Genomes of planktonic Acidimicrobiales: widening horizons for marine Actinobacteria by metagenomics

Abstract

The genomes of four novel marine Actinobacteria have been assembled from large metagenomic data sets derived from the Mediterranean deep chlorophyll maximum (DCM). These are the first marine representatives belonging to the order Acidimicrobiales and only the second group of planktonic marine Actinobacteria to be described. Their streamlined genomes and photoheterotrophic lifestyle suggest that they are planktonic, free-living microbes. A novel rhodopsin clade, acidirhodopsins, related to freshwater actinorhodopsins, was found in these organisms. Their genomes suggest a capacity to assimilate C2 compounds, some using the glyoxylate bypass and others with the ethylmalonyl-coenzyme A (CoA) pathway. They are also able to derive energy from dimethylsulfopropionate (DMSP), sulfonate, and carbon monoxide oxidation, all commonly available in the marine habitat. These organisms appear to be prevalent in the deep photic zone at or around the DCM. The presence of sister clades to the marine Acidimicrobiales in freshwater aquatic habitats provides a new example of marine-freshwater transitions with potential evolutionary insights.

Importance: Despite several studies showing the importance and abundance of planktonic Actinobacteria in the marine habitat, a representative genome was only recently described. In order to expand the genomic repertoire of marine Actinobacteria, we describe here the first Acidimicrobidae genomes of marine origin and provide insights about their ecology. They display metabolic versatility in the acquisition of carbon and appear capable of utilizing diverse sources of energy. One of the genomes harbors a new kind of rhodopsin related to the actinorhodopsin clade of freshwater origin that is widespread in the oceans. Our data also support their preference to inhabit the deep chlorophyll maximum and the deep photic zone. This work contributes to the perception of marine actinobacterial groups as important players in the marine environment with distinct and important contributions to nutrient cycling in the oceans.

FIG 1

Phylogeny of the MedAcidi group of marine Actinobacteria. (a) Maximum-likelihood phylogeny of 16S rRNA of the assembled MedAcidi genomes and related sequences from clone libraries. Sequences from the order Actinomycetales are used to root the tree. The 16S rRNAs from the MedAcidi groups are highlighted by colored boxes. (b) Maximum-likelihood phylogeny using a concatenation of 106 conserved proteins: the assembled genomes of the MedAcidi group are highlighted by colored boxes. Bootstrap values (%) are indicated at each node. Reference organisms shown in both trees are connected by dashed lines.

FIG 2

Rhodopsin phylogeny. A maximum-likelihood tree of all known types of rhodopsins is shown. Sequences belonging to the new clade of acidirhodopsins are highlighted. Sequences originating from marine and freshwater habitats are indicated by colored squares. Bootstrap values (%) are shown on the nodes.

FIG 3

Metabolic overview of the marine actinobacterium MedAcidi-G1. Major pathways are indicated in boxes. DMSP, dimethylsulfopropionate; MMPA, methylmercaptopropionate; THF, tetrahydrofolate; DHAP, dihydroxyacetone phosphate.

FIG 4

Metabolic overview of the marine actinobacterium MedAcidi-G3. Major pathways are indicated in boxes. Some reactions that have not been found in this genome but are found in the other MedAcidi genomes are shown in grey. DMSP, dimethylsulfopropionate; MMPA, methylmercaptopropionate; THF, tetrahydrofolate; ggt, gamma-glutamyl transpeptidase; DHAP, dihydroxyacetone phosphate.

FIG 5

Metagenomic fragment recruitment. (a) Relative abundances of genomes of marine Acidimicrobiales and “Ca. Actinomarinales” across two data sets from the Mediterranean deep chlorophyll maximum, Hawaii Ocean Time-series (HOTS), Bermuda Atlantic Time-series (BATS), and the Red Sea. Data are expressed as RPKG (reads recruited per Kb of genome per Gb of metagenome). (b) Recruitment plots of two representative Acidimicrobiales genomes (MedAcidi-G1 and MedAcidi-G3) and one “Ca. Actinomarinales” genome (“Ca. Actinomarina minuta”) compared to two metagenomes (MedDCM-2012 and MedDCM-2013) are shown. The dashed horizontal line indicates 95% nucleotide sequence identity. (c) Relative abundances of 16S rRNA sequences of marine Acidimicrobiales and “Ca. Actinomarinales” across the same data sets. All data sets that are from a deep chlorophyll maximum are marked with a green circle. Data are expressed as hits/Gb of metagenome.