Dataset Information

Diel-Regulated Transcriptional Cascades of Microbial Eukaryotes in the North Pacific Subtropical Gyre

ABSTRACT: Open-ocean surface waters host a diverse community of single-celled eukaryotic plankton (protists) consisting of phototrophs, heterotrophs, and mixotrophs. The productivity and biomass of these organisms oscillate over diel cycles, and yet the underlying transcriptional processes are known for few members of the community. Here, we examined a 4-day diel time series of transcriptional abundance profiles for the protist community (0.2–100 μm in cell size) in the North Pacific Subtropical Gyre near Station ALOHA. De novo assembly of poly-A+ selected metatranscriptomes yielded over 30 million contigs with taxonomic and functional annotations assigned to 54 and 25% of translated contigs, respectively. The completeness of the resulting environmental eukaryotic taxonomic bins was assessed, and 48 genera were further evaluated for diel patterns in transcript abundances. These environmental transcriptome bins maintained reproducible temporal partitioning of total gene family abundances, with haptophyte and ochrophyte genera generally showing the greatest diel partitioning of their transcriptomes. The haptophyte Phaeocystis demonstrated the highest proportion of transcript diel periodicity, while most other protists had intermediate levels of periodicity regardless of their trophic status. Dinoflagellates, except for the parasitoid genus Amoebophrya, exhibit the fewest diel oscillations of transcript abundances. Diel-regulated gene families were enriched in key metabolic pathways; photosynthesis, carbon fixation, and fatty acid biosynthesis gene families had peak times concentrated around dawn, while gene families involved in protein turnover (proteasome and protein processing) are most active during the high intensity daylight hours. TCA cycle, oxidative phosphorylation and fatty acid degradation predominantly peaked near dusk. We identified temporal pathway enrichments unique to certain taxa, including assimilatory sulfate reduction at dawn in dictyophytes and signaling pathways at early evening in haptophytes, pointing to possible taxon-specific channels of carbon and nutrients through the microbial community. These results illustrate the synchrony of transcriptional regulation to the diel cycle and how the protist community of the North Pacific Subtropical Gyre structures their transcriptomes to guide the daily flux of matter and energy through the gyre ecosystem.

SUBMITTER: Groussman R

PROVIDER: S-EPMC8511712 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Similar Datasets

Project description:Sinking particles mediate the transport of carbon and energy to the deep-sea, yet the specific microbes associated with sedimenting particles in the ocean's interior remain largely uncharacterized. In this study, we used particle interceptor traps (PITs) to assess the nature of particle-associated microbial communities collected at a variety of depths in the North Pacific Subtropical Gyre. Comparative metagenomics was used to assess differences in microbial taxa and functional gene repertoires in PITs containing a preservative (poisoned traps) compared to preservative-free traps where growth was allowed to continue in situ (live traps). Live trap microbial communities shared taxonomic and functional similarities with bacteria previously reported to be enriched in dissolved organic matter (DOM) microcosms (e.g., Alteromonas and Methylophaga), in addition to other particle and eukaryote-associated bacteria (e.g., Flavobacteriales and Pseudoalteromonas). Poisoned trap microbial assemblages were enriched in Vibrio and Campylobacterales likely associated with eukaryotic surfaces and intestinal tracts as symbionts, pathogens, or saprophytes. The functional gene content of microbial assemblages in poisoned traps included a variety of genes involved in virulence, anaerobic metabolism, attachment to chitinaceaous surfaces, and chitin degradation. The presence of chitinaceaous surfaces was also accompanied by the co-existence of bacteria which encoded the capacity to attach to, transport and metabolize chitin and its derivatives. Distinctly different microbial assemblages predominated in live traps, which were largely represented by copiotrophs and eukaryote-associated bacterial communities. Predominant sediment trap-assocaited eukaryotic phyla included Dinoflagellata, Metazoa (mostly copepods), Protalveolata, Retaria, and Stramenopiles. These data indicate the central role of eukaryotic taxa in structuring sinking particle microbial assemblages, as well as the rapid responses of indigenous microbial species in the degradation of marine particulate organic matter (POM) in situ in the ocean's interior.

Project description:The summertime North Pacific subtropical gyre has widespread phytoplankton blooms between Hawaii and the subtropical front (?30°N) that appear as chlorophyll (chl) increases in satellite ocean color data. Nitrogen-fixing diatom symbioses (diatom-diazotroph associations: DDAs) often increase 10(2)-10(3) fold in these blooms and contribute to elevated export flux. In 2008 and 2009, two cruises targeted satellite chlorophyll blooms to examine DDA species abundance, chlorophyll concentration, biogenic silica concentration, and hydrography. Generalized observations that DDA blooms occur when the mixed layer depth is < 70 m are supported, but there is no consistent relationship between mixed layer depth, bloom intensity, or composition; regional blooms between 22-34°N occur within a broader temperature range (21-26°C) than previously reported. In both years, the Hemiaulus-Richelia and Rhizosolenia-Richelia DDAs increased 10(2)-10(3) over background concentrations within satellite-defined bloom features. The two years share a common trend of Hemiaulus dominance of the DDAs and substantial increases in the >10 µm chl a fraction (?40-90+% of total chl a). Integrated diatom abundance varied 10-fold over <10 km. Biogenic silica concentration tracked diatom abundance, was dominated by the >10 µm size fraction, and increased up to 5-fold in the blooms. The two years differed in the magnitude of the surface chl a increase (2009>2008), the abundance of pennate diatoms within the bloom (2009>2008), and the substantially greater mixed layer depth in 2009. Only the 2009 bloom had sufficient chl a in the >10 µm fraction to produce the observed ocean color chl increase. Blooms had high spatial variability; ocean color images likely average over numerous small events over time and space scales that exceed the individual event scale. Summertime DDA export flux noted at the Hawaii time-series Sta. ALOHA is probably a generalized feature of the eastern N. Pacific north to the subtropical front.

Dataset Information

Diel-Regulated Transcriptional Cascades of Microbial Eukaryotes in the North Pacific Subtropical Gyre

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets