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Viral metagenome in soil

Jacob H Munson-McGee, Shengyun Peng, Samantha Dewerff, Ramunas Stepanauskas, Rachel J Whitaker, Joshua S Weitz, Mark J Young
The application of viral and cellular metagenomics to natural environments has expanded our understanding of the structure, functioning, and diversity of microbial and viral communities. The high diversity of many communities, e.g., soils, surface ocean waters, and animal-associated microbiomes, make it difficult to establish virus-host associations at the single cell (rather than population) level, assign cellular hosts, or determine the extent of viral host range from metagenomics studies alone. Here, we combine single-cell sequencing with environmental metagenomics to characterize the structure of virus-host associations in a Yellowstone National Park (YNP) hot spring microbial community...
February 21, 2018: ISME Journal
S François, D Filloux, M Frayssinet, P Roumagnac, D P Martin, M Ogliastro, R Froissart
Metagenomics studies have revolutionized the field of biology by revealing the presence of many previously unisolated and uncultured micro-organisms. However, one of the main problems encountered in metagenomic studies is the high percentage of sequences that cannot be assigned taxonomically using commonly used similarity-based approaches (e.g. BLAST or HMM). These unassigned sequences are allegorically called « dark matter » in the metagenomic literature and are often referred to as being derived from new or unknown organisms...
January 15, 2018: Virus Research
Kurt E Williamson, Jeffry J Fuhrmann, K Eric Wommack, Mark Radosevich
Viral abundance in soils can range from below detection limits in hot deserts to over 1 billion per gram in wetlands. Abundance appears to be strongly influenced by water availability and temperature, but a lack of informational standards creates difficulties for cross-study analysis. Soil viral diversity is severely underestimated and undersampled, although current measures of viral richness are higher for soils than for aquatic ecosystems. Both morphometric and metagenomic analyses have raised questions about the prevalence of nontailed, ssDNA viruses in soils...
September 29, 2017: Annual Review of Virology
Li-Li Han, Dan-Ting Yu, Li-Mei Zhang, Ju-Pei Shen, Ji-Zheng He
Viral community structures in complex agricultural soils are largely unknown. Electron microscopy and viromic analyses were conducted on six typical Chinese agricultural soil samples. Tailed bacteriophages, spherical and filamentous viral particles were identified by the morphological analysis. Based on the metagenomic analysis, single-stranded DNA viruses represented the largest viral component in most of the soil habitats, while the double-stranded DNA viruses belonging to the Caudovirales order were predominanted in Jiangxi-maize soils...
March 22, 2017: Scientific Reports
Anne-Lie Blomström, Cecilia Lalander, Allan John Komakech, Björn Vinnerås, Sofia Boqvist
BACKGROUND: Vermicomposting is a mesophilic process using earthworms to efficiently and at low cost process large volumes of organic waste. It has been suggested to not only increase soil fertility but also increase biomass of beneficial bacteria while reducing harmful bacteria. The aim of this study was to set up a strategy to investigate and characterise the viral as well as the bacterial composition of a vermicomposting system. MATERIAL AND METHODS: The vermicomposting unit used in this study was placed at the Makerere University Agricultural Research Institute Kabanyolo on the outskirts of Kampala, Uganda, and was fed with 80% cattle manure and 20% food waste...
2016: Infection Ecology & Epidemiology
Ana Georgina Cobián Güemes, Merry Youle, Vito Adrian Cantú, Ben Felts, James Nulton, Forest Rohwer
Viruses are the most abundant and the most diverse life form. In this meta-analysis we estimate that there are 4.80×10(31) phages on Earth. Further, 97% of viruses are in soil and sediment-two underinvestigated biomes that combined account for only ∼2.5% of publicly available viral metagenomes. The majority of the most abundant viral sequences from all biomes are novel. Our analysis drawing on all publicly available viral metagenomes observed a mere 257,698 viral genotypes on Earth-an unrealistically low number-which attests to the current paucity of viral metagenomic data...
September 29, 2016: Annual Review of Virology
Surendra Vikram, Leandro D Guerrero, Thulani P Makhalanyane, Phuong T Le, Mary Seely, Don A Cowan
In hyperarid ecosystems, macroscopic communities are often restricted to cryptic niches, such as hypoliths (microbial communities found beneath translucent rocks), which are widely distributed in hyperarid desert environments. While hypolithic communities are considered to play a major role in productivity, the functional guilds implicated in these processes remain unclear. Here, we describe the metagenomic sequencing, assembly and analysis of hypolithic microbial communities from the Namib Desert. Taxonomic analyses using Small Subunit phylogenetic markers showed that bacterial phylotypes (93%) dominated the communities, with relatively small proportions of archaea (0...
June 2016: Environmental Microbiology
Hayedeh Behzad, Takashi Gojobori, Katsuhiko Mineta
Recent metagenomic studies of environments, such as marine and soil, have significantly enhanced our understanding of the diverse microbial communities living in these habitats and their essential roles in sustaining vast ecosystems. The increase in the number of publications related to soil and marine metagenomics is in sharp contrast to those of air, yet airborne microbes are thought to have significant impacts on many aspects of our lives from their potential roles in atmospheric events such as cloud formation, precipitation, and atmospheric chemistry to their major impact on human health...
May 2015: Genome Biology and Evolution
Laura Sanguino, Laure Franqueville, Timothy M Vogel, Catherine Larose
The ecological pressure that viruses place on microbial communities is not only based on predation, but also on gene transfer. In order to determine the potential impact of viruses and transduction, we need a better understanding of the dynamics of interactions between viruses and their hosts in the environment. Data on environmental viruses are scarce, and methods for tracking their interactions with prokaryotes are needed. Clustered regularly interspaced short palindromic repeats (CRISPRs), which contain viral sequences in bacterial genomes, might help document the history of virus-host interactions in the environment...
May 2015: FEMS Microbiology Ecology
Mohammad A Tariq, Francesca L C Everest, Lauren A Cowley, Anthony De Soyza, Giles S Holt, Simon H Bridge, Audrey Perry, John D Perry, Stephen J Bourke, Stephen P Cummings, Clare V Lanyon, Jeremy J Barr, Darren L Smith
Pseudomonas aeruginosa (Pa), normally a soil commensal, is an important opportunistic pathogen in Cystic Fibrosis (CF) and non-Cystic Fibrosis Bronchiectasis (nCFBR). Persistent infection correlates with accelerated decline in lung function and early mortality. The horizontal transfer of DNA by temperate bacteriophages can add gene function and selective advantages to their bacterial host within the constrained environment of the lower lung. In this study, we chemically induce temperate bacteriophages from clonal cultures of Pa and identify their mixed viral communities employing metagenomic approaches...
2015: Frontiers in Microbiology
K Eri Wommack, Daniel J Nasko, Jessica Chopyk, Eric G Sakowski
The discovery of abundant viruses in the oceans and on land has ushered in a quarter century of groundbreaking advancements in our understanding of viruses within ecosystems. Two types of observations from environmental samples--direct counts of viral particles and viral metagenomic sequences--have been critical to these discoveries. Accurate direct counts have established ecosystem-scale trends in the impacts of viral infection on microbial host populations and have shown that viral communities within aquatic and soil environments respond to both short term and seasonal environmental change...
March 2015: Journal of Microbiology / the Microbiological Society of Korea
Li Deng, J Cesar Ignacio-Espinoza, Ann C Gregory, Bonnie T Poulos, Joshua S Weitz, Philip Hugenholtz, Matthew B Sullivan
Microbes and their viruses drive myriad processes across ecosystems ranging from oceans and soils to bioreactors and humans. Despite this importance, microbial diversity is only now being mapped at scales relevant to nature, while the viral diversity associated with any particular host remains little researched. Here we quantify host-associated viral diversity using viral-tagged metagenomics, which links viruses to specific host cells for high-throughput screening and sequencing. In a single experiment, we screened 10(7) Pacific Ocean viruses against a single strain of Synechococcus and found that naturally occurring cyanophage genome sequence space is statistically clustered into discrete populations...
September 11, 2014: Nature
Evelien M Adriaenssens, Lonnie Van Zyl, Pieter De Maayer, Enrico Rubagotti, Ed Rybicki, Marla Tuffin, Don A Cowan
Hypolithic microbial communities are specialized desert communities inhabiting the underside of translucent rocks. Here, we present the first study of the viral fraction of these communities isolated from the hyperarid Namib Desert. The taxonomic composition of the hypolithic viral communities was investigated and a functional assessment of the sequences determined. Phylotypic analysis showed that bacteriophages belonging to the order Caudovirales, in particular the family Siphoviridae, were most prevalent...
February 2015: Environmental Microbiology
Aaron J Prussin, Linsey C Marr, Kyle J Bibby
Despite the obvious importance of viral transmission and ecology to medicine, epidemiology, ecology, agriculture, and microbiology, the study of viral bioaerosols and community structure has remained a vastly underexplored area, due to both unresolved technical challenges and unrecognized importance. High-throughput, culture-independent techniques such as viral metagenomics are beginning to revolutionize the study of viral ecology. With recent developments in viral metagenomics, characterization of viral bioaerosol communities provides an opportunity for high-impact future research...
August 2014: FEMS Microbiology Letters
Viral G Akbari, Rupal D Pandya, Satya P Singh
The assessment of the microbial diversity of the entire community of a given habitat requires the extraction of the total environmental DNA. Metagenomic investigations of a petroleum-polluted habitat have its unique challenges. The specific methods were developed for the extraction of high-quality metagenome in good quantity from the petroleum-polluted saline and non-saline sites in Gujarat (India). The soil samples were washed to remove the toxic, hazardous organic pollutants which might interfere with the recovery of the metagenomic DNA...
October 2014: Environmental Monitoring and Assessment
Sandra Appelt, Laura Fancello, Matthieu Le Bailly, Didier Raoult, Michel Drancourt, Christelle Desnues
Coprolites are fossilized fecal material that can reveal information about ancient intestinal and environmental microbiota. Viral metagenomics has allowed systematic characterization of viral diversity in environmental and human-associated specimens, but little is known about the viral diversity in fossil remains. Here, we analyzed the viral community of a 14th-century coprolite from a closed barrel in a Middle Ages site in Belgium using electron microscopy and metagenomics. Viruses that infect eukaryotes, bacteria, and archaea were detected, and we confirmed the presence of some of them by ad hoc suicide PCR...
May 2014: Applied and Environmental Microbiology
Min-Soo Kim, Tae Woong Whon, Jin-Woo Bae
The introduction of metagenomics into the field of virology has facilitated the exploration of viral communities in various natural habitats. Understanding the viral ecology of a variety of sample types throughout the biosphere is important per se, but it also has potential applications in clinical and diagnostic virology. However, the procedures used by viral metagenomics may produce technical errors, such as amplification bias, while public viral databases are very limited, which may hamper the determination of the viral diversity in samples...
September 2013: Genomics & Informatics
Sharath Srinivasiah, Jacqueline Lovett, Shawn Polson, Jaysheel Bhavsar, Dhritiman Ghosh, Krishnakali Roy, Jeffry J Fuhrmann, Mark Radosevich, K Eric Wommack
Viruses are the most abundant and diverse biological entities within soils, yet their ecological impact is largely unknown. Defining how soil viral communities change with perturbation or across environments will contribute to understanding the larger ecological significance of soil viruses. A new approach to examining the composition of soil viral communities based on random PCR amplification of polymorphic DNA (RAPD-PCR) was developed. A key methodological improvement was the use of viral metagenomic sequence data for the design of RAPD-PCR primers...
September 2013: Applied and Environmental Microbiology
Kyle Bibby, Jordan Peccia
The large diversity of viruses that exist in human populations are potentially excreted into sewage collection systems and concentrated in sewage sludge. In the U.S., the primary fate of processed sewage sludge (class B biosolids) is application to agricultural land as a soil amendment. To characterize and understand infectious risks associated with land application, and to describe the diversity of viruses in human populations, shotgun viral metagenomics was applied to 10 sewage sludge samples from 5 wastewater treatment plants throughout the continental U...
February 19, 2013: Environmental Science & Technology
Laura Fancello, Sébatien Trape, Catherine Robert, Mickaël Boyer, Nikolay Popgeorgiev, Didier Raoult, Christelle Desnues
Here, we present the first metagenomic study of viral communities from four perennial ponds (gueltas) located in the central Sahara (Mauritania). Three of the four gueltas (Ilij, Molomhar and Hamdoun) are located at the source of three different wadis belonging to the same hydrologic basin, whereas the fourth (El Berbera) belongs to a different basin. Overall, sequences belonging to tailed bacteriophages were the most abundant in all four metagenomes although electron microscopy and sequencing confirmed the presence of other viral groups, such as large DNA viruses...
February 2013: ISME Journal
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