An assessment of actinobacterial diversity in the marine environment

Abstract

The 16S rRNA gene sequence diversity within the Phylum Actinobacteria was assessed from four sources: PCR-generated V6 sequence tags derived from seawater samples, metagenomic data from the Global Ocean Sampling (GOS) expedition, marine-derived sequences maintained in the Ribosomal Database Project (RDP), and select cultured strains for which sequence data is not yet available in the RDP. This meta-analysis revealed remarkable levels of phylogenetic diversity and confirms the existence of major, deeply rooted, and as of yet uncharacterized lineages within the phylum. A dramatic incongruence among cultured strains and those detected using cultureindependent techniques was also revealed. Redundancy among the actinobacteria detected using culture-independent techniques suggests that greater sequence coverage or improved DNA extraction efficiencies may be required to detect the rare phylotypes that can be readily cultured from marine samples. Conversely, new strategies need to be developed for the cultivation of frequently observed but yet to be cultured marine actinobacteria.

Actinorhodopsin genes discovered in diverse freshwater habitats and among cultivated freshwater Actinobacteria

“…Here, signals from SSU rRNA genes are used from metagenomic samples and cultivated Actinobacteria to gain insight into the distribution of ActR genes among members of this phylum. Three SSU rRNA data sets were used for this exercise and the first comes from previous work by Jensen and Lauro (2008), who thoroughly analyzed actinobacterial SSU rRNA sequence diversity from assembled GOS metagenomic data (Rusch et al, 2007) and kindly provided us their data set from non-marine sites. The phylogenetic affinity, as determined by us, for each of the 121 partial and full-length sequences from this data set is summarized in Figure 5.…”

Genome Sequence of “Candidatus Aquiluna” sp. Strain IMCC13023, a Marine Member of the Actinobacteria Isolated from an Arctic Fjord

“…embers of the class Actinobacteria, such as the marine Actinobacteria clade (OM1 clade) (10), have been recognized as significant, if not major, contributors to marine microbial communities through culture-independent studies, including pyrosequencing of 16S rRNA genes, metagenome sequencing, and metaproteomics (5,7,8,13,14). "Candidatus Aquiluna rubra" in the family Microbacteriaceae of the Actinobacteria was initially proposed as an indigenous freshwater species based on the cultivation study from freshwater lakes (4).…”

Genetic Screening Strategy for Rapid Access to Polyether Ionophore Producers and Products in Actinomycetes

“…Given that the length of 16S rRNA gene sequences used for this purpose was 600 bp, the distribution of the distance setting 30 created sequence clusters that shared at least 95% identity. Each singleton and cluster was defined as an operational taxonomic unit (OTU) (23). One sequence from each OTU was used to construct a phylogenetic tree with related reference sequences as described above.…”