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Journal: PeerJ Preprints

Abbreviation

Publisher

PeerJ

Journal Volumes

ISSN

2167-9843

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2014 - 20152
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Publications 1 - 2 of 2
  • A standardized, extensible framework for optimizing classification improves marker-gene taxonomic assignments
    Item type: Working Paper
    Bokulich, Nicholas; Rideout, Jai Ram; Kopylova, Evguenia; et al. (2015)
    PeerJ Preprints
    Background: Taxonomic classification of marker-gene (i.e., amplicon) sequences represents an important step for molecular identification of microorganisms. Results: We present three advances in our ability to assign and interpret taxonomic classifications of short marker gene sequences: two new methods for taxonomy assignment, which reduce runtime up to two-fold and achieve high-precision genus-level assignments; an evaluation of classification methods that highlights differences in performance with different marker genes and at different levels of taxonomic resolution; and an extensible framework for evaluating and optimizing new classification methods, which we hope will serve as a model for standardized and reproducible bioinformatics methods evaluations. Conclusions: Our new methods are accessible in QIIME 1.9.0, and our evaluation framework will support ongoing optimization of classification methods to complement rapidly evolving short-amplicon sequencing and bioinformatics technologies. Static versions of all of the analysis notebooks generated with this framework, which contain all code and analysis results, can be viewed at http://bit.ly/srta-012 .
  • Soil carbon research and global environmental challenges
    Item type: Working Paper
    Hartemink, Alfred E.; Lal, Rattan; Gerzabek, Martin H.; et al. (2014)
    PeerJ Preprints
    The role of soil organic carbon (SOC) in maintaining soil conditions and its resulting services is well established. Currently, over 1,000 articles per year are being published in peer-reviewed journals, and increasing at about 10% per year. It was not until the 1980s when the relation between soils and climate change was noted, and it was realized that soils play a key role as a sink and source of greenhouse gases (GHGs) ( Bouwman 1990, Scharpenseel, Ayoub and Schomaker 1990, Jenny 1980). A large number of research projects have been initiated globally in which soil C is a key component, and there have been some excellent reviews ( Lal 2004, Stockmann et al. 2013, Melillo et al. 2011). Yet, there is a lack of focus in soil C research in relation to current environmental challenges. Here we recommend research priorities to advance the knowledge base and use of soil C in relation to global human and environmental challenges: food and fiber production, water scarcity and purification, energy production, climate change, biodiversity, recycling waste, and environmental degradation. We have listed the priorities under three themes: (i) Soil C in space and time, (ii) Soil C properties and processes, and (ii) Soil C depletion and management.
Publications 1 - 2 of 2