PMC

(a–d), Microscopic fluorescence in situ hybridization (FISH) image of samples from the Mediterranean deep chlorophyll maximum (MedDCM). The micrographs show two pairs of identical microscopic fields, with samples stained with DAPI (left) and with the new lineage specific low GC Actinobacteria probe (LGC722) labeled with Cy3 (right). Yellow arrows (left) indicate autofluorescent Prochlorococcus, and white arrows (right) mark LGC722 signal also detected by DAPI. Bar: 10 μm (all four panels). (e), Abundance and bacterial structure size by flow cytometry. The size structure of the heterotrophic bacterioplankton population is shown. Size distribution of targeted Actinobacteria according to FISH measurements is shown in black. Note that the left tail of the size distribution is mostly due to instrumental noise and not due to bacterioplankton size.

(a), Worldwide distribution of 16S ribosomal rRNA of ‘Candidatus Actinomarina'. Several metagenomes and the Ribosomal Database Project (RDP) database were examined. Locations where the 16S rRNA gene of ‘Candidatus Actinomarina' was detected in the RDP database (%identity >98% and coverage >98% of complete gene) are shown in circles shaded according to the number of sequences (see key on the right). The number of reads detected in several metagenomes (GOS Open Ocean, Coastal, Coral Reef, Estuary, Warm Seep) are shown in percentages of total rRNA reads (%identity >98% and coverage 98% of metagenomic read) (see key on the right). Also shown (in white squares) are locations where no reads were detected. The world map shown here is a modified version of a freely available map made with Natural Earth at www.naturalearthdata.com. (b), Fragment recruitment. Metagenomic reads recruited (TBLASTX) by the ‘Candidatus Actinomarina' contigs in three metagenomes, the Mediterranean deep chlorophyll maximum (DCM), BATS and HOTS. (c), Depth profile. Percentage of metagenomic reads assigned to ‘Candidatus Actinomarina' genome in a depth profile of the HOTS and the BATS stations in comparison to Synechococcus.

(a), Linear representation of ‘Candidatus Actinomarina' contigs showing their overlaps. Estimates of the genome size based on different indicators are shown to the right with some reference small genome sizes. Two groups of contigs are highlighted in grey and are shown in greater detail in the panels below. (b), Multiple, highly related lineages. A group of contigs with overlaps indicating nucleotide identity (BLASTN, top) and translated protein identity (TBLASTX, below). A color scale is shown below. (c), Synteny amongst two rhodopsin containing contigs. The rhodopsin gene is shown in red. Overlaps are colored according to the color scale as shown (comparison performed with TBLASTX). (d), Marine Actinobacterial Clade Rhodopsins (MACrhodopsins). A maximum likelihood tree of all known types of rhodopsins is shown. The number of sequences in each clade of rhodopsins is indicated in brackets. 29 sequences from several Global Ocean Sampling (GOS) datasets were also identified using the novel sequences from the Mediterranean deep chlorophyll maximum and are part of the MACrhodopsin clade. Bootstrap values (shown as percentages) are indicated by circles (see key on bottom right).

(a), Comparison of marine low GC Actinobacterial contigs containing rRNA genes to scaffolds from the Global Ocean Sampling (GOS) dataset (using BLASTN). The oceanic habitat (C-Coastal, CRA-Coral Reef Atoll, O-Open Ocean, E-Estuary), sampling locations (NAEC: North American East Coast, GI-Galapagos Islands, ETP-Eastern Tropical Pacific, PA-Polynesia Archipelagos) and the GOS dataset identifier are shown next to each GOS scaffold. Numbers in brackets indicate additional identical sequences found at the same location. All ribosomal RNA genes are highlighted in color and sequence identity amongst the contigs is shown in shades of grey (see color scale). (b), 16S rRNA phylogeny. 16S rRNA gene sequences from the assembled contigs and GOS scaffolds in the context of the entire Actinobacteria phylum, with Firmicutes as the outgroup. Actinobacterial Sub-Classes are in bold uppercase and Orders in bold italics. Sub-orders are shown in different colors in the tree and labeled (key is shown on bottom right). Freshwater actinobacterial clades are additionally marked with an asterisk. ‘Ca. Microthrix parvicella', to which the Actinobacteria OM1 clade is related, is marked with a blue star. The novel branch with sequences attributed to sub-class ‘Candidatus Actinomarinidae' is shown in red. Bootstrap values (shown as percentages) for all major branches are shown in colored circles (see key bottom left).