40 results on '"Lisa Zeigler Allen"'
Search Results
2. Diploid genomic architecture of Nitzschia inconspicua, an elite biomass production diatom
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Aaron Oliver, Sheila Podell, Agnieszka Pinowska, Jesse C. Traller, Sarah R. Smith, Ryan McClure, Alex Beliaev, Pavlo Bohutskyi, Eric A. Hill, Ariel Rabines, Hong Zheng, Lisa Zeigler Allen, Alan Kuo, Igor V. Grigoriev, Andrew E. Allen, David Hazlebeck, and Eric E. Allen more...
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Medicine ,Science - Abstract
Abstract A near-complete diploid nuclear genome and accompanying circular mitochondrial and chloroplast genomes have been assembled from the elite commercial diatom species Nitzschia inconspicua. The 50 Mbp haploid size of the nuclear genome is nearly double that of model diatom Phaeodactylum tricornutum, but 30% smaller than closer relative Fragilariopsis cylindrus. Diploid assembly, which was facilitated by low levels of allelic heterozygosity (2.7%), included 14 candidate chromosome pairs composed of long, syntenic contigs, covering 93% of the total assembly. Telomeric ends were capped with an unusual 12-mer, G-rich, degenerate repeat sequence. Predicted proteins were highly enriched in strain-specific marker domains associated with cell-surface adhesion, biofilm formation, and raphe system gliding motility. Expanded species-specific families of carbonic anhydrases suggest potential enhancement of carbon concentration efficiency, and duplicated glycolysis and fatty acid synthesis pathways across cytosolic and organellar compartments may enhance peak metabolic output, contributing to competitive success over other organisms in mixed cultures. The N. inconspicua genome delivers a robust new reference for future functional and transcriptomic studies to illuminate the physiology of benthic pennate diatoms and harness their unique adaptations to support commercial algae biomass and bioproduct production. more...
- Published
- 2021
- Full Text
- View/download PDF
Catalog
3. Publisher Correction: Influence of nutrient supply on plankton microbiome biodiversity and distribution in a coastal upwelling region
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Chase C. James, Andrew D. Barton, Lisa Zeigler Allen, Robert H. Lampe, Ariel Rabines, Anne Schulberg, Hong Zheng, Ralf Goericke, Kelly D. Goodwin, and Andrew E. Allen
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Science - Published
- 2022
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4. The Baltic Sea Virome: Diversity and Transcriptional Activity of DNA and RNA Viruses
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Lisa Zeigler Allen, John P. McCrow, Karolina Ininbergs, Christopher L. Dupont, Jonathan H. Badger, Jeffery M. Hoffman, Martin Ekman, Andrew E. Allen, Birgitta Bergman, and J. Craig Venter
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marine microbiology ,viral ecology ,viral metagenomics ,viral metatranscriptomics ,viral/host inference ,Microbiology ,QR1-502 - Abstract
ABSTRACT Metagenomic and metatranscriptomic data were generated from size-fractionated samples from 11 sites within the Baltic Sea and adjacent marine waters of Kattegat and freshwater Lake Torneträsk in order to investigate the diversity, distribution, and transcriptional activity of virioplankton. Such a transect, spanning a salinity gradient from freshwater to the open sea, facilitated a broad genome-enabled investigation of natural as well as impacted aspects of Baltic Sea viral communities. Taxonomic signatures representative of phages within the widely distributed order Caudovirales were identified with enrichments in lesser-known families such as Podoviridae and Siphoviridae. The distribution of phage reported to infect diverse and ubiquitous heterotrophic bacteria (SAR11 clades) and cyanobacteria (Synechococcus sp.) displayed population-level shifts in diversity. Samples from higher-salinity conditions (>14 practical salinity units [PSU]) had increased abundances of viruses for picoeukaryotes, i.e., Ostreococcus. These data, combined with host diversity estimates, suggest viral modulation of diversity on the whole-community scale, as well as in specific prokaryotic and eukaryotic lineages. RNA libraries revealed single-stranded DNA (ssDNA) and RNA viral populations throughout the Baltic Sea, with ssDNA phage highly represented in Lake Torneträsk. Further, our data suggest relatively high transcriptional activity of fish viruses within diverse families known to have broad host ranges, such as Nodoviridae (RNA), Iridoviridae (DNA), and predicted zoonotic viruses that can cause ecological and economic damage as well as impact human health. IMPORTANCE Inferred virus-host relationships, community structures of ubiquitous ecologically relevant groups, and identification of transcriptionally active populations have been achieved with our Baltic Sea study. Further, these data, highlighting the transcriptional activity of viruses, represent one of the more powerful uses of omics concerning ecosystem health. The use of omics-related data to assess ecosystem health holds great promise for rapid and relatively inexpensive determination of perturbations and risk, explicitly with regard to viral assemblages, as no single marker gene is suitable for widespread taxonomic coverage. more...
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- 2017
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5. Functional tradeoffs underpin salinity-driven divergence in microbial community composition.
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Chris L Dupont, John Larsson, Shibu Yooseph, Karolina Ininbergs, Johannes Goll, Johannes Asplund-Samuelsson, John P McCrow, Narin Celepli, Lisa Zeigler Allen, Martin Ekman, Andrew J Lucas, Åke Hagström, Mathangi Thiagarajan, Björn Brindefalk, Alexander R Richter, Anders F Andersson, Aaron Tenney, Daniel Lundin, Andrey Tovchigrechko, Johan A A Nylander, Daniel Brami, Jonathan H Badger, Andrew E Allen, Douglas B Rusch, Jeff Hoffman, Erling Norrby, Robert Friedman, Jarone Pinhassi, J Craig Venter, and Birgitta Bergman more...
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Medicine ,Science - Abstract
Bacterial community composition and functional potential change subtly across gradients in the surface ocean. In contrast, while there are significant phylogenetic divergences between communities from freshwater and marine habitats, the underlying mechanisms to this phylogenetic structuring yet remain unknown. We hypothesized that the functional potential of natural bacterial communities is linked to this striking divide between microbiomes. To test this hypothesis, metagenomic sequencing of microbial communities along a 1,800 km transect in the Baltic Sea area, encompassing a continuous natural salinity gradient from limnic to fully marine conditions, was explored. Multivariate statistical analyses showed that salinity is the main determinant of dramatic changes in microbial community composition, but also of large scale changes in core metabolic functions of bacteria. Strikingly, genetically and metabolically different pathways for key metabolic processes, such as respiration, biosynthesis of quinones and isoprenoids, glycolysis and osmolyte transport, were differentially abundant at high and low salinities. These shifts in functional capacities were observed at multiple taxonomic levels and within dominant bacterial phyla, while bacteria, such as SAR11, were able to adapt to the entire salinity gradient. We propose that the large differences in central metabolism required at high and low salinities dictate the striking divide between freshwater and marine microbiomes, and that the ability to inhabit different salinity regimes evolved early during bacterial phylogenetic differentiation. These findings significantly advance our understanding of microbial distributions and stress the need to incorporate salinity in future climate change models that predict increased levels of precipitation and a reduction in salinity. more...
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- 2014
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6. Metagenomic exploration of viruses throughout the Indian Ocean.
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Shannon J Williamson, Lisa Zeigler Allen, Hernan A Lorenzi, Douglas W Fadrosh, Daniel Brami, Mathangi Thiagarajan, John P McCrow, Andrey Tovchigrechko, Shibu Yooseph, and J Craig Venter
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Medicine ,Science - Abstract
The characterization of global marine microbial taxonomic and functional diversity is a primary goal of the Global Ocean Sampling Expedition. As part of this study, 19 water samples were collected aboard the Sorcerer II sailing vessel from the southern Indian Ocean in an effort to more thoroughly understand the lifestyle strategies of the microbial inhabitants of this ultra-oligotrophic region. No investigations of whole virioplankton assemblages have been conducted on waters collected from the Indian Ocean or across multiple size fractions thus far. Therefore, the goals of this study were to examine the effect of size fractionation on viral consortia structure and function and understand the diversity and functional potential of the Indian Ocean virome. Five samples were selected for comprehensive metagenomic exploration; and sequencing was performed on the microbes captured on 3.0-, 0.8- and 0.1 µm membrane filters as well as the viral fraction ( more...
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- 2012
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7. Single virus genomics: a new tool for virus discovery.
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Lisa Zeigler Allen, Thomas Ishoey, Mark A Novotny, Jeffrey S McLean, Roger S Lasken, and Shannon J Williamson
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Medicine ,Science - Abstract
Whole genome amplification and sequencing of single microbial cells has significantly influenced genomics and microbial ecology by facilitating direct recovery of reference genome data. However, viral genomics continues to suffer due to difficulties related to the isolation and characterization of uncultivated viruses. We report here on a new approach called 'Single Virus Genomics', which enabled the isolation and complete genome sequencing of the first single virus particle. A mixed assemblage comprised of two known viruses; E. coli bacteriophages lambda and T4, were sorted using flow cytometric methods and subsequently immobilized in an agarose matrix. Genome amplification was then achieved in situ via multiple displacement amplification (MDA). The complete lambda phage genome was recovered with an average depth of coverage of approximately 437X. The isolation and genome sequencing of uncultivated viruses using Single Virus Genomics approaches will enable researchers to address questions about viral diversity, evolution, adaptation and ecology that were previously unattainable. more...
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- 2011
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8. Going deeper: metagenome of a hadopelagic microbial community.
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Emiley A Eloe, Douglas W Fadrosh, Mark Novotny, Lisa Zeigler Allen, Maria Kim, Mary-Jane Lombardo, Joyclyn Yee-Greenbaum, Shibu Yooseph, Eric E Allen, Roger Lasken, Shannon J Williamson, and Douglas H Bartlett more...
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Medicine ,Science - Abstract
The paucity of sequence data from pelagic deep-ocean microbial assemblages has severely restricted molecular exploration of the largest biome on Earth. In this study, an analysis is presented of a large-scale 454-pyrosequencing metagenomic dataset from a hadopelagic environment from 6,000 m depth within the Puerto Rico Trench (PRT). A total of 145 Mbp of assembled sequence data was generated and compared to two pelagic deep ocean metagenomes and two representative surface seawater datasets from the Sargasso Sea. In a number of instances, all three deep metagenomes displayed similar trends, but were most magnified in the PRT, including enrichment in functions for two-component signal transduction mechanisms and transcriptional regulation. Overrepresented transporters in the PRT metagenome included outer membrane porins, diverse cation transporters, and di- and tri-carboxylate transporters that matched well with the prevailing catabolic processes such as butanoate, glyoxylate and dicarboxylate metabolism. A surprisingly high abundance of sulfatases for the degradation of sulfated polysaccharides were also present in the PRT. The most dramatic adaptational feature of the PRT microbes appears to be heavy metal resistance, as reflected in the large numbers of transporters present for their removal. As a complement to the metagenome approach, single-cell genomic techniques were utilized to generate partial whole-genome sequence data from four uncultivated cells from members of the dominant phyla within the PRT, Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes and Planctomycetes. The single-cell sequence data provided genomic context for many of the highly abundant functional attributes identified from the PRT metagenome, as well as recruiting heavily the PRT metagenomic sequence data compared to 172 available reference marine genomes. Through these multifaceted sequence approaches, new insights have been provided into the unique functional attributes present in microbes residing in a deeper layer of the ocean far removed from the more productive sun-drenched zones above. more...
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- 2011
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9. A Five-Fold Expansion of the Global RNA Virome Reveals Multiple New Clades of RNA Bacteriophages
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Uri Neri, Yuri I. Wolf, Simon Roux, Antonio Pedro Camargo, Benjamin D. Lee, Darius Kazlauskas, I. Min Chen, Natalia Ivanova, Lisa Zeigler Allen, David Paez-Espino, Donald A. Bryant, Devaki Bhaya, RNA Virus Discovery Consortium, Mart Krupovic, Valerian V. Dolja, Nikos C. Kyrpides, Eugene Koonin, and Uri Gophna more...
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History ,Polymers and Plastics ,Business and International Management ,Industrial and Manufacturing Engineering - Published
- 2022
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10. Draft Genome Sequence of Desulfurobacterium sp. Strain AV08, a Thermophilic Chemolithoautotroph Isolated from a Deep-Sea Hydrothermal Vent
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Julie A. Huber, Alice Levesque, Lisa Zeigler Allen, Margrethe H. Serres, and Emilie J. Skoog
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Whole genome sequencing ,geography ,geography.geographical_feature_category ,Strain (chemistry) ,Thermophile ,Seamount ,fungi ,Genome Sequences ,Deep sea ,Oceanography ,Immunology and Microbiology (miscellaneous) ,Volcano ,Desulfurobacterium ,Genetics ,Molecular Biology ,Geology ,health care economics and organizations ,geographic locations ,Hydrothermal vent - Abstract
A thermophilic chemolithoautotrophic bacterium was isolated from vent fluids at Axial Seamount, an active deep-sea volcano in the northeast Pacific Ocean. We present the draft genome sequence of Desulfurobacterium sp. strain AV08. more...
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- 2021
11. Diploid Genomic Architecture of Nitzschia Hildebrandi, An Elite Biomass Production Diatom
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Ryan McClure, Lisa Zeigler Allen, Andrew E. Allen, Pavlo Bohutskyi, Sheila Podell, Jesse C. Traller, Kuo A, Zheng H, Eric E. Allen, Ariel Rabines, Grigoriev, Agnieszka Pinowska, Smith, Eric A. Hill, David A. Hazlebeck, Alexander S. Beliaev, and Aaron Oliver more...
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Diatom ,Nitzschia ,Botany ,Genomic architecture ,Biomass ,Ploidy ,Biology ,biology.organism_classification - Abstract
A near-complete diploid nuclear genome and accompanying circular mitochondrial and chloroplast genomes have been assembled from the elite commercial diatom species Nitzschia hildebrandi. The 50 Mbp haploid size of the nuclear genome is nearly double that of model diatom Phaeodactylum tricornutum, but 30% smaller than closer relative Fragilariopsis cylindrus. Diploid assembly, which was facilitated by low levels of allelic heterozygosity (2.7%), included 14 candidate chromosome pairs composed of long, syntenic contigs, covering 93% of the total assembly. Telomeric ends were capped with an unusual 12-mer, G-rich, degenerate repeat sequence. Predicted proteins were highly enriched in strain-specific marker domains associated with cell-surface adhesion, biofilm formation, and raphe system gliding motility. Expanded species-specific families of carbonic anhydrases suggest potential enhancement of carbon concentration efficiency, and duplicated glycolysis and fatty acid synthesis pathways across cytosolic and organellar compartments may enhance peak metabolic output, contributing to competitive success over other organisms in mixed cultures. The N. hildebrandi genome delivers a robust new reference for future functional and transcriptomic studies to illuminate the physiology of benthic pennate diatoms and harness their unique adaptations to support commercial algae biomass and bioproduct production. more...
- Published
- 2021
- Full Text
- View/download PDF
12. Diploid genomic architecture of Nitzschia inconspicua, an elite biomass production diatom
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Alan Kuo, Eric A. Hill, Jesse C. Traller, Sheila Podell, Agnieszka Pinowska, Lisa Zeigler Allen, Eric E. Allen, Aaron Oliver, David A. Hazlebeck, Pavlo Bohutskyi, Ariel Rabines, Sarah R. Smith, Ryan McClure, Igor V. Grigoriev, Hong Zheng, Andrew E. Allen, and Alexander S. Beliaev more...
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0106 biological sciences ,Gliding motility ,01 natural sciences ,Genome ,Repetitive Sequences ,Contig Mapping ,Genome Size ,Biomass ,Phylogeny ,Carbonic Anhydrases ,Genetics ,0303 health sciences ,Multidisciplinary ,biology ,Genomics ,Mitochondrial ,Medicine ,Ploidy ,Sequence Analysis ,Biotechnology ,Nuclear gene ,Science ,Chloroplast ,Synteny ,Article ,03 medical and health sciences ,Open Reading Frames ,Affordable and Clean Energy ,Phaeodactylum tricornutum ,Genome, Chloroplast ,Genome size ,030304 developmental biology ,Repetitive Sequences, Nucleic Acid ,Comparative genomics ,Diatoms ,Nucleic Acid ,DNA ,Sequence Analysis, DNA ,biology.organism_classification ,Diploidy ,Diatom ,Genome, Mitochondrial ,Plant biotechnology ,Plant sciences ,010606 plant biology & botany - Abstract
A near-complete diploid nuclear genome and accompanying circular mitochondrial and chloroplast genomes have been assembled from the elite commercial diatom species Nitzschia inconspicua. The 50 Mbp haploid size of the nuclear genome is nearly double that of model diatom Phaeodactylum tricornutum, but 30% smaller than closer relative Fragilariopsis cylindrus. Diploid assembly, which was facilitated by low levels of allelic heterozygosity (2.7%), included 14 candidate chromosome pairs composed of long, syntenic contigs, covering 93% of the total assembly. Telomeric ends were capped with an unusual 12-mer, G-rich, degenerate repeat sequence. Predicted proteins were highly enriched in strain-specific marker domains associated with cell-surface adhesion, biofilm formation, and raphe system gliding motility. Expanded species-specific families of carbonic anhydrases suggest potential enhancement of carbon concentration efficiency, and duplicated glycolysis and fatty acid synthesis pathways across cytosolic and organellar compartments may enhance peak metabolic output, contributing to competitive success over other organisms in mixed cultures. The N. inconspicua genome delivers a robust new reference for future functional and transcriptomic studies to illuminate the physiology of benthic pennate diatoms and harness their unique adaptations to support commercial algae biomass and bioproduct production. more...
- Published
- 2021
13. Seafloor Incubation Experiment with Deep-Sea Hydrothermal Vent Fluid Reveals Effect of Pressure and Lag Time on Autotrophic Microbial Communities
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David A. Butterfield, Caroline S. Fortunato, Christopher K. Algar, Giora Proskurowski, Begüm D. Topçuoğlu, Lucy C. Stewart, B. I. Larson, Joseph J. Vallino, Noah Lawrence-Slavas, Lisa Zeigler Allen, James F. Holden, Julie A. Huber, and Emily Reddington more...
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Biogeochemical cycle ,Time Factors ,Seamount ,Stable-isotope probing ,hydrothermal vent ,Applied Microbiology and Biotechnology ,Deep sea ,03 medical and health sciences ,Hydrothermal Vents ,RNA, Ribosomal, 16S ,Environmental Microbiology ,Pressure ,Seawater ,Autotroph ,Spotlight ,RNA-SIP ,Ships ,030304 developmental biology ,instrumentation ,0303 health sciences ,geography ,metagenomics ,Autotrophic Processes ,Bacteriological Techniques ,geography.geographical_feature_category ,metatranscriptomics ,Ecology ,Primary producers ,Bacteria ,Base Sequence ,030306 microbiology ,Microbiota ,fungi ,Metagenomics ,deep sea ,Environmental chemistry ,autotrophy ,Environmental science ,Metagenome ,geographic locations ,Food Science ,Biotechnology ,Hydrothermal vent - Abstract
Diverse microbial communities drive biogeochemical cycles in Earth’s ocean, yet studying these organisms and processes is often limited by technological capabilities, especially in the deep ocean. In this study, we used a novel marine microbial incubator instrument capable of in situ experimentation to investigate microbial primary producers at deep-sea hydrothermal vents., Depressurization and sample processing delays may impact the outcome of shipboard microbial incubations of samples collected from the deep sea. To address this knowledge gap, we developed a remotely operated vehicle (ROV)-powered incubator instrument to carry out and compare results from in situ and shipboard RNA stable isotope probing (RNA-SIP) experiments to identify the key chemolithoautotrophic microbes and metabolisms in diffuse, low-temperature venting fluids from Axial Seamount. All the incubations showed microbial uptake of labeled bicarbonate primarily by thermophilic autotrophic Epsilonbacteraeota that oxidized hydrogen coupled with nitrate reduction. However, the in situ seafloor incubations showed higher abundances of transcripts annotated for aerobic processes, suggesting that oxygen was lost from the hydrothermal fluid samples prior to shipboard analysis. Furthermore, transcripts for thermal stress proteins such as heat shock chaperones and proteases were significantly more abundant in the shipboard incubations, suggesting that depressurization induced thermal stress in the metabolically active microbes in these incubations. Together, the results indicate that while the autotrophic microbial communities in the shipboard and seafloor experiments behaved similarly, there were distinct differences that provide new insight into the activities of natural microbial assemblages under nearly native conditions in the ocean. IMPORTANCE Diverse microbial communities drive biogeochemical cycles in Earth’s ocean, yet studying these organisms and processes is often limited by technological capabilities, especially in the deep ocean. In this study, we used a novel marine microbial incubator instrument capable of in situ experimentation to investigate microbial primary producers at deep-sea hydrothermal vents. We carried out identical stable isotope probing experiments coupled to RNA sequencing both on the seafloor and on the ship to examine thermophilic, microbial autotrophs in venting fluids from an active submarine volcano. Our results indicate that microbial communities were significantly impacted by the effects of depressurization and sample processing delays, with shipboard microbial communities being more stressed than seafloor incubations. Differences in metabolism were also apparent and are likely linked to the chemistry of the fluid at the beginning of the experiment. Microbial experimentation in the natural habitat provides new insights into understanding microbial activities in the ocean. more...
- Published
- 2021
14. Past, present and future-sample environments for materials research studies in scattering and spectroscopy; a UK perspective
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Nicholas J. Terrill, Wim Bras, Andrew J. Dent, Lisa Zeigler Allen, B. R. Dobson, and Andrew M. Beale
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Scattering ,Research studies ,Added value ,General Materials Science ,Sample (statistics) ,Condensed Matter Physics ,Data science - Abstract
Small angle x-ray scattering and x-ray absorption fine structure are two techniques that have been employed at synchrotron sources ever since their inception. Over the course of the development of the techniques, the introduction of sample environments for added value experiments has grown dramatically. This article reviews past successes, current developments and an exploration of future possibilities for these two x-ray techniques with an emphasis on the developments in the United Kingdom between 1980–2020. more...
- Published
- 2021
15. Seafloor incubation experiment with deep-sea hydrothermal vent fluid reveals effect of pressure and lag time on autotrophic microbial communities
- Author
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Noah Lawrence-Slavas, B. I. Larson, Julie A. Huber, Joseph J. Vallino, James F. Holden, Caroline S. Fortunato, David A. Butterfield, Emily Reddington, Lucy C. Stewart, Giora Proskurowski, Lisa Zeigler Allen, Begüm D. Topçuoğlu, and Christopher K. Algar more...
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chemistry.chemical_compound ,geography ,geography.geographical_feature_category ,Nitrate ,chemistry ,Thermophile ,Environmental chemistry ,Seamount ,Hydrostatic pressure ,Stable-isotope probing ,Autotroph ,Deep sea ,Hydrothermal vent - Abstract
Depressurization and sample processing delays may impact the outcome of shipboard microbial incubations of samples collected from the deep sea. To address this knowledge gap, we developed an ROV-powered incubator instrument to carry out and compare results from in situ and shipboard RNA Stable Isotope Probing (RNA-SIP) experiments to identify the key chemolithoautotrophic microbes and metabolisms in diffuse, low-temperature venting fluids from Axial Seamount. All the incubations showed microbial uptake of labelled bicarbonate primarily by thermophilic autotrophic Epsilonbacteraeota that oxidized hydrogen coupled with nitrate reduction. However, the in situ seafloor incubations showed higher abundances of transcripts annotated for aerobic processes suggesting that oxygen was lost from the hydrothermal fluid samples prior to shipboard analysis. Furthermore, transcripts for thermal stress proteins such as heat shock chaperones and proteases were significantly more abundant in the shipboard incubations suggesting that hydrostatic pressure ameliorated thermal stress in the metabolically active microbes in the seafloor incubations. Together, results indicate that while the autotrophic microbial communities in the shipboard and seafloor experiments behaved similarly, there were distinct differences that provide new insight into the activities of natural microbial assemblages under near-native conditions in the ocean. more...
- Published
- 2020
- Full Text
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16. NOAA-CalCOFI Ocean Genomics (NCOG) Sample Collection v1
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Ariel Rabines, Rob Lampe, Lisa Zeigler Allen, and Andrew E Allen
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Oceanography ,Environmental science ,Genomics ,Sample collection - Abstract
This protocol describes our sampling strategy and techniques for the NOAA-CalCOFI Ocean Genomics (NCOG) project. In summary, seawater for DNA and RNA from multiple depths is filtered onto Sterivex filters at each station. Although the protocol is specific to this project, it is easily adaptable for other field-based sampling. more...
- Published
- 2020
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17. Minimum Information about an Uncultivated Virus Genome (MIUViG)
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Seth R. Bordenstein, Frederik Schulz, Pelin Yilmaz, Rebecca Vega Thurber, Natalia Ivanova, Christelle Desnues, Shinichi Sunagawa, Karyna Rosario, Simon Roux, Steven W. Wilhelm, Nicole S. Webster, Mart Krupovic, Lisa Zeigler Allen, Catherine Putonti, K. Eric Wommack, Tanja Woyke, Eugene V. Koonin, Joanne B. Emerson, Jed A. Fuhrman, Hiroyuki Ogata, Ramy K. Aziz, Arvind Varsani, Marie-Agnès Petit, Bonnie L. Hurwitz, Evelien M. Adriaenssens, Andrew M. Kropinski, Katrine Whiteson, Thomas Rattei, Kyung Bum Lee, Peer Bork, David Paez-Espino, Mark J. Young, Jens H. Kuhn, Ben Temperton, Rebecca A. Daly, Natalya Yutin, Emiley A. Eloe-Fadrosh, Manuel Martinez-Garcia, Curtis A. Suttle, Susannah G. Tringe, Alejandro Reyes, Bas E. Dutilh, Nikos C. Kyrpides, Rex R. Malmstrom, Ilene Karsch Mizrachi, Kelly C. Wrighton, Rob Lavigne, Mya Breitbart, Lynn M. Schriml, Philip Hugenholtz, Melissa B. Duhaime, François Enault, Pascal Hingamp, Francisco Rodriguez-Valera, Clara Amid, Matthew B. Sullivan, Jessica M. Labonté, Grieg F. Steward, J. Rodney Brister, Takashi Yoshida, Guy Cochrane, DOE Joint Genome Institute [Walnut Creek], University of Liverpool, Theoretical Biology & Bioinformatics [Utrecht], University Medical Center [Utrecht], Radboud University Medical Center [Nijmegen], National Center for Biotechnology Information (NCBI), University of Guelph, Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris] (IP), National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Arizona State University [Tempe] (ASU), University of Cape Town, European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Cairo University, Vanderbilt University [Nashville], European Molecular Biology Laboratory [Heidelberg] (EMBL), University of South Florida [Tampa] (USF), Colorado State University [Fort Collins] (CSU), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), University of Michigan [Ann Arbor], University of Michigan System, University of California [Davis] (UC Davis), University of California (UC), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), University of Southern California (USC), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), University of Queensland [Brisbane], University of Arizona, Texas A&M University [Galveston], National Institute of Genetics (NIG), Universidad de Alicante, Kyoto University, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, University of Chicago, Department of Microbiology and Ecosystem Science [Vienna], University of Vienna [Vienna], Universidad de los Andes [Bogota] (UNIANDES), Universidad Miguel Hernández [Elche] (UMH), University of Maryland School of Medicine, University of Maryland System, University of Hawai‘i [Mānoa] (UHM), Ohio State University [Columbus] (OSU), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), University of British Columbia (UBC), University of Exeter, Oregon State University (OSU), Australian Institute of Marine Science [Townsville] (AIMS Townsville), Australian Institute of Marine Science (AIMS), University of California [Irvine] (UC Irvine), The University of Tennessee [Knoxville], University of Delaware [Newark], Max Planck Institute for Marine Microbiology, Max-Planck-Gesellschaft, Montana State University (MSU), J. Craig Venter Institute, University of California [San Diego] (UC San Diego), This work was supported by the Laboratory Directed Research and Development Program of Lawrence Berkeley National Laboratory under US Department of Energy Contract No. DE-AC02-05CH11231 for S.R., the Netherlands Organization for Scientific Research (NWO) Vidi grant 864.14.004 for B.E.D., the Intramural Research Program of the National Library of Medicine, National Institutes of Health for E.V.K., I.K.M., J.R.B. and N.Y., the Virus-X project (EU Horizon 2020, No. 685778) for F.E. and M.K., Battelle Memorial Institute's prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID) under Contract No. HHSN272200700016I for J.H.K., the GOA grant 'Bacteriophage Biosystems' from KU Leuven for R.L., the European Molecular Biology Laboratory for C.A. and G.R.C., Cairo University Grant 2016-57 for R.K.A., National Science Foundation award 1456778, National Institutes of Health awards R01 AI132581 and R21 HD086833, and The Vanderbilt Microbiome Initiative award for S.R.B., National Science Foundation awards DEB-1239976 for M.B. and K.R. and DEB-1555854 for M.B., the NSF Early Career award DEB-1555854 and NSF Dimensions of Biodiversity #1342701 for K.C.W. and R.A.D., the Agence Nationale de la Recherche JCJC grant ANR-13-JSV6-0004 and Investissements d'Avenir Méditerranée Infection 10-IAHU-03 for C.D., the Gordon and Betty Moore Foundation Marine Microbiology Initiative No. 3779 and the Simons Foundation for J.A.F., the French government 'Investissements d'Avenir' program OCEANOMICS ANR-11-BTBR-0008 and European FEDER Fund 1166-39417 for P. Hingamp, Australian Research Council Laureate Fellowship FL150100038 to P. Hugenholtz the National Science Foundation award 1801367 and C-DEBI Research Grant for J.M.L., the Gordon and Betty Moore Foundation grant 5334 and Ministry of Economy and Competitivity refs. CGL2013-40564-R and SAF2013-49267-EXP for M.M.-G., the Grant-in-Aid for Scientific Research on Innovative Areas from the Ministry of Education, Culture, Science, Sports, and Technology (MEXT) of Japan No. 16H06429, 16K21723, and 16H06437 for H.O. and T.Y., National Science Foundation award DBI-1661357 to C.P., the Ministry of Economy and Competitivity ref CGL2016-76273-P (cofunded with FEDER funds) for F.R.-V., the Gordon and Betty Moore Foundation awards 3305 and 3790 and NSF Biological Oceanography OCE 1536989 for M.B.S., the ETH Zurich and Helmut Horten Foundation and the Novartis Foundation for Medical-Biological Research (17B077) for S.S., a BIOS-SCOPE award from Simons Foundation International and NERC award NE/P008534/1 to B.T., NSF Biological Oceanography Grant 1635913 for R.V.T., the Australian Research Council Future Fellowship FT120100480 for N.S.W., a Gilead Sciences Cystic Fibrosis Research Scholarship for K.L.W., Gordon and Better Moore Foundation Grant 4971 for S.W.W., the NSF EPSCoR grant 1736030 for K.E.W., the National Science Foundation award DEB-4W4596 and National Institutes of Health award R01 GM117361 for M.J.Y., the Gordon and Betty Moore Foundation No. 7000 and the National Oceanic and Atmospheric Administration (NOAA) under award NA15OAR4320071 for L.Z.A. DDBJ is supported by ROIS and MEXT. The work conducted by the US Department of Energy Joint Genome Institute is supported by the Office of Science of the US Department of Energy under contract no. DE-AC02-05CH11231. The views and conclusions contained in this document are those of the authors and should not be interpreted as necessarily representing the official policies, either expressed or implied, of the US Department of Health and Human Services or of the institutions and companies affiliated with the authors. B.E.D., A.K., M.K., J.H.K., R.L. and A.V. are members of the ICTV Executive Committee, but the views and opinions expressed are those of the authors and not those of the ICTV., Universidad de Alicante. Departamento de Fisiología, Genética y Microbiología, Ecología Microbiana Molecular, Institut Pasteur [Paris], University of South Florida (USF), University of California, Laboratoire Microorganismes : Génome et Environnement - Clermont Auvergne (LMGE), Université Clermont Auvergne (UCA)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Kyoto University [Kyoto], Universidad de los Andes [Bogota], Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), University of California [Irvine] (UCI), J Craig Venter Institute, Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Sub Bioinformatics, and Theoretical Biology and Bioinformatics more...
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[SDV]Life Sciences [q-bio] ,Microbiología ,2.2 Factors relating to physical environment ,Applied Microbiology and Biotechnology ,Genome ,0302 clinical medicine ,Databases, Genetic ,Tumours of the digestive tract Radboud Institute for Molecular Life Sciences [Radboudumc 14] ,phage ,Viral ,0303 health sciences ,Genetic Databases ,Environmental microbiology ,pipeline ,Genome project ,dynamics ,Genomics ,annotation ,Viruses ,Molecular Medicine ,tacomony ,Infection ,Genetic databases ,Biotechnology ,Virus Cultivation ,In silico ,Biomedical Engineering ,Phage biology ,Bioengineering ,Computational biology ,Genome, Viral ,Biology ,Virus ,dna viruses ,Article ,Uncultivated virus genomes ,Databases ,03 medical and health sciences ,Annotation ,Genetic ,Virology ,MD Multidisciplinary ,Genetics ,030304 developmental biology ,Human Genome ,Biological classification ,commitee ,prediction ,Metagenomics ,Minimum Information about any (x) Sequence (MIxS) ,030217 neurology & neurosurgery ,discovery - Abstract
We present an extension of the Minimum Information about any (x) Sequence (MIxS) standard for reporting sequences of uncultivated virus genomes. Minimum Information about an Uncultivated Virus Genome (MIUViG) standards were developed within the Genomic Standards Consortium framework and include virus origin, genome quality, genome annotation, taxonomic classification, biogeographic distribution and in silico host prediction. Community-wide adoption of MIUViG standards, which complement the Minimum Information about a Single Amplified Genome (MISAG) and Metagenome-Assembled Genome (MIMAG) standards for uncultivated bacteria and archaea, will improve the reporting of uncultivated virus genomes in public databases. In turn, this should enable more robust comparative studies and a systematic exploration of the global virosphere., Nature Biotechnology, 37 (1), ISSN:1546-1696, ISSN:1087-0156 more...
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- 2018
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18. Molecular Approaches for an Operational Marine Biodiversity Observation Network
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Andrew E. Allen, Frank E. Muller-Karger, Anni Djurhuus, Lisa Zeigler Allen, Gabrielle Canonico Hyde, Kelly D. Goodwin, and John P. McCrow
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Sustainable development ,Marine conservation ,business.industry ,Metagenomics ,Computer science ,Scale (chemistry) ,Environmental resource management ,Sustainability ,Biodiversity ,Sample collection ,business ,Ecosystem services - Abstract
Biological health underpins ecosystem services, including the production of food from the sea. Therefore, many policy frameworks rely on biological observations to guide the sustainable use of marine resources. For example, a marine biodiversity observation network can provide evidence of ecosystem degradation, remediation success, and progress toward goals of sustainable development. The utility of biodiversity observations is limited, however, if measurements are not standardized to allow comparisons across space and time or if they are too difficult or expensive to make routinely or at large scale. Molecular approaches (e.g., metagenomics, metabarcoding, eDNA, metatranscriptomics) offer efficiencies in sample collection and processing and provide analysis across trophic levels compared to traditional methods. Increased affordability and throughput of nucleic acid sequencing allow integration of molecular biological techniques into operational monitoring with the potential benefit of expanding the spatial and temporal scale of biological observations. more...
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- 2019
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19. Contributors
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Olubukola Adebambo, Tundi Agardy, Andrew E. Allen, Andrew H. Altieri, Francisco Andrade, Michela Angiolillo, Stephanie Avery-Gomm, Jiayu Bai, Joel Baker, Luís Gabriel A. Barboza, Thayanne Lima Barros, John M. Baxter, Daniel T.I. Bayley, Luca G. Bellucci, Charles Birkeland, Alex Bond, Andy M. Booth, Stephanie Borrelle, Jessica Bradford, Paula Bueno, Gabrielle Canonico Hyde, Bing Chen, Jing Cheng, Andrés Cózar, Rory Crawford, Larry B. Crowder, Jordi Dachs, Rosa M. Darbra, Matej David, Jon C. Day, Monica C. Del Aguila Feijoo, Robert J. Diaz, Anni Djurhuus, Zhijun Dong, Stuart Johnston Edwards, Charles N. Ehler, Elias Elhaimer, Karen Filbee-Dexter, Ramón Filgueira, Merv Fingas, Greg Foster, Catarina Frazão Santos, João P.G.L. Frias, Daniel A. Friess, Barbara C.G. Gimenez, Silvia Giuliani, Stephan Gollasch, Thomas P. Good, Kelly D. Goodwin, Lúcia Guilhermino, Jeff Hatfield, Eliza C. Heery, Peter Hodum, Tahazzud Hossain, Liang Jing, Peter J. Kershaw, Kira Krumhansl, Dan Laffoley, Shing Yip Lee, Kenneth Lee, Julie A. Lively, Rainer Lohmann, Lynette H.L. Loke, Heather L. Major, Mark Mallory, Julie Masura, Ethan J. Matchinski, Karen D. McCoy, John P. McCrow, Flemming Merkel, Andrew O.M. Mogg, Courtney E. Morrison, Frank E. Muller-Karger, Michael K. Orbach, Simone Panigada, Daniel Pauly, Morten F. Pedersen, Marta Picciulin, Jurgenne H. Primavera, Jennifer F. Provencher, Martí Puig, Nikolina Rako-Gospić, Michelle Reynolds, Fabian Ritter, David Rodríguez-Rodríguez, Alex D. Rogers, Jessica Romo, Nameeta Sharma, Richard B. Sherley, Dena Spatz, Laura Steeves, Nora F.Y. Tam, Stephanie Taylor, Peter A. Todd, Hanneke Van Lavieren, Luís R. Vieira, Stephen Votier, Jill Wakefield, Tony R. Walker, Yafen Wang, Jenny Weitzman, Lauren Wenzel, Thomas Wernberg, Xudong Ye, Lisa Zeigler Allen, Dirk Zeller, Baiyu Zhang, Katherine Zischka, and Sanam Zomorodi more...
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- 2019
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20. Speciation and ecological success in dimly lit waters: horizontal gene transfer in a green sulfur bacteria bloom unveiled by metagenomic assembly
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Tomàs Llorens-Marès, Zhenfeng Liu, Lisa Zeigler Allen, Douglas B. Rusch, Christopher L. Dupont, Donald A. Bryant, Emilio O. Casamayor, and Matthew T. Craig
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0301 basic medicine ,Gene Transfer, Horizontal ,Chlorobium ,Microbiology ,Enrichment culture ,03 medical and health sciences ,chemistry.chemical_compound ,Bacterial Proteins ,Microbial ecology ,RNA, Ribosomal, 16S ,Photosynthesis ,Bacteriochlorophylls ,Ecosystem ,Ecology, Evolution, Behavior and Systematics ,biology ,Geomicrobiology ,Ecology ,biology.organism_classification ,Lakes ,030104 developmental biology ,Environmental biotechnology ,chemistry ,Spain ,Horizontal gene transfer ,Green sulfur bacteria ,Original Article ,Metagenomics ,Bacteriochlorophyll ,Sulfur - Abstract
11 páginas, 6 figuras., A natural planktonic bloom of a brown-pigmented photosynthetic green sulfur bacteria (GSB) from the disphotic zone of karstic Lake Banyoles (NE Spain) was studied as a natural enrichment culture from which a nearly complete genome was obtained after metagenomic assembly. We showed in situ a case where horizontal gene transfer (HGT) explained the ecological success of a natural population unveiling ecosystem-specific adaptations. The uncultured brown-pigmented GSB was 99.7% identical in the 16S rRNA gene sequence to its green-pigmented cultured counterpart Chlorobium luteolum DSM 273T. Several differences were detected for ferrous iron acquisition potential, ATP synthesis and gas vesicle formation, although the most striking trait was related to pigment biosynthesis strategy. Chl. luteolum DSM 273T synthesizes bacteriochlorophyll (BChl) c, whereas Chl. luteolum CIII incorporated by HGT a 18-kbp cluster with the genes needed for BChl e and specific carotenoids biosynthesis that provided ecophysiological advantages to successfully colonize the dimly lit waters. We also genomically characterized what we believe to be the first described GSB phage, which based on the metagenomic coverage was likely in an active state of lytic infection. Overall, we observed spread HGT and we unveiled clear evidence for virus-mediated HGT in a natural population of photosynthetic GSB., This research was funded by grant DARKNESS CGL2012- 32747 from the Spanish Office of Science (MINECO) to EOC and by the Global Ocean Sampling Project supported by the Beyster Family Foundation Fund of the San Diego Foundation and the Life Technology Foundation (to JCVI). Work on BChl e biosynthesis and the genomics of GSB in the laboratory of DAB was supported by the Division of Chemical Sciences, Geosciences, and Biosciences, Office of Basic Energy Sciences of the U.S. Department of Energy through Grant DE-FG02-94ER20137. more...
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- 2016
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21. The Baltic Sea Virome: Diversity and Transcriptional Activity of DNA and RNA Viruses
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Andrew E. Allen, Christopher L. Dupont, Jonathan H. Badger, J. Craig Venter, Birgitta Bergman, Lisa Zeigler Allen, John P. McCrow, Martin Ekman, Jeffery M. Hoffman, and Karolina Ininbergs
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0301 basic medicine ,Viral metagenomics ,viral ecology ,viral metatranscriptomics ,Physiology ,Ecology (disciplines) ,media_common.quotation_subject ,030106 microbiology ,lcsh:QR1-502 ,Biology ,marine microbiology ,Biochemistry ,Microbiology ,lcsh:Microbiology ,03 medical and health sciences ,chemistry.chemical_compound ,Genetics ,Human virome ,14. Life underwater ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,media_common ,Ecology ,Applied and Environmental Science ,RNA ,Editor's Pick ,QR1-502 ,Computer Science Applications ,viral/host inference ,030104 developmental biology ,Baltic sea ,chemistry ,Metagenomics ,Modeling and Simulation ,viral metagenomics ,DNA ,Diversity (politics) ,Research Article - Abstract
Inferred virus-host relationships, community structures of ubiquitous ecologically relevant groups, and identification of transcriptionally active populations have been achieved with our Baltic Sea study. Further, these data, highlighting the transcriptional activity of viruses, represent one of the more powerful uses of omics concerning ecosystem health. The use of omics-related data to assess ecosystem health holds great promise for rapid and relatively inexpensive determination of perturbations and risk, explicitly with regard to viral assemblages, as no single marker gene is suitable for widespread taxonomic coverage., Metagenomic and metatranscriptomic data were generated from size-fractionated samples from 11 sites within the Baltic Sea and adjacent marine waters of Kattegat and freshwater Lake Torneträsk in order to investigate the diversity, distribution, and transcriptional activity of virioplankton. Such a transect, spanning a salinity gradient from freshwater to the open sea, facilitated a broad genome-enabled investigation of natural as well as impacted aspects of Baltic Sea viral communities. Taxonomic signatures representative of phages within the widely distributed order Caudovirales were identified with enrichments in lesser-known families such as Podoviridae and Siphoviridae. The distribution of phage reported to infect diverse and ubiquitous heterotrophic bacteria (SAR11 clades) and cyanobacteria (Synechococcus sp.) displayed population-level shifts in diversity. Samples from higher-salinity conditions (>14 practical salinity units [PSU]) had increased abundances of viruses for picoeukaryotes, i.e., Ostreococcus. These data, combined with host diversity estimates, suggest viral modulation of diversity on the whole-community scale, as well as in specific prokaryotic and eukaryotic lineages. RNA libraries revealed single-stranded DNA (ssDNA) and RNA viral populations throughout the Baltic Sea, with ssDNA phage highly represented in Lake Torneträsk. Further, our data suggest relatively high transcriptional activity of fish viruses within diverse families known to have broad host ranges, such as Nodoviridae (RNA), Iridoviridae (DNA), and predicted zoonotic viruses that can cause ecological and economic damage as well as impact human health. IMPORTANCE Inferred virus-host relationships, community structures of ubiquitous ecologically relevant groups, and identification of transcriptionally active populations have been achieved with our Baltic Sea study. Further, these data, highlighting the transcriptional activity of viruses, represent one of the more powerful uses of omics concerning ecosystem health. The use of omics-related data to assess ecosystem health holds great promise for rapid and relatively inexpensive determination of perturbations and risk, explicitly with regard to viral assemblages, as no single marker gene is suitable for widespread taxonomic coverage. more...
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- 2017
22. Diversity and genome dynamics of marine cyanophages using metagenomic analyses
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Lisa Zeigler Allen, Yingfei Ma, and Brian Palenik
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Genetics ,Contig ,Phylogenetic tree ,Phylogenetics ,Metagenomics ,Genetic variation ,Cyanophage ,Biology ,Synechococcus ,biology.organism_classification ,Agricultural and Biological Sciences (miscellaneous) ,Ecology, Evolution, Behavior and Systematics ,Homology (biology) - Abstract
Cyanophages are abundant in the oceanic environment and directly impact cyanobacterial distributions, physiological processes and evolution. Two samples collected from coastal Maine in July and September 2009 were enriched for Synechococcus cells using flow cytometry and examined through metagenomic sequencing. Homology-based sequence prediction indicated cyanophages, largely myoviruses, accounted for almost half the reads and provided insights into environmental infection events. T4-phage core-gene phylogenetic reconstruction revealed unique diversity among uncultured cyanophages and reference isolates resulting in identification of a new phylogenetic cluster. Genomic comparison of reference cyanophage strains S-SM2 and Syn1 with putative homologous contigs recovered from metagenomes provided evidence that gene insertion, deletion and recombination have occurred among, and are likely important for diversification of, natural populations. Identification of putative genetic exchange between cyanophage and non-cyanophage viruses, i.e. Micromonas virus and Pelagibacter phage, supports hypotheses related to a significant role for viruses in mediating transfer of genetic material between taxonomically diverse organisms with overlapping ecological niches. more...
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- 2014
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23. Influence of nutrients and currents on the genomic composition of microbes across an upwelling mosaic
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Kenneth H. Nealson, Mathangi Thiagarajan, Shannon J. Williamson, Doug Rusch, J. Craig Venter, Jonathan H. Badger, Eric E. Allen, John P. McCrow, Ian T. Paulsen, Andrew E. Allen, Liam D. H. Elbourne, and Lisa Zeigler Allen more...
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Time Factors ,Nitrogen ,Oceans and Seas ,Population ,Cyanobacteria ,Microbiology ,California ,Phylogenetics ,Ecosystem ,Seawater ,education ,Ecology, Evolution, Behavior and Systematics ,Phylogeny ,education.field_of_study ,metagenomics ,biology ,Bacteria ,Ecology ,Bacteroidetes ,Community structure ,marine ,Plankton ,biology.organism_classification ,California Current ,upwelling ,Metagenomics ,Upwelling ,Original Article - Abstract
Metagenomic data sets were generated from samples collected along a coastal to open ocean transect between Southern California Bight and California Current waters during a seasonal upwelling event, providing an opportunity to examine the impact of episodic pulses of cold nutrient-rich water into surface ocean microbial communities. The data set consists of ∼5.8 million predicted proteins across seven sites, from three different size classes: 0.1–0.8, 0.8–3.0 and 3.0–200.0 μm. Taxonomic and metabolic analyses suggest that sequences from the 0.1–0.8 μm size class correlated with their position along the upwelling mosaic. However, taxonomic profiles of bacteria from the larger size classes (0.8–200 μm) were less constrained by habitat and characterized by an increase in Cyanobacteria, Bacteroidetes, Flavobacteria and double-stranded DNA viral sequences. Functional annotation of transmembrane proteins indicate that sites comprised of organisms with small genomes have an enrichment of transporters with substrate specificities for amino acids, iron and cadmium, whereas organisms with larger genomes have a higher percentage of transporters for ammonium and potassium. Eukaryotic-type glutamine synthetase (GS) II proteins were identified and taxonomically classified as viral, most closely related to the GSII in Mimivirus, suggesting that marine Mimivirus-like particles may have played a role in the transfer of GSII gene functions. Additionally, a Planctomycete bloom was sampled from one upwelling site providing a rare opportunity to assess the genomic composition of a marine Planctomycete population. The significant correlations observed between genomic properties, community structure and nutrient availability provide insights into habitat-driven dynamics among oligotrophic versus upwelled marine waters adjoining each other spatially. more...
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- 2012
24. Diversity and genome dynamics of marine cyanophages using metagenomic analyses
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Yingfei, Ma, Lisa Zeigler, Allen, and Brian, Palenik
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Gene Transfer, Horizontal ,Oceans and Seas ,Molecular Sequence Data ,Genetic Variation ,Bacteriophages ,Seawater ,Genome, Viral ,Metagenomics ,Maine ,Cyanobacteria ,Host Specificity ,Phylogeny - Abstract
Cyanophages are abundant in the oceanic environment and directly impact cyanobacterial distributions, physiological processes and evolution. Two samples collected from coastal Maine in July and September 2009 were enriched for Synechococcus cells using flow cytometry and examined through metagenomic sequencing. Homology-based sequence prediction indicated cyanophages, largely myoviruses, accounted for almost half the reads and provided insights into environmental infection events. T4-phage core-gene phylogenetic reconstruction revealed unique diversity among uncultured cyanophages and reference isolates resulting in identification of a new phylogenetic cluster. Genomic comparison of reference cyanophage strains S-SM2 and Syn1 with putative homologous contigs recovered from metagenomes provided evidence that gene insertion, deletion and recombination have occurred among, and are likely important for diversification of, natural populations. Identification of putative genetic exchange between cyanophage and non-cyanophage viruses, i.e. Micromonas virus and Pelagibacter phage, supports hypotheses related to a significant role for viruses in mediating transfer of genetic material between taxonomically diverse organisms with overlapping ecological niches. more...
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- 2015
25. Functional Tradeoffs Underpin Salinity-Driven Divergence in Microbial Community Composition
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R. Alexander Richter, Narin Celepli, Björn Brindefalk, Karolina Ininbergs, Aaron Tenney, Daniel Brami, Lisa Zeigler Allen, Robert Friedman, Andrey Tovchigrechko, Martin Ekman, Jonathan H. Badger, Erling Norrby, Jeff Hoffman, Johannes Asplund-Samuelsson, Christopher L. Dupont, Daniel Lundin, Birgitta Bergman, John P. McCrow, Douglas B. Rusch, Johannes B. Goll, Andrew E. Allen, Åke Hagström, J. Craig Venter, John Larsson, Johan A. A. Nylander, Mathangi Thiagarajan, Jarone Pinhassi, Anders F. Andersson, Andrew Lucas, and Shibu Yooseph more...
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Baltic States ,Salinity ,Biodiversity ,lcsh:Medicine ,Marine and Aquatic Sciences ,Biochemistry ,Marine bacteriophage ,Microbial Physiology ,RNA, Ribosomal, 16S ,Naturvetenskap ,lcsh:Science ,Phylogeny ,Freshwater Ecology ,Multidisciplinary ,Ecology ,Microbiota ,Marine Ecology ,Genomics ,Functional Genomics ,Phylogenetics ,Metabolic Pathways ,Natural Sciences ,Water Microbiology ,Research Article ,Microbial Taxonomy ,Marine Biology ,Biology ,Microbiology ,Microbial Ecology ,Ecosystem ,Evolutionary Systematics ,Seawater ,14. Life underwater ,Taxonomy ,Ekologi ,Evolutionary Biology ,Bacterial Evolution ,Bacteria ,lcsh:R ,Bacterial Taxonomy ,Marine habitats ,Bacteriology ,Marine Environments ,Metabolism ,Microbial population biology ,13. Climate action ,Metagenomics ,Microbial Evolution ,Earth Sciences ,Metagenome ,lcsh:Q ,Ecological Environments - Abstract
Bacterial community composition and functional potential change subtly across gradients in the surface ocean. In contrast, while there are significant phylogenetic divergences between communities from freshwater and marine habitats, the underlying mechanisms to this phylogenetic structuring yet remain unknown. We hypothesized that the functional potential of natural bacterial communities is linked to this striking divide between microbiomes. To test this hypothesis, metagenomic sequencing of microbial communities along a 1,800 km transect in the Baltic Sea area, encompassing a continuous natural salinity gradient from limnic to fully marine conditions, was explored. Multivariate statistical analyses showed that salinity is the main determinant of dramatic changes in microbial community composition, but also of large scale changes in core metabolic functions of bacteria. Strikingly, genetically and metabolically different pathways for key metabolic processes, such as respiration, biosynthesis of quinones and isoprenoids, glycolysis and osmolyte transport, were differentially abundant at high and low salinities. These shifts in functional capacities were observed at multiple taxonomic levels and within dominant bacterial phyla, while bacteria, such as SAR11, were able to adapt to the entire salinity gradient. We propose that the large differences in central metabolism required at high and low salinities dictate the striking divide between freshwater and marine microbiomes, and that the ability to inhabit different salinity regimes evolved early during bacterial phylogenetic differentiation. These findings significantly advance our understanding of microbial distributions and stress the need to incorporate salinity in future climate change models that predict increased levels of precipitation and a reduction in salinity. more...
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- 2014
26. Lineage specific gene family enrichment at the microscale in marine systems
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Lisa Zeigler Allen, Andrew E. Allen, and John P. McCrow
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Microbiology (medical) ,Genetics ,Geologic Sediments ,Bacteria ,Lineage (evolution) ,Ecology (disciplines) ,Eukaryota ,Genomics ,Biology ,biology.organism_classification ,Microbiology ,Archaea ,Infectious Diseases ,Evolutionary biology ,Metagenomics ,Viruses ,Gene family ,Seawater ,Picoplankton ,Reference genome - Abstract
Recent advances in metagenomics have generated numerous insights related to the cell biology, ecology, evolution, and biogeochemistry of microbial life in the ocean. Notably, advances in single cell genomics (SCG), fluorescence activated cell sorting (FACS) capture of specific populations and metagenomic assembly are providing valuable information related to within and between lineage genomic content. Improved reference genome databases have assisted biogeographic studies of particular taxa, including in some cases different ecotypes. Several studies targeting picoplankton, associated with various particle size classes, have begun to define contrasting trends in gene family evolution between free-living compared to particle associated microbes. Also viruses and eukaryotic microbes are increasingly considered in metagenomic studies and specific associations between viruses, bacteria, archaea, and eukaryotic microbes are emerging. more...
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- 2014
27. A metagenomic framework for the study of airborne microbial communities
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J. Craig Venter, Jeff Hoffman, Lisa Zeigler-Allen, Shannon J. Williamson, Cynthia Andrews-Pfannkoch, Jeffrey B. McQuaid, Johannes B. Goll, Douglas Fadrosh, John I. Glass, Aaron Tenney, Robert Friedman, Shibu Yooseph, Mark Raymond Adams, Mathangi Thiagarajan, and Daniel Brami more...
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DNA, Bacterial ,Microorganism ,Biodiversity ,Air Microbiology ,lcsh:Medicine ,Biology ,18S ribosomal RNA ,Microbiology ,RNA, Ribosomal, 16S ,Environmental monitoring ,Taxonomic rank ,lcsh:Science ,Phylogeny ,Principal Component Analysis ,Multidisciplinary ,Bacteria ,Ecology ,lcsh:R ,Bacterial taxonomy ,Genes, rRNA ,Nucleic acid amplification technique ,Metagenomics ,lcsh:Q ,Nucleic Acid Amplification Techniques ,Environmental Monitoring ,Research Article - Abstract
Understanding the microbial content of the air has important scientific, health, and economic implications. While studies have primarily characterized the taxonomic content of air samples by sequencing the 16S or 18S ribosomal RNA gene, direct analysis of the genomic content of airborne microorganisms has not been possible due to the extremely low density of biological material in airborne environments. We developed sampling and amplification methods to enable adequate DNA recovery to allow metagenomic profiling of air samples collected from indoor and outdoor environments. Air samples were collected from a large urban building, a medical center, a house, and a pier. Analyses of metagenomic data generated from these samples reveal airborne communities with a high degree of diversity and different genera abundance profiles. The identities of many of the taxonomic groups and protein families also allows for the identification of the likely sources of the sampled airborne bacteria. more...
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- 2013
28. Contrasting genomic properties of free-living and particle-attached microbial assemblages within a coastal ecosystem
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Lydie Herfort, Lisa Zeigler Allen, Andrew E. Allen, Holly M. Simon, and Maria W. Smith
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Microbiology (medical) ,environmental water ,Thaumarchaeota ,particle-attached and free-living microbes ,Nitrosopumilus ,lcsh:QR1-502 ,microbial communities ,Deep sea ,Microbiology ,lcsh:Microbiology ,03 medical and health sciences ,Columbia River coastal margin ,Water column ,Photic zone ,14. Life underwater ,Original Research Article ,030304 developmental biology ,0303 health sciences ,geography ,geography.geographical_feature_category ,biology ,030306 microbiology ,Ecology ,Estuary ,biology.organism_classification ,13. Climate action ,Metagenomics ,metagenome analysis ,Archaea - Abstract
The Columbia River (CR) is a powerful economic and environmental driver in the US Pacific Northwest. Microbial communities in the water column were analyzed from four diverse habitats: 1) an estuarine turbidity maximum (ETM); 2) a chlorophyll maximum of the river plume; 3) an upwelling-associated hypoxic zone; and 4) the deep ocean bottom. Three size fractions, 0.1-0.8, 0.8-3 and 3-200 μm were collected for each habitat in August 2007, and used for DNA isolation and 454 sequencing, resulting in 12 metagenomes of >5 million reads (>1.6 Gbp). To characterize the dominant microorganisms and metabolisms contributing to coastal biogeochemistry, we used predicted peptide and rRNA data. The 3- and 0.8-μm metagenomes, representing particulate fractions, were taxonomically diverse across habitats. The 3-μm size fractions contained a high abundance of eukaryota with diatoms dominating the hypoxic water and plume, while cryptophytes were more abundant in the ETM. The 0.1-μm metagenomes represented mainly free-living bacteria and archaea. The most abundant archaeal hits were observed in the deep ocean and hypoxic water (19% of prokaryotic peptides in the 0.1-μm metagenomes), and were homologous to Nitrosopumilus maritimus (ammonia-oxidizing Thaumarchaeota). Bacteria dominated metagenomes of all samples. In the euphotic zone (estuary, plume and hypoxic ocean), the most abundant bacterial taxa (≥40 % of prokaryotic peptides) represented aerobic photoheterotrophs. In contrast, the low-oxygen, deep water metagenome was enriched with sequences for strict and facultative anaerobes. Interestingly, many of the same anaerobic bacterial families were enriched in the 3-μm size fraction of the ETM (2-10X more abundant relative to the 0.1-μm metagenome), indicating possible formation of anoxic microniches within particles. Results from this study provide a metagenome perspective on ecosystem-scale metabolism in an upwelling-influenced river-dominated coastal margin. more...
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- 2013
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29. Isolation and Genome Analysis of Single Virions using 'Single Virus Genomics'
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Jeffrey S. McLean, Shannon J. Williamson, Thomas Ishoey, Roger S. Lasken, Lisa Zeigler Allen, and Mark Novotny
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Cancer genome sequencing ,Comparative genomics ,Genetics ,Whole Genome Amplification ,Microscopy, Confocal ,General Immunology and Microbiology ,General Chemical Engineering ,General Neuroscience ,Virion ,Genomics ,Nucleic acid amplification technique ,Genome, Viral ,Biology ,Flow Cytometry ,Genome ,Bacteriophage lambda ,General Biochemistry, Genetics and Molecular Biology ,genomic DNA ,Metagenomics ,DNA, Viral ,T-Phages ,Nucleic Acid Amplification Techniques - Abstract
Whole genome amplification and sequencing of single microbial cells enables genomic characterization without the need of cultivation (1-3). Viruses, which are ubiquitous and the most numerous entities on our planet (4) and important in all environments (5), have yet to be revealed via similar approaches. Here we describe an approach for isolating and characterizing the genomes of single virions called 'Single Virus Genomics' (SVG). SVG utilizes flow cytometry to isolate individual viruses and whole genome amplification to obtain high molecular weight genomic DNA (gDNA) that can be used in subsequent sequencing reactions. more...
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- 2013
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30. Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform
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Adam P. Hall, Michael G. Ziegler, Pavel A. Pevzner, Kenneth H. Nealson, Scott Durkin, Sharon L. Reed, Robert Friedman, Jonathan H. Badger, Glenn Tesler, Anna Edlund, Lisa Zeigler Allen, Joyclyn Yee-Greenbaum, Mary-Jane Lombardo, Roger S. Lasken, Francesca J. Torriani, J. Craig Venter, Jeffrey S. McLean, Valery M. Lesin, Sergey Nurk, Daniel Brami, and Mark Novotny more...
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Genetics ,Comparative genomics ,Cross Infection ,Genetic strain ,Sequence assembly ,High-Throughput Nucleotide Sequencing ,Method ,Genomics ,Biology ,Genome ,Deep sequencing ,DNA sequencing ,Microbiology ,Metagenomics ,Biofilms ,Bacteroidaceae Infections ,Humans ,Single-Cell Analysis ,Porphyromonas gingivalis ,Genetics (clinical) ,Genome, Bacterial - Abstract
Ongoing efforts to understand the genomic diversity of microbes in nature and in human health are hampered by the limited availability of cultivated organisms and their genomes (The Human Microbiome Jumpstart Reference Strains Consortium 2010). Only 1%–10% of known bacterial species (Rappe and Giovannoni 2003) are thought to be currently cultivated, although great progress is being made for some bacterial communities; for example, about half of bacterial species within the human oral cavity have been cultivated (Dewhirst et al. 2010). The recent advancements in DNA sequencing of single bacterial cells (Raghunathan et al. 2005) have accelerated the discovery of uncultivated microbes (Lasken 2012), providing genomic assemblies for species previously known only from 16S rRNA clone libraries and metagenomic data (Marcy et al. 2007; Podar et al. 2007; Binga et al. 2008; Eloe et al. 2011; Youssef et al. 2011; Dupont et al. 2012). This newly developed methodology provides a culture-independent approach to capture the genomes of uncultivated organisms, which can then be integrated into many intensive genomics-based studies. A high-throughput strategy was recently established to sequence and assemble single-cell genomes of bacteria (Chitsaz et al. 2011) and viruses (Allen et al. 2011), including novel uncultivated bacteria from environmental samples (Chitsaz et al. 2011; Eloe et al. 2011; Dupont et al. 2012). The workflow consists of (1) delivery of single bacterial cells into 384-well microtiter wells by fluorescence activated cell sorting (FACS); (2) use of a robotic platform to perform 384-well automated cell lysis and amplification of DNA by the multiple displacement amplification (MDA) method (Dean et al. 2001, 2002; Hosono et al. 2003) to create libraries of genomic DNA derived from single cells; (3) PCR and cycle sequencing of 16S rRNA genes to profile the taxonomy and diversity of the libraries; (4) selection of candidate amplified genomes for whole-genome sequencing; and (5) sequencing and assembly of selected genomes using assembly tools designed specifically for MDA-amplified single cells (Chitsaz et al. 2011; Bankevich et al. 2012). A highly integrated robotic platform, described in this study for the first time, was used to increase the throughput, ease, and overall cost of processing single cells. Here we have focused this approach on the indoor environment. Despite the fact that a typical person spends ∼90% of their time indoors (Klepeis et al. 2001), there is little known about the microbial diversity of this environment. Of particular interest is the prevalence of species affecting human health, including both opportunistic and primary pathogens. Recent studies of indoor environments using culture-independent molecular methods indicate an unexpectedly high bacterial diversity on surfaces within daycare facilities and public bathroom facilities (Lee et al. 2007; Flores et al. 2011), where the majority of organisms in the latter environment were human associated (Flores et al. 2011). Another study shows that bacterial diversity is lower in indoor air at a healthcare facility compared with outdoor air; however, the indoor air contained a higher number of potential human pathogens as shown by 16S rRNA gene sequence analyses (Kembel et al. 2012). Biofilms in particular are thought to be reservoirs of disease-causing organisms in both outdoor and indoor environments. Several pathogens, including Escherichia coli, Vibrio cholerae (Shikuma and Hadfield 2010), and Helicobacter pylori (Percival and Thomas 2009; Linke et al. 2010), have been detected in biofilms within water distribution systems. In addition, the long-term persistence of Legionella pneumophila, the causative agent of Legionnaire's disease, in biofilms within natural and human-impacted freshwater environments is well known (Walker et al. 1993; Murga et al. 2001; Declerck 2010; Giao et al. 2011). Recent 16S rRNA gene molecular surveys have revealed a significant load of Mycobacterium avium in showerhead biofilms (Feazel et al. 2009), and studies on biofilms growing on shower curtains suggest that these communities also harbor potential opportunistic pathogens that can threaten immune-compromised patients (Kelley et al. 2004). In another study, the source of a deadly outbreak of a multidrug-resistant strain of Pseudomonas aeruginosa was traced to biofilms in hand hygiene sink drains, where its viable cells could be identified (Hota et al. 2009). There is great interest, therefore, to investigate biofilms as reservoirs of pathogens at higher resolution than allowed by the most commonly used detection and identification methodologies. Culture-independent surveys using the 16S rRNA gene as a marker are currently the most widely used approach; however, genetic strain differences reflecting pathogenicity are often difficult to resolve due to this gene being highly conserved among many bacterial strains. Quantitative PCR and direct culturing are focused on either a handful of predetermined pathogens or what can be readily cultivated. Metagenomic surveys are becoming common, but so far, our ability is limited to accurately predicting taxonomic affiliation at species or strain levels from highly diverse and complex data sets. Additionally, a whole-genome comparative genomic study on the evolution and transmission of a pathogen requires substantial amounts of DNA or a cultured strain, which often cannot be obtained. It has been demonstrated in a controlled experiment with 10 pg of extracted DNA provided as a template that MDA-amplified genotyping call and accuracy rates were only slightly lower than those for genomic DNA isolated directly from cultured cells (Giardina et al. 2009). Using single-cell genomic approaches, partial to near complete genomes should be obtainable without cultivation, from difficult samples within critical indoor environments such as healthcare facilities. In-depth analyses of these genomic data can then provide accurate and detailed information of strain-specific pathogen-gene signatures and other virulence factors. The aim of this study was to investigate for the first time the bacteria present in a healthcare facility with a high-throughput single-cell genomics approach. Based on the known prevalence of pathogens in biofilms, we focused on a sink drain biofilm from a public restroom adjoining an emergency waiting room. Sequencing 16S rRNA genes PCR-amplified from 416 single-cell MDA reactions, we found 18 candidate commensal and potentially pathogenic species that were selected for 454 shallow sequencing. Initial read mapping and de novo assembly of the low-coverage 454 sequence data confirmed that we had obtained genomic sequences for the pathogen Streptococcus pneumoniae as well as bacterial species highly similar to and those reported to be potentially pathogenic, including Sphingobacterium spiritivorum (Tronel et al. 2003; Kampfer et al. 2005), Leptotrichia buccalis (Hammann et al. 1993; Hot et al. 2008), as well as the host-associated oral bacteria, Streptococcus mitis and Veillonella parvula. Of particular note, we found three MDA products with sequences for the oral pathogen Porphyromonas gingivalis, which is a periodontal pathogen involved in periodontal bone loss that has also been linked to progression of atherosclerotic disease (Pussinen et al. 2007; Yilmaz 2008). P. gingivalis possesses many virulence factors, including functions that allow it to survive intracellularly and to be transmitted between different types of host cells (Li et al. 2008). Despite being detected at a very low abundance in the oral cavity, P. gingivalis can strongly disrupt the host–microbial homeostasis (Hajishengallis et al. 2011). As with many pathogens, the environmental reservoirs and mode(s) of transmission of P. gingivalis are not fully understood, yet it is a globally important pathogen with only three sequenced genomes available at the time of this report. It was recently stated by a CDC report that nearly 50% of American adults have mild, moderate, or severe periodontitis, and this percentage rises to 70% in adults greater than age 65 (Eke et al. 2012). To our knowledge, there are no previous reports detecting P. gingivalis outside of a host. Three MDA-amplified genomes with 16S rRNA gene sequences identified as P. gingivalis were chosen for additional deep sequencing on the Illumina GA IIx platform, and the resulting reads were mapped to P. gingivalis genomes. One MDA-read data set had ∼90% sequence coverage to P. gingivalis strain TDC60, which was isolated from a patient in Japan with severe periodontitis (Watanabe et al. 2011). A new single-cell de novo assembly algorithm, SPAdes (Bankevich et al. 2012), was used to generate contigs of the highest-coverage MDA product, which produced a 2.35-Mb draft genome (PG JCVI SC001). Comparative genomics and pangenome analyses were performed with the three other available P. gingivalis genomes; virulent strains W83 (Nelson et al. 2003) and TDC60 (Watanabe et al. 2011), and the less virulent strain ATCC 33277 (Naito et al. 2008). We demonstrate that single-cell genomics is a powerful approach that can produce highly accurate sequence data, enabling comparative genomic studies of pathogens obtained from a complex heterogeneous environmental sample. more...
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- 2013
31. Diffuse flow environments within basalt- and sediment-based hydrothermal vent ecosystems harbor specialized microbial communities
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S. Craig Cary, K. Eric Wommack, Barbara J. Campbell, Shannon J. Williamson, Shawn W. Polson, Lisa Zeigler Allen, and Charles Kai-Wu Lee
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Microbiology (medical) ,lcsh:QR1-502 ,Biology ,Microbiology ,Deep sea ,lcsh:Microbiology ,Hydrothermal circulation ,03 medical and health sciences ,Hydrothermal Vents ,Gammaproteobacteria ,Original Research Article ,14. Life underwater ,diffuse flow ,16S rRNA ,Microbial Diversity ,030304 developmental biology ,0303 health sciences ,Epsilonproteobacteria ,030306 microbiology ,Ecology ,diffuse-flow ,biology.organism_classification ,pyrosequencing ,Microbial population biology ,Guaymas Basin ,Alpha diversity ,Hydrothermal vent - Abstract
Hydrothermal vents differ both in surface input and subsurface geochemistry. The effects of these differences on their microbial communities are not clear. Here, we investigated both alpha and beta diversity of diffuse flow-associated microbial communities emanating from vents at a basalt-based hydrothermal system along the East Pacific Rise (EPR) and a sediment-based hydrothermal system, Guaymas Basin. Both Bacteria and Archaea were targeted using high throughput 16S rRNA gene pyrosequencing analyses. A novel aspect of this study was the use of a universal set of 16S rRNA gene primers to characterize total and diffuse flow-specific microbial communities from varied deep-sea hydrothermal environments. Both surrounding seawater and diffuse flow water samples contained large numbers of Marine Group I (MGI) Thaumarchaea and Gammaproteobacteria taxa previously observed in deep sea systems. However, these taxa were geographically distinct and segregated according to type of spreading center. Diffuse flow microbial community profiles were highly differentiated. In particular, EPR dominant diffuse-flow taxa were most closely associated with chemolithoautotrophs and off axis water were dominated by heterotrophic-related taxa, where the opposite was true for Guaymas basin. The diversity and richness of diffuse flow specific microbial communities were strongly correlated to the relative abundance of Epsilonproteobacteria, proximity to macrofauna, and hydrothermal system type. Archaeal diversity was higher than or equivalent to bacterial diversity in about one third of the samples. Most diffuse flow-specific communities were dominated by OTUs associated with Epsilonproteobacteria, but many of the Guaymas Basin diffuse flow samples were dominated by either OTUs within the Planctomycetes or hyperthermophilic Archaea. This study emphasizes the unique microbial communities associated with geochemically and geographically distinct hydrothermal diffuse flow environments. more...
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- 2013
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32. Metagenomic investigation of microbes and viruses in patients with jaw osteonecrosis associated with bisphosphonate therapy
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Shannon J. Williamson, Lisa Zeigler-Allen, Parish P. Sedghizadeh, Douglas Fadrosh, Mathangi Thiagarajan, Farid Farahnik, Shibu Yooseph, and Hamid Salek
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Male ,Pathology ,medicine.medical_specialty ,Firmicutes ,Polymerase Chain Reaction ,Article ,Pathology and Forensic Medicine ,Actinobacteria ,Microbiology ,Lysogenic cycle ,RNA, Ribosomal, 16S ,medicine ,Humans ,Radiology, Nuclear Medicine and imaging ,Dentistry (miscellaneous) ,Saliva ,Prophage ,Aged ,Aged, 80 and over ,Bisphosphonate-associated osteonecrosis of the jaw ,biology ,Biofilm ,medicine.disease ,biology.organism_classification ,Metagenomics ,Biofilms ,Surgery ,Bisphosphonate-Associated Osteonecrosis of the Jaw ,Female ,Oral Surgery ,Osteonecrosis of the jaw - Abstract
Objective The goal of this preliminary study was to use metagenomic approaches to investigate the taxonomic diversity of microorganisms in patients with bisphosphonate-related osteonecrosis of the jaw (BRONJ). Study Design Samples of saliva for planktonic microbial analysis and biofilm cultivation were collected from 10 patients (5 with BRONJ and 5 non-BRONJ control subjects) who met all ascertainment criteria. Prophage induction experiments—16S rRNA polymerase chain reaction and 454 pyrosequencing—and epifluorescent microscopy were performed for characterization and enumeration of microbes and viruses. Results Three phyla of microbes—Proteobacteria (70%), Firmicutes (26.9%), and Actinobacteria (1.95%)—dominated all BRONJ samples and accounted for almost 99% of the total data. Viral abundance was ∼1 order of magnitude greater than microbial cell abundance and comprised mainly phage viruses. Conclusions Individuals with jaw osteonecrosis harbored different microbial assemblages than nonaffected patients, and in general viral abundance and prophage induction increased with biofilm formation, suggesting that biofilm formation encouraged lysogenic interactions between viruses and microbial hosts and may contribute to pathogenicity. more...
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- 2012
33. Metagenomic exploration of viruses throughout the Indian Ocean
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Shibu Yooseph, Hernan Lorenzi, Shannon J. Williamson, Mathangi Thiagarajan, Andrey Tovchigrechko, J. Craig Venter, John P. McCrow, Douglas Fadrosh, Daniel Brami, and Lisa Zeigler Allen
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Genotype ,lcsh:Medicine ,Genome, Viral ,Microbiology ,Microbial Ecology ,03 medical and health sciences ,Phylogenetics ,Virology ,Databases, Genetic ,Human virome ,14. Life underwater ,Amino Acid Sequence ,lcsh:Science ,Base Pairing ,Indian Ocean ,Biology ,Virus classification ,Phylogeny ,030304 developmental biology ,0303 health sciences ,Principal Component Analysis ,Multidisciplinary ,Phylogenetic tree ,biology ,Base Sequence ,Geography ,Ecology ,030306 microbiology ,lcsh:R ,Bacterial taxonomy ,Genetic Variation ,Computational Biology ,Sequence Analysis, DNA ,Genomics ,biology.organism_classification ,Plankton ,Metagenomics ,Host-Pathogen Interactions ,Viruses ,Metagenome ,Taxonomy (biology) ,lcsh:Q ,Prochlorococcus ,Research Article - Abstract
The characterization of global marine microbial taxonomic and functional diversity is a primary goal of the Global Ocean Sampling Expedition. As part of this study, 19 water samples were collected aboard the Sorcerer II sailing vessel from the southern Indian Ocean in an effort to more thoroughly understand the lifestyle strategies of the microbial inhabitants of this ultra-oligotrophic region. No investigations of whole virioplankton assemblages have been conducted on waters collected from the Indian Ocean or across multiple size fractions thus far. Therefore, the goals of this study were to examine the effect of size fractionation on viral consortia structure and function and understand the diversity and functional potential of the Indian Ocean virome. Five samples were selected for comprehensive metagenomic exploration; and sequencing was performed on the microbes captured on 3.0-, 0.8- and 0.1 µm membrane filters as well as the viral fraction ( more...
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- 2012
34. Reconstruction of a Bacterial Genome from DNA Cassettes
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Lisa Zeigler Allen, Robert M. Friedman, Shibu Yooseph, Mathangi Thiagarajan, Andrew E. Allen, Christopher L. Dupont, J. Craig Venter, John I. Glass, and Laura Sheahan
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Synthetic biology ,Microbial ecology ,Ecology ,Metagenomics ,Shotgun sequencing ,Horizontal gene transfer ,Context (language use) ,Bacterial genome size ,Computational biology ,Biology ,Genome - Abstract
This basic research program comprised two major areas: (1) acquisition and analysis of marine microbial metagenomic data and development of genomic analysis tools for broad, external community use; (2) development of a minimal bacterial genome. Our Marine Metagenomic Diversity effort generated and analyzed shotgun sequencing data from microbial communities sampled from over 250 sites around the world. About 40% of the 26 Gbp of sequence data has been made publicly available to date with a complete release anticipated in six months. Our results and those mining the deposited data have revealed a vast diversity of genes coding for critical metabolic processes whose phylogenetic and geographic distributions will enable a deeper understanding of carbon and nutrient cycling, microbial ecology, and rapid rate evolutionary processes such as horizontal gene transfer by viruses and plasmids. A global assembly of the generated dataset resulted in a massive set (5Gbp) of genome fragments that provide context to the majority of the generated data that originated from uncultivated organisms. Our Synthetic Biology team has made significant progress towards the goal of synthesizing a minimal mycoplasma genome that will have all of the machinery for independent life. This project, once completed, will provide fundamentally new knowledge about requirements for microbial life and help to lay a basic research foundation for developing microbiological approaches to bioenergy. more...
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- 2011
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35. Single virus genomics: a new tool for virus discovery
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Shannon J. Williamson, Roger S. Lasken, Lisa Zeigler Allen, Thomas Ishoey, Jeffrey S. McLean, and Mark Novotny
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Cancer genome sequencing ,viruses ,Science ,Genomics ,Marine Biology ,Genome, Viral ,Biology ,Genome ,Polymerase Chain Reaction ,Microbiology ,Microbial Ecology ,Virology ,Bacteriophage T4 ,Genome Sequencing ,Whole Genome Amplification ,Comparative genomics ,Whole genome sequencing ,Genetics ,Evolutionary Biology ,Multidisciplinary ,Microscopy, Confocal ,Ecology ,Multiple displacement amplification ,Marine Ecology ,Reproducibility of Results ,Genomic Evolution ,Sequence Analysis, DNA ,Reference Standards ,Flow Cytometry ,Bacteriophage lambda ,Genetic Loci ,Microbial Evolution ,Medicine ,Metagenomics ,Reference genome ,Research Article - Abstract
Whole genome amplification and sequencing of single microbial cells has significantly influenced genomics and microbial ecology by facilitating direct recovery of reference genome data. However, viral genomics continues to suffer due to difficulties related to the isolation and characterization of uncultivated viruses. We report here on a new approach called 'Single Virus Genomics', which enabled the isolation and complete genome sequencing of the first single virus particle. A mixed assemblage comprised of two known viruses; E. coli bacteriophages lambda and T4, were sorted using flow cytometric methods and subsequently immobilized in an agarose matrix. Genome amplification was then achieved in situ via multiple displacement amplification (MDA). The complete lambda phage genome was recovered with an average depth of coverage of approximately 437X. The isolation and genome sequencing of uncultivated viruses using Single Virus Genomics approaches will enable researchers to address questions about viral diversity, evolution, adaptation and ecology that were previously unattainable. more...
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- 2011
36. Going deeper: metagenome of a hadopelagic microbial community
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Roger S. Lasken, Shibu Yooseph, Mary-Jane Lombardo, Douglas H. Bartlett, Eric E. Allen, Lisa Zeigler Allen, Shannon J. Williamson, Mark Novotny, Joyclyn Yee-Greenbaum, Maria Kim, Emiley A. Eloe, and Douglas Fadrosh more...
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Rhodospirillales ,Molecular Sequence Data ,lcsh:Medicine ,Context (language use) ,Computational biology ,Microbial Ecology ,03 medical and health sciences ,Marine bacteriophage ,Gammaproteobacteria ,Seawater ,14. Life underwater ,lcsh:Science ,Biology ,Phylogeny ,030304 developmental biology ,Alphaproteobacteria ,0303 health sciences ,Multidisciplinary ,biology ,Ecology ,030306 microbiology ,Phylum ,Bacteroidetes ,lcsh:R ,Planctomycetes ,Marine Ecology ,Computational Biology ,food and beverages ,Genomics ,biology.organism_classification ,Flow Cytometry ,Metagenomics ,RNA, Ribosomal ,Metagenome ,lcsh:Q ,Research Article - Abstract
The paucity of sequence data from pelagic deep-ocean microbial assemblages has severely restricted molecular exploration of the largest biome on Earth. In this study, an analysis is presented of a large-scale 454-pyrosequencing metagenomic dataset from a hadopelagic environment from 6,000 m depth within the Puerto Rico Trench (PRT). A total of 145 Mbp of assembled sequence data was generated and compared to two pelagic deep ocean metagenomes and two representative surface seawater datasets from the Sargasso Sea. In a number of instances, all three deep metagenomes displayed similar trends, but were most magnified in the PRT, including enrichment in functions for two-component signal transduction mechanisms and transcriptional regulation. Overrepresented transporters in the PRT metagenome included outer membrane porins, diverse cation transporters, and di- and tri-carboxylate transporters that matched well with the prevailing catabolic processes such as butanoate, glyoxylate and dicarboxylate metabolism. A surprisingly high abundance of sulfatases for the degradation of sulfated polysaccharides were also present in the PRT. The most dramatic adaptational feature of the PRT microbes appears to be heavy metal resistance, as reflected in the large numbers of transporters present for their removal. As a complement to the metagenome approach, single-cell genomic techniques were utilized to generate partial whole-genome sequence data from four uncultivated cells from members of the dominant phyla within the PRT, Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes and Planctomycetes. The single-cell sequence data provided genomic context for many of the highly abundant functional attributes identified from the PRT metagenome, as well as recruiting heavily the PRT metagenomic sequence data compared to 172 available reference marine genomes. Through these multifaceted sequence approaches, new insights have been provided into the unique functional attributes present in microbes residing in a deeper layer of the ocean far removed from the more productive sun-drenched zones above. more...
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- 2011
37. Identifying Low pH Active and Lactate-Utilizing Taxa within Oral Microbiome Communities from Healthy Children Using Stable Isotope Probing Techniques
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Jeffrey S. McLean, Sarah J. Fansler, Paul D. Majors, Lisa Zeigler Allen, Wenyuan Shi, Kathleen McAteer, Mark E. Shirtliff, Renate Lux, and Aziz, Ramy K
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Bacterial Diseases ,Magnetic Resonance Spectroscopy ,Stable-isotope probing ,lcsh:Medicine ,Isotopes ,Lactobacillus ,lcsh:Science ,Child ,Pediatric ,0303 health sciences ,Multidisciplinary ,biology ,Bacterial ,Hydrogen-Ion Concentration ,3. Good health ,RNA, Bacterial ,Infectious Diseases ,Biochemistry ,Health ,Lactates ,Medicine ,Oral Microbiome ,Research Article ,DNA, Bacterial ,General Science & Technology ,Propionibacterium ,Oral Medicine ,Dental Plaque ,Dental Caries ,Buffers ,Dental plaque ,Microbiology ,03 medical and health sciences ,Clinical Research ,Genetics ,medicine ,Humans ,Microbiome ,Dental/Oral and Craniofacial Disease ,Biology ,030304 developmental biology ,Mouth ,Bacteria ,030306 microbiology ,lcsh:R ,Bacteriology ,DNA ,medicine.disease ,biology.organism_classification ,Metagenomics ,RNA ,Metagenome ,lcsh:Q - Abstract
Author(s): McLean, Jeffrey S; Fansler, Sarah J; Majors, Paul D; McAteer, Kathleen; Allen, Lisa Z; Shirtliff, Mark E; Lux, Renate; Shi, Wenyuan | Abstract: BackgroundMany human microbial infectious diseases including dental caries are polymicrobial in nature. How these complex multi-species communities evolve from a healthy to a diseased state is not well understood. Although many health- or disease-associated oral bacteria have been characterized in vitro, their physiology within the complex oral microbiome is difficult to determine with current approaches. In addition, about half of these species remain uncultivated to date with little known besides their 16S rRNA sequence. Lacking culture-based physiological analyses, the functional roles of uncultivated species will remain enigmatic despite their apparent disease correlation. To start addressing these knowledge gaps, we applied a combination of Magnetic Resonance Spectroscopy (MRS) with RNA and DNA based Stable Isotope Probing (SIP) to oral plaque communities from healthy children for in vitro temporal monitoring of metabolites and identification of metabolically active and inactive bacterial species.Methodology/principal findingsSupragingival plaque samples from caries-free children incubated with (13)C-substrates under imposed healthy (buffered, pH 7) and diseased states (pH 5.5 and pH 4.5) produced lactate as the dominant organic acid from glucose metabolism. Rapid lactate utilization upon glucose depletion was observed under pH 7 conditions. SIP analyses revealed a number of genera containing cultured and uncultivated taxa with metabolic capabilities at pH 5.5. The diversity of active species decreased significantly at pH 4.5 and was dominated by Lactobacillus and Propionibacterium species, both of which have been previously found within carious lesions from children.Conclusions/significanceOur approach allowed for identification of species that metabolize carbohydrates under different pH conditions and supports the importance of Lactobacilli and Propionibacterium in the development of childhood caries. Identification of species within healthy subjects that are active at low pH can lead to a better understanding of oral caries onset and generate appropriate targets for preventative measures in the early stages. more...
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- 2012
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38. Expansion of the global RNA virome reveals diverse clades of bacteriophages
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Uri Neri, Yuri I. Wolf, Simon Roux, Antonio Pedro Camargo, Benjamin Lee, Darius Kazlauskas, I. Min Chen, Natalia Ivanova, Lisa Zeigler Allen, David Paez-Espino, Donald A. Bryant, Devaki Bhaya, Mart Krupovic, Valerian V. Dolja, Nikos C. Kyrpides, Eugene V. Koonin, Uri Gophna, Adrienne B. Narrowe, Alexander J. Probst, Alexander Sczyrba, Annegret Kohler, Armand Séguin, Ashley Shade, Barbara J. Campbell, Björn D. Lindahl, Brandi Kiel Reese, Breanna M. Roque, Chris DeRito, Colin Averill, Daniel Cullen, David A.C. Beck, David A. Walsh, David M. Ward, Dongying Wu, Emiley Eloe-Fadrosh, Eoin L. Brodie, Erica B. Young, Erik A. Lilleskov, Federico J. Castillo, Francis M. Martin, Gary R. LeCleir, Graeme T. Attwood, Hinsby Cadillo-Quiroz, Holly M. Simon, Ian Hewson, Igor V. Grigoriev, James M. Tiedje, Janet K. Jansson, Janey Lee, Jean S. VanderGheynst, Jeff Dangl, Jeff S. Bowman, Jeffrey L. Blanchard, Jennifer L. Bowen, Jiangbing Xu, Jillian F. Banfield, Jody W. Deming, Joel E. Kostka, John M. Gladden, Josephine Z. Rapp, Joshua Sharpe, Katherine D. McMahon, Kathleen K. Treseder, Kay D. Bidle, Kelly C. Wrighton, Kimberlee Thamatrakoln, Klaus Nusslein, Laura K. Meredith, Lucia Ramirez, Marc Buee, Marcel Huntemann, Marina G. Kalyuzhnaya, Mark P. Waldrop, Matthew B. Sullivan, Matthew O. Schrenk, Matthias Hess, Michael A. Vega, Michelle A. O’Malley, Monica Medina, Naomi E. Gilbert, Nathalie Delherbe, Olivia U. Mason, Paul Dijkstra, Peter F. Chuckran, Petr Baldrian, Philippe Constant, Ramunas Stepanauskas, Rebecca A. Daly, Regina Lamendella, Robert J. Gruninger, Robert M. McKay, Samuel Hylander, Sarah L. Lebeis, Sarah P. Esser, Silvia G. Acinas, Steven S. Wilhelm, Steven W. Singer, Susannah S. Tringe, Tanja Woyke, T.B.K. Reddy, Terrence H. Bell, Thomas Mock, Tim McAllister, Vera Thiel, Vincent J. Denef, Wen-Tso Liu, Willm Martens-Habbena, Xiao-Jun Allen Liu, Zachary S. Cooper, Zhong Wang, Tel Aviv University (TAU), National Center for Biotechnology Information (NCBI), Lawrence Berkeley National Laboratory [Berkeley] (LBNL), University of Oxford, Vilnius University [Vilnius], J. Craig Venter Institute [La Jolla, USA] (JCVI), Pennsylvania State University (Penn State), Penn State System, Carnegie Institution for Science, Virologie des archées - Archaeal Virology, Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Oregon State University (OSU), U.G. and U.N. are supported by the European Research Council (ERC-AdG 787514). U.N. is supported by a fellowship from the Edmond J. Safra Center for Bioinformatics at Tel Aviv University. Y.I.W. and E.V.K. are supported through the Intramural Research Program of the US National Institutes of Health (National Library of Medicine). V.V.D. was partially supported by NIH/NLM/NCBI Visiting Scientist Fellowship. The work of the U.S. Department of Energy Joint Genome Institute (S.R., A.P.C., I.M.C., N.I., D.P.-E., N.C.K., and all JGI co-authors), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy under contract no. DE-AC02-05CH11231. M.K. was supported by l’Agence Nationale de la Recherche grants ANR-20-CE20-009-02 and ANR-21-CE11-0001-01. D.K. was funded by the European Social Fund under no. 09.3.3-LMT-K-712-14-0027. D.A.B. is supported by grant NNX16SJ62G from the NASA Exobiology program, and by grant DE-FG02-94ER20137 from the Photosynthetic Systems Program, Division of Chemical Sciences, Geosciences, and Biosciences (CSGB), Office of Basic Energy Sciences of the U.S. Department of Energy. We gratefully acknowledge the contributions of many scientists and principal investigators, who sent extracted genetic material for isolate genomes, environmental metagenomes, and metatranscriptomes, or sequencing results as part of the Department of Energy Joint Genome Institute Community Science Program and allowed us to include in our study the RNA virus sequences detected in these publicly available data sets regardless of publication status., The RNA Virus Discovery Consortium members are Adrienne B. Narrowe, Alexander J. Probst, Alexander Sczyrba, Annegret Kohler, Armand Séguin, Ashley Shade, Barbara J. Campbell, Björn D. Lindahl, Brandi Kiel Reese, Breanna M. Roque, Chris DeRito, Colin Averill, Daniel Cullen, David A.C. Beck, David A. Walsh, David M. Ward, Dongying Wu, Emiley Eloe-Fadrosh, Eoin L. Brodie, Erica B. Young, Erik A. Lilleskov, Federico J. Castillo, Francis M. Martin, Gary R. LeCleir, Graeme T. Attwood, Hinsby Cadillo-Quiroz, Holly M. Simon, Ian Hewson, Igor V. Grigoriev, James M. Tiedje, Janet K. Jansson, Janey Lee, Jean S. VanderGheynst, Jeff Dangl, Jeff S. Bowman, Jeffrey L. Blanchard, Jennifer L. Bowen, Jiangbing Xu, Jillian F. Banfield, Jody W. Deming, Joel E. Kostka, John M. Gladden, Josephine Z. Rapp, Joshua Sharpe, Katherine D. McMahon, Kathleen K. Treseder, Kay D. Bidle, Kelly C. Wrighton, Kimberlee Thamatrakoln, Klaus Nusslein, Laura K. Meredith, Lucia Ramirez, Marc Buee, Marcel Huntemann, Marina G. Kalyuzhnaya, Mark P. Waldrop, Matthew B. Sullivan, Matthew O. Schrenk, Matthias Hess, Michael A. Vega, Michelle A. O’Malley, Monica Medina, Naomi E. Gilbert, Nathalie Delherbe, Olivia U. Mason, Paul Dijkstra, Peter F. Chuckran, Petr Baldrian, Philippe Constant, Ramunas Stepanauskas, Rebecca A. Daly, Regina Lamendella, Robert J. Gruninger, Robert M. McKay, Samuel Hylander, Sarah L. Lebeis, Sarah P. Esser, Silvia G. Acinas, Steven S. Wilhelm, Steven W. Singer, Susannah S. Tringe, Tanja Woyke, T.B.K. Reddy, Terrence H. Bell, Thomas Mock, Tim McAllister, Vera Thiel, Vincent J. Denef, Wen-Tso Liu, Willm Martens-Habbena, Xiao-Jun Allen Liu, Zachary S. Cooper, and Zhong Wang, ANR-20-CE20-0009,VIROMET,Devoiler le virome des archées methanogenes(2020), and ANR-21-CE11-0001,ArcFus,Protéines de classe II de fusion membranaire chez les archées(2021) more...
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Bactriophage ,RNA Virus ,Virome ,Functional protein annotation ,Metatranscriptomics ,RNA dependent RNA polymerase ,Viral Ecology ,viral phylogeny ,Virus ,Virus - Host prediction ,DNA-Directed RNA Polymerases ,Genome, Viral ,RNA-Dependent RNA Polymerase ,General Biochemistry, Genetics and Molecular Biology ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,RNA ,RNA Viruses ,Bacteriophages ,Phylogeny - Abstract
International audience; High-throughput RNA sequencing offers broad opportunities to explore the Earth RNA virome. Mining 5,150 diverse metatranscriptomes uncovered >2.5 million RNA virus contigs. Analysis of >330,000 RNA-dependent RNA polymerases (RdRPs) shows that this expansion corresponds to a 5-fold increase of the known RNA virus diversity. Gene content analysis revealed multiple protein domains previously not found in RNA viruses and implicated in virus-host interactions. Extended RdRP phylogeny supports the monophyly of the five established phyla and reveals two putative additional bacteriophage phyla and numerous putative additional classes and orders. The dramatically expanded phylum Lenarviricota, consisting of bacterial and related eukaryotic viruses, now accounts for a third of the RNA virome. Identification of CRISPR spacer matches and bacteriolytic proteins suggests that subsets of picobirnaviruses and partitiviruses, previously associated with eukaryotes, infect prokaryotic hosts. more...
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39. A metagenomic framework for the study of airborne microbial communities.
- Author
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Shibu Yooseph, Cynthia Andrews-Pfannkoch, Aaron Tenney, Jeff McQuaid, Shannon Williamson, Mathangi Thiagarajan, Daniel Brami, Lisa Zeigler-Allen, Jeff Hoffman, Johannes B Goll, Douglas Fadrosh, John Glass, Mark D Adams, Robert Friedman, and J Craig Venter more...
- Subjects
Medicine ,Science - Abstract
Understanding the microbial content of the air has important scientific, health, and economic implications. While studies have primarily characterized the taxonomic content of air samples by sequencing the 16S or 18S ribosomal RNA gene, direct analysis of the genomic content of airborne microorganisms has not been possible due to the extremely low density of biological material in airborne environments. We developed sampling and amplification methods to enable adequate DNA recovery to allow metagenomic profiling of air samples collected from indoor and outdoor environments. Air samples were collected from a large urban building, a medical center, a house, and a pier. Analyses of metagenomic data generated from these samples reveal airborne communities with a high degree of diversity and different genera abundance profiles. The identities of many of the taxonomic groups and protein families also allows for the identification of the likely sources of the sampled airborne bacteria. more...
- Published
- 2013
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40. Assessing viral taxonomic composition in benthic marine ecosystems: reliability and efficiency of different bioinformatic tools for viral metagenomic analyses
- Author
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Antonio Dell'Anno, Cinzia Corinaldesi, L. Zeigler Allen, Giulia Riccioni, Michael Tangherlini, Michael Tangherlini, Antonio Dell'Anno, Lisa Zeigler Allen, Giulia Riccioni, and Cinzia Corinaldesi
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0301 basic medicine ,Range (biology) ,viruses ,Oceans and Seas ,030106 microbiology ,Biome ,Biology ,Article ,03 medical and health sciences ,Phylogenetics ,Human virome ,Marine ecosystem ,Ecosystem ,Computational platforms and environments, Microbial ecology ,Phylogeny ,Multidisciplinary ,Ecology ,Computational Biology ,030104 developmental biology ,Benthic zone ,Metagenomics ,Viruses ,Databases, Nucleic Acid ,Water Microbiology - Abstract
In benthic deep-sea ecosystems, which represent the largest biome on Earth, viruses have a recognised key ecological role, but their diversity is still largely unknown. Identifying the taxonomic composition of viruses is crucial for understanding virus-host interactions, their role in food web functioning and evolutionary processes. Here, we compared the performance of various bioinformatic tools (BLAST, MG-RAST, NBC, VMGAP, MetaVir, VIROME) for analysing the viral taxonomic composition in simulated viromes and viral metagenomes from different benthic deep-sea ecosystems. The analyses of simulated viromes indicate that all the BLAST tools, followed by MetaVir and VMGAP, are more reliable in the affiliation of viral sequences and strains. When analysing the environmental viromes, tBLASTx, MetaVir, VMGAP and VIROME showed a similar efficiency of sequence annotation; however, MetaVir and tBLASTx identified a higher number of viral strains. These latter tools also identified a wider range of viral families than the others, providing a wider view of viral taxonomic diversity in benthic deep-sea ecosystems. Our findings highlight strengths and weaknesses of available bioinformatic tools for investigating the taxonomic diversity of viruses in benthic ecosystems in order to improve our comprehension of viral diversity in the oceans and its relationships with host diversity and ecosystem functioning. more...
- Published
- 2016
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