful ecological interpretations. Here we experimentally optimized steps for generating quantitatively-amplified viral metagenomes to better capture both ssDNA and dsDNA viruses across three distinct soil habitats along a permafrost thaw gradient. First, we assessed differing DNA extraction methods (PowerSoil, Wizard mini columns, and cetyl trimethylammonium bromide) for quantity and quality of viral DNA. This established PowerSoil as best for yield and quality of DNA from our samples, though ∼1/3 of the viral populations captured by each extraction kit were unique, suggesting appreciable differential biases among DNA extraction kits. Second, we evaluated the impact of purifying viral particles after resuspension (by cesium chloride gradients; CsCl) and of viral lysis method (heat vs bead-beating) on the resultant viromes. DNA yields after CsCl particle-purification were largely non-detectable, while unpurified samples yielded 1–2-fold more DNA after lysis by heat than by bead-beating. Virome quality was assessed by the number and size of metagenome-assembled viral contigs, which showed no increase after CsCl-purification, but did from heat lysis relative to bead-beating. We also evaluated sample preparation protocols for ssDNA virus recovery. In both CsCl-purified and non-purified samples, ssDNA viruses were successfully recovered by using the Accel-NGS 1S Plus Library Kit. While ssDNA viruses were identified in all three soil types, none were identified in the samples that used bead-beating, suggesting this lysis method may impact recovery. Further, 13 ssDNA vOTUs were identified compared to 582 dsDNA vOTUs, and the ssDNA vOTUs only accounted for ∼4% of the assembled reads, implying dsDNA viruses were dominant in these samples. This optimized approach was combined with the previously published viral resuspension protocol into a sample-to-virome protocol for soils now available at protocols.io, where community feedback creates ‘living’ protocols. This collective approach will be particularly valuable given the high physicochemical variability of soils, which will may require considerable soil type-specific optimization. This optimized protocol provides a starting place for developing quantitatively-amplified viromic datasets and will help enable viral ecogenomic studies on organic-rich soils.
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Affiliation(s)
- Gareth Trubl
- Department of Microbiology, The Ohio State University, Columbus, OH, United States of America.,Current affiliation: Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States of America
| | - Simon Roux
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, CA, United States of America
| | - Natalie Solonenko
- Department of Microbiology, The Ohio State University, Columbus, OH, United States of America
| | - Yueh-Fen Li
- Department of Microbiology, The Ohio State University, Columbus, OH, United States of America
| | - Benjamin Bolduc
- Department of Microbiology, The Ohio State University, Columbus, OH, United States of America
| | - Josué Rodríguez-Ramos
- Department of Microbiology, The Ohio State University, Columbus, OH, United States of America.,Current affiliation: Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, United States of America
| | - Emiley A Eloe-Fadrosh
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, CA, United States of America
| | - Virginia I Rich
- Department of Microbiology, The Ohio State University, Columbus, OH, United States of America
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH, United States of America.,Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, United States of America
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8
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Lee DK, Na E, Park S, Park JH, Lim J, Kwon SW. In Vitro Tracking of Intracellular Metabolism-Derived Cancer Volatiles via Isotope Labeling. ACS CENTRAL SCIENCE 2018; 4:1037-1044. [PMID: 30159401 PMCID: PMC6107874 DOI: 10.1021/acscentsci.8b00296] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Indexed: 05/28/2023]
Abstract
Cancer detection relying on the release of volatile biomarkers has been extensively studied, but the individual biochemical processes of the cells from which biogenic volatiles originate have not been thoroughly elucidated to date. Inadequate determination of the metabolic origin of the volatile biomarkers has limited the progress of the scientific and practical applications of volatile biomarkers. To overcome the current limitations, we developed a metabolism tracking approach combining stable isotope labeling and flux analysis of volatiles to trace the intracellular metabolism-derived volatiles and to reveal their relation to cancer metabolic pathways. Specifically, after the 13C labeling of lung cancer cell, the isotopic ratio of whole cellular carbon was measured by nanoscale secondary ion mass spectrometry-based imaging. The kinetic modeling with the time-dependent isotopic ratio determined the period during which cancer cells reach the metabolic steady state, at which time all of the potential volatiles derived from intracellular metabolism were fully enriched isotopically. By measuring the isotopic enrichment of volatiles at the end-stage of isotopic flux, we found that 2-pentadecanone appeared to be derived from the metabolic cascade starting from glucose to fatty acid synthesis. Furthermore, this biosynthetic pathway was determined to be distinct in cancer, as it was upregulated in colon, breast, and pancreatic cancer cells but not in normal cells. The investigation of the metabolic footprint of 2-pentadecanone demonstrates that our novel approach could be applied to trace the metabolic origin of biogenic volatile organic compounds. This analytical strategy represents a potential cutting-edge tool in elucidating the biochemical authenticity of cancer volatiles and further expanding our understanding of the metabolic network of airborne metabolites in vitro.
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Affiliation(s)
- Dong-Kyu Lee
- Research
Institute of Pharmaceutical Sciences, Seoul
National University, Seoul 08826, Republic of Korea
| | - Euiyeon Na
- College
of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Seongoh Park
- Department
of Statistics, Seoul National University, Seoul 08826, Republic of Korea
| | - Jeong Hill Park
- Research
Institute of Pharmaceutical Sciences, Seoul
National University, Seoul 08826, Republic of Korea
- College
of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Johan Lim
- Department
of Statistics, Seoul National University, Seoul 08826, Republic of Korea
| | - Sung Won Kwon
- Research
Institute of Pharmaceutical Sciences, Seoul
National University, Seoul 08826, Republic of Korea
- College
of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
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