Diel Rhythms of Marine Picoplanktonic Communities Assessed by Comparative Metaproteomics

Abstract

Background Diel cycle is of enormous biological importance in that it imposes temporal structure on ecosystem productivity. In the world oceans, microorganisms form complex communities that carry out about half of photosynthesis and the bulk of life-sustaining nutrient cycling. Within these natural microbial assemblages, photoautotrophs, such as Cyanobacteria , display diel rhythmicity in gene expression. To what extent autotrophs and heterotrophs are impacted by light and dark oscillations and how this collectively influences community structure and functionality remains poorly documented. In this study, we compared eight day/night metaproteome profiles of Cyanobacteria and both free-living and attached bacterial fractions from picoplanktonic communities sampled over two consecutive days from the surface north-west Mediterranean Sea. Results Our results showed similar taxonomic structure in both free-living and particle-attached bacteria, dominated by Alphaproteobacteria and Gammaproteobacteria . Temporal rhythmicity in protein expression was observed in both Synechococcales and Rhodobacterales in light-dependent processes such as photosynthesis or UV-stress response. Other biological processes, such as phosphorus or amino acid metabolisms, were also found to cycle in phototrophs. In contrast, proteins from the ubiquitous Pelagibacterales remained stable independently of the day/night oscillations. Conclusion This work integrated for the first time diel comparative metaproteomics on both free-living and particle attached bacterial fractions in coastal oligotrophic environment. Our findings demonstrated a taxa-specific response to diel cycle with a more controlled protein regulation for phototrophs. This study provided additional evidences that timekeeping mechanisms might be widespread among bacteria, broadening our knowledge on diel microbial assemblage dynamics.

Clarifying the murk: unveiling bacterial dynamics in response to crude oil pollution, Corexit-dispersant, and natural sunlight in the Gulf of Mexico

“…Until now, only one metaproteomics study has successfully described a list of proteins involved in the response to oil (Bargiela et al, 2015). Since then, environmental metaproteomics has been greatly improved thanks to development of high resolution mass spectrometry, protein search database construction, and bioinformatic tools to accurately annotate and link the taxonomy and functions of identified proteins, limiting the well-known protein inference issue (Matallana-Surget et al, 2018;Geŕon et al, 2019;Saito et al, 2019;Werner et al, 2019).…”

“…For 16S amplicon analysis, a total of 500 mL to 2 L of water from each mesocosm were filtered through a 0.22 µM Millipore Durapore GVWP filter then placed in cryo-tubes with sterile 0.1 mm silica and 0.5 mm glass beads and sucrose buffer (20 mM EDTA, 400 mM NaCl, 0.75 M sucrose, 50 mM Tris-HCl pH 9.0). For metaproteomics analysis, large volumes of seawater are required, as detailed previously (Matallana-Surget et al, 2018;Geŕon et al, 2019). Consequently, the complete volume of each bag (~60 to 68L) was filtered to guarantee a high-quality proteomics dataset.…”

“…Peptide samples were analyzed on an ultra-high-performance liquid chromatography-high-resolution tandem mass spectroscopy (UHPLC-HRMS/MS) system, including a Eksigent NanoLC 400 and AB SCIEX TripleTOF 5600. Two micrograms of peptides were analyzed using acquisition parameters previously reported (Geŕon et al, 2019), and MS/MS spectra were acquired with the instrument operating in data-dependent acquisition (DDA), with micro injection (75 min LC separation) modes. The metaproteomic raw data are available in the iProx public platform (Project ID: PXD048022).…”

“…The OTU tables obtained by the 16S rRNA reads were used to create the protein search databases for the analysis of the 8 metaproteomes. Those fasta files were generated with mPies v 0.9, our recently in house developed mPies program is freely available at https://github.com/johanneswerner/mPies/ (Werner et al, 2019), following the same TAX-DB workflow, as previously described in our recent methodological publications (Geŕon et al, 2019;Werner et al, 2019). Taxonomic classification based on the 16S amplicon sequencing for this metaproteomics workflow is only needed as a guide for the phylum, class, or order level, as previously described (Geŕon et al, 2019;Werner et al, 2019).…”

“…Identified proteins were further annotated using mPies as previously described in our former papers (Geŕon et al, 2019;Werner et al, 2019). For taxonomic and functional annotation, mPies used Diamond to align each identified protein sequences against the non-redundant NCBI DB and the UniProt DB (Swiss-Prot), respectively, and retrieved up to 20 best hits based on alignment score (>80).…”