Abstract
Background The Roseobacter clade is a widespread, metabolically versatile, and easily cultured lineage of marine microbes. Furthermore, cultured isolates are generally considered to be representative of the naturally occurring diversity in the environment. Roseobacter is thus considered an ideal clade for exploring and understanding microbial function in a representative model system. Nevertheless, recent studies question whether cultured strains are truly representative of natural populations. Support for one of these studies was based on the potentially biased samples of a Global Ocean Sampling (GOS) expedition [1]. The marine metagenomic studies of the GOS expeditions initially focused on microbes collected from a single filter range (0.1um – 0.8um) and it has been previously suggested that this excludes many Roseobacters, thus biasing the dataset towards smaller cells.
Highlights
The Roseobacter clade is a widespread, metabolically versatile, and cultured lineage of marine microbes
We examined correlations between bacterial taxonomic diversity and the three size classes to understand the potential for diversity biases between filter ranges
The 16S rRNA gene sequences from these datasets were extracted using Metaxa and subsequently analyzed using MOTHUR, which provided fine-level resolution taxonomic assignments. This analysis reveals a potential bias as the ranges of Roseobacter subgroup diversity in this dataset varied between size classes
Summary
The Roseobacter clade is a widespread, metabolically versatile, and cultured lineage of marine microbes. The influence of sample biases on estimations of marine microbial diversity Caroline Rempe1*, Charles R Budinoff2, T Chad Effler2, Alison Buchan1,2 From 11th Annual UT-ORNL-KBRIN Bioinformatics Summit 2012 Louisville, KY, USA. Background The Roseobacter clade is a widespread, metabolically versatile, and cultured lineage of marine microbes.
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