Metagenomic and Small-Subunit rRNA Analyses Reveal the Genetic Diversity of Bacteria, Archaea, Fungi, and Viruses in Soil
Noah Fierer,Noah Fierer,Mya Breitbart,James Nulton,Peter Salamon,Catherine A. Lozupone,Ryan T. Jones,Michael S. Robeson,Robert Edwards,Ben Felts,Steve Rayhawk,Rob Knight,Forest Rohwer,Robert B. Jackson +13 more
TLDR
In this first study to comprehensively survey viral communities using a metagenomic approach, it is found that soil viruses are taxonomically diverse and distinct from the communities of viruses found in other environments that have been surveyed using a similar approach.Abstract:
Recent studies have highlighted the surprising richness of soil bacterial communities; however, bacteria are not the only microorganisms found in soil. To our knowledge, no study has compared the diversities of the four major microbial taxa, i.e., bacteria, archaea, fungi, and viruses, from an individual soil sample. We used metagenomic and small-subunit RNA-based sequence analysis techniques to compare the estimated richness and evenness of these groups in prairie, desert, and rainforest soils. By grouping sequences at the 97% sequence similarity level (an operational taxonomic unit [OTU]), we found that the archaeal and fungal communities were consistently less even than the bacterial communities. Although total richness levels are difficult to estimate with a high degree of certainty, the estimated number of unique archaeal or fungal OTUs appears to rival or exceed the number of unique bacterial OTUs in each of the collected soils. In this first study to comprehensively survey viral communities using a metagenomic approach, we found that soil viruses are taxonomically diverse and distinct from the communities of viruses found in other environments that have been surveyed using a similar approach. Within each of the four microbial groups, we observed minimal taxonomic overlap between sites, suggesting that soil archaea, bacteria, fungi, and viruses are globally as well as locally diverse.read more
Citations
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The Metagenomics RAST Server: A Public Resource for the Automatic Phylogenetic and Functional Analysis of Metagenomes
Folker Meyer,Folker Meyer,Daniel Paarmann,Mark D'Souza,Robert Olson,Elizabeth M. Glass,Michael Kubal,Tobias Paczian,Alexis A. Rodriguez,Rick Stevens,Rick Stevens,Andreas Wilke,Jared Wilkening,Robert Edwards,Robert Edwards +14 more
TL;DR: The open-source metagenomics RAST service provides a new paradigm for the annotation and analysis of metagenomes that is stable, extensible, and freely available to all researchers.
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Next-Generation DNA Sequencing Methods
TL;DR: An astounding potential exists for next-generation DNA sequencing technologies to bring enormous change in genetic and biological research and to enhance the authors' fundamental biological knowledge.
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The impact of next-generation sequencing technology on genetics.
TL;DR: Next-generation sequencing technologies are surveyed and it is considered how they can provide a more complete picture of how the genome shapes the organism.
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Belowground biodiversity and ecosystem functioning
TL;DR: Recent progress in understanding belowground biodiversity and its role in determining the ecological and evolutionary responses of terrestrial ecosystems to current and future environmental change are reviewed.
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Using network analysis to explore co-occurrence patterns in soil microbial communities
TL;DR: The potential of exploring inter-taxa correlations to gain a more integrated understanding of microbial community structure and the ecological rules guiding community assembly is demonstrated.
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