Microbial diversity in the deep sea and the underexplored “rare biosphere”

By Mitchell L Sogin, Hilary G. Morrison, J. Huber, D. Welch, Susan M. Huse, Phillip R. Neal, J. Arrieta, G. Herndl. Proceedings of the National Academy of Sciences of the United States of America, 2006

3,775 citations recorded by the source corpus.

Subfields: Ecology, Environmental Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/5cdacc4d269df393d3472dc188e15d3dad166507

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Citations in the corpus

Microbial community gene expression in ocean surface waters (2008, result): “This finding is consistent with other large-scale metagenomic surveys that showed no sign of sequencing saturation for similar marine microbial communities (31, 32).”
Marine biodiversity and ecosystem function relationships: The potential for practical monitoring applications (2015, neutral): “…generation sequencing technologies applied to 16S rRNA genes have not only increased the current databases, but also allows the identi ﬁ cation of rare bacterial taxa for which ecological signi ﬁ cance is even more uncertain than that of the dominant taxa (Sogin et al., 2006; Gobet et al., 2012).”
Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies (2012, background): “In 2006, Roche’s 454 GS 20 pyrosequencing (5) became the first high-throughput sequencing technology to be successfully applied for large scale biodiversity analysis and was key to uncovering the ‘rare biosphere’ (6).”
The impact of next-generation sequencing technology on genetics. (2008, background): “Aside from the human body, metagenomic studies are ongoing in several important ecosystems, including global soil [27,28], deep mine [29] and the ocean [30, 31 ].”
Interactions between gut microbiota, host genetics and diet relevant to development of metabolic syndromes in mice (2010, methodology): “This suggests that phylotypes in the same phylogenetic cluster may share similar functions relevant to host phenotypes, and that the ‘rare biosphere’ is not negligible (Sogin et al., 2006).”
A DNA-Based Registry for All Animal Species: The Barcode Index Number (BIN) System (2013, methodology): “CROP uses an optimized Needleman-Wunsch [29] algorithm to perform pairwise alignments and the Quickdist [30] algorithm to generate distances.”
A High-Throughput DNA Sequence Aligner for Microbial Ecology Studies (2009, methodology): “60 bp long) have used MUSCLE to generate MSAs for up to 20,000 sequences [3,10,11].”
Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity (2014, background): “There have been two distinct approaches to considering the rare biosphere in microbial ecology: (i) deep sequencing to detect as many rare members as possible (6) and (ii) omission of the entire rare “tail” to clarify overarching community patterns, whether arbitrary (e.”
Strengths and Limitations of 16S rRNA Gene Amplicon Sequencing in Revealing Temporal Microbial Community Dynamics (2014, background): “better appreciation of extant biodiversity [5]; however, the 16S”
A Primer on Metagenomics (2010, neutral): “called rare biosphere [22,23].”