Microbial Population Structures in the Deep Marine Biosphere

By J. Huber, D. M. Mark Welch, Hilary G. Morrison, Susan M. Huse, Phillip R. Neal, D. Butterfield, Mitchell L Sogin. Science, 2007

930 citations recorded by the source corpus.

Subfields: Ecology, Environmental Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/2c05bd7563eae3614d48204395a2f571de134746

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Citations in the corpus

Next-generation DNA sequencing methods. (2008, background): “These studies include previously sampled environments such as the ocean (2, 19, 42) and an acid mine site (13), but soil (14, 27) and coral reefs (54) also were studied by Roche/454 pyrosequencing.”
Grazing practices affect the soil microbial community composition in a Tibetan alpine meadow (2018, background): “These regions can provide sufficient phylogenetic affinity identification and high classification accuracies (Claesson et al., 2010; Huber et al., 2007; Pei et al., 2010; Sogin et al., 2011).”
Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers (2008, background): “(31) performs poorly relative to the other regions, as do the regions that overlap V6 such as R1114 (with 250-base reads) and F1099, reaching recovery levels below 10% on the gut datasets.”
Beyond the Calvin cycle: autotrophic carbon fixation in the ocean. (2011, background): “…in ecosystems where intensive mixing of hydrothermal fluid and seawater takes place, like the shallow subsurface, and indeed, Epsilonproteobacteria related to Sulfurovum and Sulfurimonas spp. are often found to dominate such ecosystems (Campbell et al. 2006, Huber et al. 2007, Hügler et al. 2010).”
Fast UniFrac: Facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data (2009, background): “For example, many recent pyrosequencing studies in a range of environments have used taxon-based methods to compare samples (Sogin et al ., 2006; Huber et al ., 2007; Roesch et al ., 2007), primarily because of these challenges.”
Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies (2011, background): “allocate vast sequencing resources to numerous samples [3].”
Microbial community structure and its functional implications (2009, background): “, and characterizing the rare ones with molecular tools typically requires a focused study, such as high-throughput tag sequencin”
Microbial community profiling for human microbiome projects: Tools, techniques, and challenges. (2009, methodology): “Several different barcoding strategies have been used with pyrosequencing (Binladen et al. 2007; Hoffmann et al. 2007; Huber et al. 2007; Parameswaran et al. 2007; Fierer et al. 2008; Hamady et al. 2008).”
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample (2010, methodology): “By using a variant of the barcoding strategy used for 454 (12 – 14) with the Illumina platform (Fig.”
Deciphering Diversity Indices for a Better Understanding of Microbial Communities. (2017, methodology): “The approach to use high-throughput next-generation sequencing in combination with taxonomic classification of 16S rRNA genes maximizes the bacterial species identification with high-resolution power [9-12].”
A Bioinformatician's Guide to Metagenomics (2008, methodology): “Pyrosequencing has recently been applied to PCR-amplified 16S rRNA genes, providing 100- or 200-bp 16S “pyrotags” to evaluate community composition (61, 63, 126).”
A Method for Studying Protistan Diversity Using Massively Parallel Sequencing of V9 Hypervariable Regions of Small-Subunit Ribosomal RNA Genes (2009, methodology): “…8 sample sites (16 total) were assigned a unique forward primer incorporating the 1380 or 1389 primer sequence, the 454 Life Science Adaptor A, and the distinct 5-base key to allow us to bioinformatically separate information from each sample after sequencing as described in Huber et al., 2007 [7].”
Use of Ichip for High-Throughput In Situ Cultivation of “Uncultivable” Microbial Species (2010, background): “The number of microbial species in nature is unknown but is likely large, with thousands of species present in a single gram of soil or aquatic sediment (10, 11, 26).”