The 'Neglected' Soil Virome - Potential Role and Impact.

@article{Pratama2018TheS,
  title={The 'Neglected' Soil Virome - Potential Role and Impact.},
  author={Akbar Adjie Pratama and Jan Dirk van Elsas},
  journal={Trends in microbiology},
  year={2018},
  volume={26 8},
  pages={
          649-662
        }
}
Bacteriophages are among the most abundant and diverse biological units in the biosphere. They have contributed to our understanding of the central dogma of biology and have been instrumental in the evolutionary success of bacterial pathogens. In contrast to our current understanding of marine viral communities, the soil virome and its function in terrestrial ecosystems has remained relatively understudied. Here, we examine, in a comparative fashion, the knowledge gathered from studies… 
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References

SHOWING 1-10 OF 94 REFERENCES
Dark Matter of the Biosphere: the Amazing World of Bacteriophage Diversity
  • G. Hatfull
  • Medicine, Biology
    Journal of Virology
  • 2015
TLDR
This view reveals substantial diversity even among phages known to infect a common host strain, but the relationships are complex, with mosaic genomic architectures generated by illegitimate recombination over a long period of evolutionary history.
Environmental drivers of viral community composition in Antarctic soils identified by viromics
TLDR
The pattern of viral community structure with higher levels of diversity at lower altitude and pH, and co-occurring viral families, suggests that these cold desert soil viruses interact with each other, the host, and the environment in an intricate manner, playing a potentially crucial role in maintaining host diversity and functioning of the microbial ecosystem in the extreme environments of Antarctic soil.
Origins of Highly Mosaic Mycobacteriophage Genomes
TLDR
The genomic sequences of ten newly isolated mycobacteriophages suggest that the bacteriophage population as a whole is amazingly diverse and may represent the largest unexplored reservoir of sequence information in the biosphere.
Phages across the biosphere: contrasts of viruses in soil and aquatic environments.
TLDR
This review briefly summarizes recent investigations of viral abundance and diversity in soil environments.
Marine viruses: truth or dare.
  • M. Breitbart
  • Biology, Medicine
    Annual review of marine science
  • 2012
TLDR
This review is structured as a scientific "truth or dare," revealing several well-established "truths" about marine viruses and presenting a few "dares" for the research community to undertake in future studies.
Using Signature Genes as Tools To Assess Environmental Viral Ecology and Diversity
TLDR
Signature genes have been used in combination with PCR-based fingerprinting and/or sequencing strategies to investigate spatial, temporal, and seasonal variations and diversity in a wide range of habitats.
The enigmatic archaeal virosphere
TLDR
This Review summarizes recent advances in understanding of the genomic and morphological diversity of archaeal viruses and the molecular biology of their life cycles and virus–host interactions, including interactions witharchaeal CRISPR–Cas systems.
Rising to the challenge: accelerated pace of discovery transforms marine virology
TLDR
Recent technological advances in marine virology including the use of near-quantitative, reproducible metagenomics for large-scale investigation of viral communities and the emergence of gene-based viral ecology are discussed.
Horizontal gene transfer in the phytosphere.
Here, the ecological aspects of gene transfer processes between bacteria in the phytosphere are examined in the context of emerging evidence for the dominant role that horizontal gene transfer (HGT)…
Metagenomic analysis of the viral community in Namib Desert hypoliths.
TLDR
The composition of the viral hypolith fraction containing many Bacillus-infecting phages was not completely consistent with Namib hypolith phylotypic surveys of the bacterial hosts, in which the cyanobacterial genus Chroococcidiopsis was found to be dominant.
...
1
2
3
4
5
...