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Viral metagenome in soil

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https://www.readbyqxmd.com/read/27834174/a-metagenomic-analysis-displays-the-diverse-microbial-community-of-a-vermicomposting-system-in-uganda
#1
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
https://www.readbyqxmd.com/read/27741409/viruses-as-winners-in-the-game-of-life
#2
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
https://www.readbyqxmd.com/read/26470632/metagenomic-analysis-provides-insights-into-functional-capacity-in-a-hyperarid-desert-soil-niche-community
#3
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
https://www.readbyqxmd.com/read/25953766/challenges-and-opportunities-of-airborne-metagenomics
#4
REVIEW
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
https://www.readbyqxmd.com/read/25908869/linking-environmental-prokaryotic-viruses-and-their-host-through-crisprs
#5
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
https://www.readbyqxmd.com/read/25741327/a-metagenomic-approach-to-characterize-temperate-bacteriophage-populations-from-cystic-fibrosis-and-non-cystic-fibrosis-bronchiectasis-patients
#6
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
https://www.readbyqxmd.com/read/25732739/counts-and-sequences-observations-that-continue-to-change-our-understanding-of-viruses-in-nature
#7
REVIEW
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
https://www.readbyqxmd.com/read/25043051/viral-tagging-reveals-discrete-populations-in-synechococcus-viral-genome-sequence-space
#8
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
https://www.readbyqxmd.com/read/24912085/metagenomic-analysis-of-the-viral-community-in-namib-desert-hypoliths
#9
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
https://www.readbyqxmd.com/read/24891293/challenges-of-studying-viral-aerosol-metagenomics-and-communities-in-comparison-with-bacterial-and-fungal-aerosols
#10
REVIEW
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
https://www.readbyqxmd.com/read/24869956/extraction-of-the-metagenomic-dna-and-assessment-of-the-bacterial-diversity-from-the-petroleum-polluted-sites
#11
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
https://www.readbyqxmd.com/read/24509925/viruses-in-a-14th-century-coprolite
#12
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
https://www.readbyqxmd.com/read/24124407/comparative-viral-metagenomics-of-environmental-samples-from-korea
#13
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
https://www.readbyqxmd.com/read/23793630/direct-assessment-of-viral-diversity-in-soils-by-random-pcr-amplification-of-polymorphic-dna
#14
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
https://www.readbyqxmd.com/read/23346855/identification-of-viral-pathogen-diversity-in-sewage-sludge-by-metagenome-analysis
#15
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
https://www.readbyqxmd.com/read/23038177/viruses-in-the-desert-a-metagenomic-survey-of-viral-communities-in-four-perennial-ponds-of-the-mauritanian-sahara
#16
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
https://www.readbyqxmd.com/read/22773646/temporal-dynamics-and-decay-of-putatively-allochthonous-and-autochthonous-viral-genotypes-in-contrasting-freshwater-lakes
#17
Ian Hewson, Jorge G Barbosa, Julia M Brown, Ryan P Donelan, James B Eaglesham, Erin M Eggleston, Brenna A LaBarre
Aquatic viruses play important roles in the biogeochemistry and ecology of lacustrine ecosystems; however, their composition, dynamics, and interactions with viruses of terrestrial origin are less extensively studied. We used a viral shotgun metagenomic approach to elucidate candidate autochthonous (i.e., produced within the lake) and allochthonous (i.e., washed in from other habitats) viral genotypes for a comparative study of their dynamics in lake waters. Based on shotgun metagenomes prepared from catchment soil and freshwater samples from two contrasting lakes (Cayuga Lake and Fayetteville Green Lake), we selected two putatively autochthonous viral genotypes (phycodnaviruses likely infecting algae and cyanomyoviruses likely infecting picocyanobacteria) and two putatively allochthonous viral genotypes (geminiviruses likely infecting terrestrial plants and circoviruses infecting unknown hosts but common in soil libraries) for analysis by genotype-specific quantitative PCR (TaqMan) applied to DNAs from viruses in the viral size fraction of lake plankton, i...
September 2012: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/21183634/metagenomic-analysis-of-the-viral-communities-in-fermented-foods
#18
Eun-Jin Park, Kyoung-Ho Kim, Guy C J Abell, Min-Soo Kim, Seong Woon Roh, Jin-Woo Bae
Viruses are recognized as the most abundant biological components on Earth, and they regulate the structure of microbial communities in many environments. In soil and marine environments, microorganism-infecting phages are the most common type of virus. Although several types of bacteriophage have been isolated from fermented foods, little is known about the overall viral assemblages (viromes) of these environments. In this study, metagenomic analyses were performed on the uncultivated viral communities from three fermented foods, fermented shrimp, kimchi, and sauerkraut...
February 2011: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/20551686/tentative-characterization-of-new-environmental-giant-viruses-by-maldi-tof-mass-spectrometry
#19
Bernard La Scola, Angélique Campocasso, Rolande N'Dong, Ghislain Fournous, Lina Barrassi, Christophe Flaudrops, Didier Raoult
OBJECTIVE: Metagenomic studies have revealed that Acanthamoeba polyphaga Mimivirus relatives are common in the environment; however, only three Acanthamoeba-growing giant viruses have been isolated from hundreds of environmental samples. We attempted herein to isolate new Acanthamoeba-growing giant viruses from environmental samples. METHODS: We inoculated 105 environmental samples by our usual procedure but with the addition of selected antibiotics to inhibit bacterial overgrowth...
2010: Intervirology
https://www.readbyqxmd.com/read/20118353/prevalence-of-bacillus-anthracis-like-organisms-and-bacteriophages-in-the-intestinal-tract-of-the-earthworm-eisenia-fetida
#20
R Schuch, A J Pelzek, S Kan, V A Fischetti
Stable infection of Bacillus anthracis laboratory strains with environmental bacteriophages confers survival phenotypes in soil and earthworm intestinal niches (R. Schuch and V. A. Fischetti, PLoS One 4:e6532, 2009). Here, the natural occurrence of two such B. anthracis-infective bacteriophages, Wip1 and Wip4, was examined in the intestines of Eisenia fetida earthworms as part of a 6-year longitudinal study at a Pennsylvania forest site. The Wip1 tectivirus was initially dominant before being supplanted by the Wip4 siphovirus, which was then dominant for the next 3 years...
April 2010: Applied and Environmental Microbiology
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