Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw

By R. Mackelprang, Mark P. Waldrop, K. DeAngelis, M. David, Krystle L. Chavarría, S. Blazewicz, Edward M. Rubin, Janet K. Jansson. Nature, 2011

689 citations recorded by the source corpus.

Subfields: Atmospheric Science, Ecology, Environmental Chemistry

View Paper: https://www.semanticscholar.org/paper/f716259d764ab24ec37e390ae09c711177b5ba4f

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Citations in the corpus

Modeling Soil Processes: Review, Key Challenges, and New Perspectives (2016, background): “Many empirical studies have begun to make this link (Hawkes et al., 2005; Prosser and Nicol, 2008; Mackelprang et al., 2011), the large number of interacting biological and physical processes pose a key challenge for modeling soil biological activity (Blagodatsky and Smith, 2012).”
The Potential of Metagenomic Approaches for Understanding Soil Microbial Processes (2014, methodology): “A few studies have used the Illumina sequencing platform for generating shotgun metagenomes from soils (Fierer et al., 2012b; Mackelprang et al., 2011), and one has combined both sequencing platforms (Uroz et al.”
MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm (2014, background): “A number of approaches have been developed to bin assembled sequences from metagenomic data [2,4-9].”
Tackling soil diversity with the assembly of large, complex metagenomes (2014, background): “DNA sequencing has begun to reveal the enormous biological diversity and heterogeneity within these systems, making them difficult to study in situ (2, 4, 5).”
Permafrost Meta-Omics and Climate Change (2016, background): “It was also found that nitrogen fixation genes were highly abundant in frozen permafrost, but they decreased significantly after short-term thaw (Mackelprang et al. 2011).”
MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data (2016, methodology): “The authors of [6] compared 250 million DNA reads from permafrost samples against the KEGG database [7] (containing less than 10 million sequences) using BLASTX [8] and this reportedly took 800000 CPU hours at a supercomputer center [9].”
Extracellular enzymes in terrestrial, freshwater, and marine environments: perspectives on system variability and common research needs (2013, background): “Metagenomic profiling (Mackelprang et al. 2011; Teeling et al. 2012) and single-cell genomic sequencing (Martinez-Garcia et al. 2012) have provided insight into community and individual potential for enzyme production, but the extent to which—and conditions under which—this potential is expressed…”
Cross-biome metagenomic analyses of soil microbial communities and their functional attributes (2012, background): “Using shotgun metagenomic sequencing, the direct sequencing of the collective genomes found in a given environmental sample, researchers have gained important insight into the potential functions of microbial communities from individual soil types (16, 17) and soils that have been experimentally man”
Relic DNA is abundant in soil and obscures estimates of soil microbial diversity (2016, background): “These 37 methods have advanced our understanding of terrestrial microbiology in a myriad of 38 ways, by: i) revealing that thousands of unique microbial taxa can inhabit a single gram 39 of soil (1-3); ii) uncovering novel soil microbial diversity (4, 5); and iii) identifying putative 40 functions o”