Combined pigment and metatranscriptomic analysis reveals highly synchronized diel patterns of phenotypic light response across domains in the open oligotrophic ocean

Abstract

Sunlight is the most important environmental control on diel fluctuations in phytoplankton activity, and understanding diel microbial processes is essential to the study of oceanic biogeochemical cycles. Yet, little is known about the in situ temporal dynamics of phytoplankton metabolic activities and their coordination across different populations. We investigated diel orchestration of phytoplankton activity in photosynthesis, photoacclimation, and photoprotection by analyzing pigment and quinone distributions in combination with metatranscriptomes in surface waters of the North Pacific Subtropical Gyre (NPSG). We found diel cycles in pigment abundances resulting from the balance of their synthesis and consumption. These dynamics suggest that night represents a metabolic recovery phase, refilling cellular pigment stores, while photosystems are remodeled towards photoprotection during daytime. Transcript levels of genes involved in photosynthesis and pigment metabolism had synchronized diel expression patterns among all taxa, reflecting the driving force light imparts upon photosynthetic organisms in the ocean, while other environmental factors drive niche differentiation. For instance, observed decoupling of diel oscillations in transcripts and related pigments indicates that pigment abundances are modulated by environmental factors extending beyond gene expression/regulation reinforcing the need to combine metatranscriptomics with proteomics and metabolomics to fully understand the timing of these critical processes in situ.

Fig. 1. Schematic representation of the structure of photosystem II in photosynthetic membranes.

The relative locations of the major pigments and quinones as well as the pathway of electrons through these molecules is shown.

Fig. 2. Diel oscillations of pigments and pigment-related transcripts.

a Molecular structure of investigated pigments and respiratory quinones associated with the photosystem. b Time-of-day average of fold change relative to 18:00 h (local time) of chloro- and carotenoid pigments, quinones, as well as transcripts associated with the metabolism of the pigment and quinone molecules. Error bars represent the standard deviation of averaged values for each time of day (n ≥ 6). Molecular structures and pigment and quinone data are colored according to compound group. If colors for transcripts match those of pigments or quinones, transcripts are related to the metabolism of the respective molecule.

Fig. 3. Relationship between periodic pigment-associated gene expression in phytoplankton transcripts and actual pigment abundances.

a Peak times of expression of all transcripts assigned to KEGG pathways associated with pigment metabolism (triangles) and pigment molecule abundances (circles). Purple symbols denote transcripts or pigment molecules identified as significantly periodic (24-h period), whereas gray symbols denote peak times without a significant diel component in peak expression or pigment abundance, respectively. b Spearman’s rank correlation matrix of the different pigment and quinone classes (blue text) and aggregated genes within the KEGG pathways photosynthesis (PS), carotenoid biosynthesis (CaBiosyn), chlorophyll and porphyrin metabolism (ChlPhyMet), photosynthesis - antenna proteins (PSA), plastoquinol biosynthesis (Plql), ubiquinone and other terpenoid-quinone biosynthesis (Ubiq) separated into prokaryotes (Prok) and eukaryotes (Euk). Circle size and color is related to correlation value. Asterisks denote correlation significance (***p < 0.001).

Fig. 4. Conceptualized temporal separation of phytoplankton pigment, plastoquinone and transcript abundances during the dark–light cycle in surface waters (15 m) at station ALOHA.

The timing was set based on Fig. 2 with the center of the polygon indicating the approximate peak time. In addition, the particulate organic carbon (POC) and photosynthetically available radiation (PAR) profiles averaged for one day/night cycle are shown. Surface PAR data were obtained from the HOT program database (http://hahana.soest.hawaii.edu/hoelegacy/hoelegacy.html), POC data from White et al. [105] and TAG (triacylglycerols & diacylglycerol acyltransferase) data from Becker et al. [19].