Microbes drive ecosystems under constraints imposed by viruses. However, a lack of virus genome information hinders our ability to answer fundamental, biological questions concerning microbial ...communities. Here we apply single-virus genomics (SVGs) to assess whether portions of marine viral communities are missed by current techniques. The majority of the here-identified 44 viral single-amplified genomes (vSAGs) are more abundant in global ocean virome data sets than published metagenome-assembled viral genomes or isolates. This indicates that vSAGs likely best represent the dsDNA viral populations dominating the oceans. Species-specific recruitment patterns and virome simulation data suggest that vSAGs are highly microdiverse and that microdiversity hinders the metagenomic assembly, which could explain why their genomes have not been identified before. Altogether, SVGs enable the discovery of some of the likely most abundant and ecologically relevant marine viral species, such as vSAG 37-F6, which were overlooked by other methodologies.
About the Authors: Nolwenn M. Dheilly * E-mail: nolwenn.dheilly@stonybrook.edu (NMD); jmartinez@bigelow.org (JMM) Affiliation: School of Marine and Atmospheric Sciences, Stony Brook University, Stony ...Brook, New York, United States of America ORCID logo http://orcid.org/0000-0002-3675-5013 Joaquín Martínez Martínez * E-mail: nolwenn.dheilly@stonybrook.edu (NMD); jmartinez@bigelow.org (JMM) Affiliation: Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, United States of America ORCID logo http://orcid.org/0000-0002-2295-0264 Karyna Rosario Affiliation: College of Marine Science, University of South Florida, Saint Petersburg, Florida, United States of America ORCID logo http://orcid.org/0000-0001-9847-4113 Paul J. Brindley Affiliations Department of Microbiology, Immunology and Tropical Medicine, George Washington University, Washington, DC, United States of America, Research Center for Neglected Diseases of Poverty, School of Medicine & Health Sciences, George Washington University, Washington, DC, United States of America ORCID logo http://orcid.org/0000-0003-1765-0002 Raina N. Fichorova Affiliation: Genital Tract Biology Division, Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America ORCID logo http://orcid.org/0000-0002-9980-5735 Jonathan Z. Kaye Affiliation: Gordon and Betty Moore Foundation, Palo Alto, California, United States of America Kevin D. Kohl Affiliation: Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America ORCID logo http://orcid.org/0000-0003-1126-2949 Laura J. Knoll Affiliation: Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America Julius Lukeš Affiliation: Institute of Parasitology, Biology Centre, Czech Academy of Sciences and Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic ORCID logo http://orcid.org/0000-0002-0578-6618 Susan L. Perkins Affiliation: Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America ORCID logo http://orcid.org/0000-0002-5400-5662 Robert Poulin Affiliation: Department of Zoology, University of Otago, Dunedin, New Zealand Lynn Schriml Affiliation: Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America ORCID logo http://orcid.org/0000-0001-8910-9851 Luke R. Thompson Affiliations Department of Biological Sciences and Northern Gulf Institute, University of Southern Mississippi, Hattiesburg, Mississippi, United States of America, Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, La Jolla, California, United States of America ORCID logo http://orcid.org/0000-0002-3911-1280 Citation: Dheilly NM, Martínez Martínez J, Rosario K, Brindley PJ, Fichorova RN, Kaye JZ, et al. Methods to tackle the grand challenges of parasite microbiome research. https://doi.org/10.1371/journal.ppat.1008028.t001 A primary advantage of a centralized platform like the PMP is the collation of large aggregates of associated metadata that can be harnessed to uncover, and eventually understand, patterns of microbial diversity and ecology 40, 35. ...detailed metadata associated with each study and sample are absolutely critical to maximize the utility of each. ...when possible, experimental evolution of parasites and hosts in the presence or absence of the identified microbes can been used to test the effect of specific microbes on the evolution of the system and to identify mechanisms involved in parasite–microbe interaction. The PMP will necessitate both significant funding to conduct challenging research as well as engagement from the community to provide high-quality samples and to share detailed and accurate metadata information. ...we propose constituting a community of researchers that meet annually for workshops and symposia.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Metagenomics has opened new windows on investigating viral diversity and functions. Viromic studies typically require large sample volumes and filtration through 0.2 μm pore-size filters, ...consequently excluding or under-sampling tailed and very large viruses. We have optimized a targeted viromic approach that employs fluorescence-activated sorting and whole genome amplification to produce dsDNA-enriched libraries from discrete viral populations from a 1-ml water sample. Using this approach on an environmental sample from the Patagonian Shelf, we produced three distinct libraries. One of the virus libraries was dominated (79.65% of sequences with known viral homology) by giant viruses from the Mimiviridae and Phycodnaviridae families, while the two other viromes were dominated by smaller phycodnaviruses, cyanophages and other bacteriophages. The estimated genotypic richness and diversity in our sorted viromes, with 52-163 estimated genotypes, was much lower than in previous virome reports. Fragment recruitment of metagenome reads to selected reference viral genomes yields high genome coverage, suggesting little amplification and sequencing bias against some genomic regions. These results underscore the value of our approach as an effective way to target and investigate specific virus groups. In particular, it will help reveal the diversity and abundance of giant viruses in marine ecosystems.
The dynamics of solute dispersion and mixing in unsaturated flows is analyzed from photobleaching experiments in two‐dimensional porous micromodels. This technique allows producing pulse line ...(delta‐Dirac) injections of a conservative tracer by bleaching a finite volume of fluorescent without disturbing the flow field. The temporal evolution of the concentration field and the spatial distribution of the air and water phases can be monitored at pore scale. We study the dispersion and mixing of a line of tracer under different water saturations. While dispersion in saturated porous media follows an approximately Fickian scaling, a shift to ballistic scaling is observed as soon as saturation is lowered. Hence, at the time scale of observation, dispersion in our unsaturated flows is dominated by the ballistic separation of tracer blobs within the water phase, between trapped clusters and preferential flow paths. While diffusion plays a minor role in the longitudinal dispersion during the time scale of the experiments, its interplay with fluid deformation is apparent in the dynamics of mixing. The scalar dissipation rates show an initial stretching regime, during which mixing is enhanced by fluid deformation, followed by a dissipation regime, during which diffusion overcomes compression induced by stretching. The transition between these two regimes occurs at the mixing time, when concentration gradients are maximum. We propose a predictive analytical model, based on shear‐enhanced diffusion, that captures the dynamics of mixing from basic unsaturated porous media parameters, suggesting that this type of model may be a useful framework at larger scales.
Key Points
Photobleaching experiments in two‐dimensional micromodels
Ballistic dispersion at short‐term as soon as saturation is lowered
Mixing is enhanced by fluid deformation, stretching regime, followed by a dissipation regime
Absolute abundances of prokaryotes are typically determined by FISH. Due to the lack of a universal conserved gene among all viruses, metagenomic fragment recruitment is commonly used to estimate the ...relative viral abundance. However, the paucity of absolute virus abundance data hinders our ability to fully understand how viruses drive global microbial populations. The cosmopolitan marine
is host for the highly widespread HTVC010P pelagiphage isolate and the extremely abundant uncultured virus vSAG 37-F6 recently discovered by single-virus genomics. Here we applied droplet digital PCR (ddPCR) to calculate the absolute abundance of these pelagiphage genotypes in the Mediterranean Sea and the Gulf of Maine. Abundances were between 360 and 8,510 virus mL-1 and 1,270-14,400 virus mL-1 for vSAG 37-F6 and HTVC010P, respectively. Illumina PCR-amplicon sequencing corroborated the absence of ddPCR non-specific amplifications for vSAG 37-F6, but showed an overestimation of 6% for HTVC010P from off-targets, genetically unrelated viruses. Absolute abundances of both pelagiphages, two of the most abundance marine viruses, suggest a large viral pelagiphage diversity in marine environments, and show the efficiency and power of ddPCR to disentangle the structure of marine viral communities. Results also highlight the need for a standardized workflow to obtain accurate quantification that allows cross data comparison.
The methanol‐to‐olefins reaction catalyzed by small‐pore cage‐based acid zeolites and zeotypes produces a mixture of short chain olefins, whose selectivity to ethene, propene and butene varies with ...the cavity architecture and with the framework composition. The product distribution of aluminosilicates and silicoaluminophosphates with the CHA and AEI structures (H‐SSZ‐13, H‐SAPO‐34, H‐SSZ‐39 and H‐SAPO‐18) has been experimentally determined, and the impact of acidity and framework flexibility on the stability of the key cationic intermediates involved in the mechanism and on the diffusion of the olefin products through the 8r windows of the catalysts has been evaluated by means of periodic DFT calculations and ab initio molecular dynamics simulations. The preferential stabilization by confinement of fully methylated hydrocarbon pool intermediates favoring the paring pathway is the main factor controlling the final olefin product distribution.
The selectivity of the methanol‐to‐olefins (MTO) reaction catalyzed by zeolites varies with cavity architecture and framework composition. The higher flexibility of the SAPO‐34 framework as compared to SSZ‐13 does not modify the relative diffusion rate of ethene and propene, but facilitates the accommodation of the bulkier cationic intermediates of the MTO reaction, increasing the production of propene and butene.
The current status of controversy regarding the use of certain preservatives in cosmetic products makes it necessary to seek new ecological alternatives that are free of adverse effects on users. In ...our study, the natural terpene thymoquinone was encapsulated in chitosan nanoparticles. The nanoparticles were characterized by DLS and TEM, showing a particle size of 20 nm. The chemical structure, thermal properties, and release profile of thymoquinone were evaluated and showed a successful stabilization and sustained release of terpenes. The antimicrobial properties of the nanoparticles were evaluated against typical microbial contaminants found in cosmetic products, showing high antimicrobial properties. Furthermore, natural moisturizing cream inoculated with the aforementioned microorganisms was formulated with thymoquinone-chitosan nanoparticles to evaluate the preservative efficiency, indicating its promising use as a preservative in cosmetics.
Porous media in which different fluid phases coexist are common in nature (e.g., vadose zone and gas‐oil reservoirs). In partially saturated porous media, the intricate spatial distributions of the ...wetting and nonwetting phases causes their flow to be focused onto preferential paths. Using a novel 2‐D experimental setup allowing pore‐scale measurement of concentration fields in a controlled unsaturated flow, we highlight mechanisms by which mixing of an invading fluid with the resident fluid is significantly enhanced when decreasing saturation. The mean scalar dissipation rate is observed to decrease slowly in time, while under saturated conditions it decays rapidly. This slow decrease is due to sustained longitudinal solute fingering, which causes concentration gradients to remain predominantly transverse to the average flow. Consequently, the effective reactivity is found to be much larger than under saturated conditions. These results provide new insights into the role that multiphase flows play on mixing/reaction in porous media.
Key Points
Enhancement of solutes mixing in unsaturated porous media
Mixing‐induced reactivity in unsaturated porous media
Vadose zone and gas‐oil reservoir
In this study we used denaturing gradient gel electrophoresis, sequencing analysis, and analytical flow cytometry to monitor the dynamics and genetic richness of Emiliania huxleyi isolates and ...cooccurring viruses during two mesocosm experiments in a Norwegian fjord in 2000 and 2003. We exploited variations in a gene encoding a protein with calcium-binding motifs (GPA) and in the major capsid protein (MCP) gene to assess allelic and genotypic richness within E. huxleyi and E. huxleyi-specific viruses (EhVs), respectively. To our knowledge, this is the first report that shows the effectiveness of the GPA gene for analysis of natural communities of E. huxleyi. Our results revealed the existence of a genetically rich, yet stable E. huxleyi and EhV community in the fjordic environment. Incredibly, the same virus and host genotypes dominated in separate studies conducted 3 years apart. Both E. huxleyi-dominated blooms contained the same six E. huxleyi alleles. In addition, despite the presence of at least six and four EhV genotypes at the start of the blooms in 2000 and 2003, respectively, the same two virus genotypes dominated the naturally occurring infections during the exponential and termination phases of the blooms in both years.
From theoretical calculations and a rational synthesis methodology, it has been possible to prepare nanocrystalline (60–80 nm) chabazite with an optimized framework Al distribution that has a ...positive impact on its catalytic properties. This is exemplified for the methanol‐to‐olefin (MTO) process. The nanosized material with the predicted Al distribution maximizes the formation of the required MTO hydrocarbon pool intermediates, while better precluding excessive diffusion pathways that favor the rapid catalyst deactivation by coke formation.
Size matters! The control of the Al distribution and the crystal size in the CHA‐type catalyst results in a five‐fold increase of the catalyst life for the methanol‐to‐olefin (MTO) reaction compared to standard CHA‐based catalysts. The optimized aluminum distribution together with the small crystallites maximize the formation of the MTO hydrocarbon pool intermediates, while diffusion pathways are also improved.
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