Organic matter processing by microbial communities throughout the Atlantic water column as revealed by metaproteomics

Abstract

The phylogenetic composition of the heterotrophic microbial community is depth stratified in the oceanic water column down to abyssopelagic layers. In the layers below the euphotic zone, it has been suggested that heterotrophic microbes rely largely on solubilized particulate organic matter as a carbon and energy source rather than on dissolved organic matter. To decipher whether changes in the phylogenetic composition with depth are reflected in changes in the bacterial and archaeal transporter proteins, we generated an extensive metaproteomic and metagenomic dataset of microbial communities collected from 100- to 5,000-m depth in the Atlantic Ocean. By identifying which compounds of the organic matter pool are absorbed, transported, and incorporated into microbial cells, intriguing insights into organic matter transformation in the deep ocean emerged. On average, solute transporters accounted for 23% of identified protein sequences in the lower euphotic and ∼39% in the bathypelagic layer, indicating the central role of heterotrophy in the dark ocean. In the bathypelagic layer, substrate affinities of expressed transporters suggest that, in addition to amino acids, peptides and carbohydrates, carboxylic acids and compatible solutes may be essential substrates for the microbial community. Key players with highest expression of solute transporters were Alphaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria, accounting for 40%, 11%, and 10%, respectively, of relative protein abundances. The in situ expression of solute transporters indicates that the heterotrophic prokaryotic community is geared toward the utilization of similar organic compounds throughout the water column, with yet higher abundances of transporters targeting aromatic compounds in the bathypelagic realm.

Keywords: Atlantic Ocean; deep sea; metaproteomics; organic matter; transporter proteins.

Fig. 1.

Mascot and SEQUEST-HT search results were combined to create nonredundant lists of protein groups, and shared COGs as well as differences in transporter abundances between the samples are shown. (A) Venn diagram illustrating the number of COG families (red) shared between the 14 metaproteomes, grouped by the distinct water layers: EUPHotic (lower euphotic, 100 m), MESO (mesopelagic, 300–850 m), upper BATHY (bathypelagic, 1,475–1,973 m), and lower BATHY (2,750–4,050 m). Proteins not grouped into COGs are indicated in black letters. (B) Distribution and abundance of selected COG functional categories associated with transport functions and cell motility. COG categories: E, amino acid transport and metabolism; P, inorganic ion transport and metabolism; G, carbohydrate transport and metabolism; N, cell motility; Q, secondary metabolites biosynthesis, transport, and catabolism. Relative protein abundances are based on NAAF values.

Fig. 2.

Vertical distribution and relative abundance (NAAF) of ATP-binding cassette (ABC), tripartite ATP-independent (TRAP-T), tripartite tricarboxylate (TTT), and TonB-dependent (TBDT) transporters. The sample IDs for metaproteomes from the euphotic zone are indicated; the coordinates and the physical and chemical characteristics of the samples are given in Table S1.

Fig. 3.

Taxonomic distribution of Bacteria and Archaea assigned to transport-related membrane proteins (TMPs). Pie charts represent semiquantitative abundance estimates based on averaged NAAF values for all TMPs at the designated water layers (see color key).

Fig. 4.

Vertical expression profiles of selected transporters analyzed in a semiquantitative manner based on NAAF values. Transporter proteins were grouped by the predicted substrate specificity of the SBP. BCAAs, branched-chain amino acids.

Fig. 5.

Vertical expression profiles of transporter proteins of abundant taxa. Expression values were calculated in a semiquantitative manner and average abundances were plotted for selected members of the substrate active community residing in the (A) lower euphotic, (B) mesopelagic, and (C) upper and (D) lower bathypelagic water layers.