Metatranscriptome analyses indicate resource partitioning between diatoms in the field

Abstract

Diverse communities of marine phytoplankton carry out half of global primary production. The vast diversity of the phytoplankton has long perplexed ecologists because these organisms coexist in an isotropic environment while competing for the same basic resources (e.g., inorganic nutrients). Differential niche partitioning of resources is one hypothesis to explain this "paradox of the plankton," but it is difficult to quantify and track variation in phytoplankton metabolism in situ. Here, we use quantitative metatranscriptome analyses to examine pathways of nitrogen (N) and phosphorus (P) metabolism in diatoms that cooccur regularly in an estuary on the east coast of the United States (Narragansett Bay). Expression of known N and P metabolic pathways varied between diatoms, indicating apparent differences in resource utilization capacity that may prevent direct competition. Nutrient amendment incubations skewed N/P ratios, elucidating nutrient-responsive patterns of expression and facilitating a quantitative comparison between diatoms. The resource-responsive (RR) gene sets deviated in composition from the metabolic profile of the organism, being enriched in genes associated with N and P metabolism. Expression of the RR gene set varied over time and differed significantly between diatoms, resulting in opposite transcriptional responses to the same environment. Apparent differences in metabolic capacity and the expression of that capacity in the environment suggest that diatom-specific resource partitioning was occurring in Narragansett Bay. This high-resolution approach highlights the molecular underpinnings of diatom resource utilization and how cooccurring diatoms adjust their cellular physiology to partition their niche space.

Keywords: diatom; metatranscriptomics; niche partitioning; nutrient physiology; phytoplankton.

Fig. 1.

Taxonomic classification of RNA-sequencing paired-end reads across the five field samples. Classification was determined by mapping to a database composed of all publicly available transcriptomes through the MMETSP as of March 17, 2014.

Fig. 2.

Quantitative metabolic fingerprint depicting the relative expression of KEGG modules for Skeletonema spp. and T. rotula in Narragansett Bay across the five sampling time points (S1–S5). Color indicates the proportion of total reads mapping to each KEGG module relative to all KEGG annotated reads.

Fig. 3.

Schematic cell model depicting the relative expression of KO gene families associated with N and P metabolic pathways for Skeletonema spp. and T. rotula in Narragansett Bay across the five sampling time points (S1–S5). Color indicates the proportion of total reads mapping to each KEGG module relative to all KEGG annotated reads.

Fig. 4.

Functional composition of the RR gene sets for T. rotula and Skeletonema spp. (A), relative expression in the incubation samples (B), and STD scores (C) for a known P-responsive gene, sodium-phosphate cotransporter, and two RR gene families. (A) RR gene sets were identified through cross-comparison of like-nutrient incubations (i.e., +N vs. −N and +P vs. −P), using ASC (fold change = 2, post-p > 0.95) (57). The relative functional categorization of the RR gene set for T. rotula and Skeletonema spp., based on KEGG ontology as assigned by the KEGG Automatic Annotation Server, is depicted at the module level relative to the portion unannotated with the KEGG. (B) Expression pattern in SGNCs of the genes from the associated gene cluster from T. rotula (T) and Skeletonema spp. (S) plotted in related incubations (i.e., RR1 shows expression from +P and −P incubations). The asterisk indicates significance between pair-wise comparisons (fold change = 2, post-p > 0.95) (57). (C) STD scores plotted across the five sample points showing STD_P for the P-significant genes and STD_N for the N-significant genes. Dashed horizontal lines at 0 and 1 indicate the +P or +N and −P or −N for corresponding significant genes.

Fig. 5.

Evolution of RR gene partitioning over time in Narragansett Bay for T. rotula and Skeletonema spp. (A) Stable gene normalized field signals for each gene identified as significantly (twofold change, post-p > 0.95) up-regulated in −P vs. +P for Skeletonema spp. (yellow) and T. rotula (orange) and in −N vs. +N for Skeletonema spp. (cyan) and T. rotula (dark blue) were proportionalized relative to the expression of those genes in nutrient incubations, yielding the STD_N and STD_P for each gene. These data are plotted for S1–S5. (B) Proportion of identified RR genes falling into the N/P > Redfield and N/P < Redfield quadrants for T. rotula (T) and Skeletonema spp. (S). FC, fold change.