Changing expression patterns of TonB-dependent transporters suggest shifts in polysaccharide consumption over the course of a spring phytoplankton bloom

T Ben Francis,Hanno Teeling,Andreas Sichert,Bernhard M Fuchs,Thomas Schweder,Rudolf I Amann,Dörte Becher,Jan-Hendrik Hehemann,Thomas Sura,Daniel Bartosik,Stephanie Markert

doi:10.1038/s41396-021-00928-8

Abstract

Algal blooms produce large quantities of organic matter that is subsequently remineralised by bacterial heterotrophs. Polysaccharide is a primary component of algal biomass. It has been hypothesised that individual bacterial heterotrophic niches during algal blooms are in part determined by the available polysaccharide substrates present. Measurement of the expression of TonB-dependent transporters, often specific for polysaccharide uptake, might serve as a proxy for assessing bacterial polysaccharide consumption over time. To investigate this, we present here high-resolution metaproteomic and metagenomic datasets from bacterioplankton of the 2016 spring phytoplankton bloom at Helgoland island in the southern North Sea, and expression profiles of TonB-dependent transporters during the bloom, which demonstrate the importance of both the Gammaproteobacteria and the Bacteroidetes as degraders of algal polysaccharide. TonB-dependent transporters were the most highly expressed protein class, split approximately evenly between the Gammaproteobacteria and Bacteroidetes, and totalling on average 16.7% of all detected proteins during the bloom. About 93% of these were predicted to take up organic matter, and for about 12% of the TonB-dependent transporters, we predicted a specific target polysaccharide class. Most significantly, we observed a change in substrate specificities of the expressed transporters over time, which was not reflected in the corresponding metagenomic data. From this, we conclude that algal cell wall-related compounds containing fucose, mannose, and xylose were mostly utilised in later bloom stages, whereas glucose-based algal and bacterial storage molecules including laminarin, glycogen, and starch were used throughout. Quantification of transporters could therefore be key for understanding marine carbon cycling.

Highlights

Seasonal phytoplankton blooms are known to be responsible for a substantial proportion of total annual atmospheric carbon fixation [1,2,3]
After assembly and binning of these to generate metagenome assembled genomes (MAGs), we identified 1261 expressed TonB-dependent transporter (TBDT) during the bloom belonging to many species of Bacteroidetes and Gammaproteobacteria, the majority of which could only be assigned a putative non-specific dissolved organic matter (DOM) uptake function
Abundances based on read frequencies were not unusual compared to earlier years, consistent with the recurrence of bacterial clades previously reported for the region around Helgoland, where taxon abundance of Bacteroidetes and Gammaproteobacteria in particular has been observed to be similar from year to year [5, 8, 10]

Summary

Introduction

Seasonal phytoplankton blooms are known to be responsible for a substantial proportion of total annual atmospheric carbon fixation [1,2,3]. Many studies have found characteristic prokaryotic clades, primarily members of the Bacteroidetes, Gammaproteobacteria, and Alphaproteobacteria, transiently achieve high abundance while consuming and remineralising algal biomass [2, 4,5,6,7]. The Bacteroidetes are often considered specialists at degrading high molecular weight (HMW) substrates such as protein and polysaccharide [12,13,14,15,16,17]. Their genomes encode homologues of the starch utilisation system (Sus), the SusC-like TonB-dependent transporter (TBDT), and the SusD-like accessory substrate-. SusCD-like transporter complexes can provide a substrate-specific ‘selfish’ uptake system for poly- and oligosaccharides (e.g. [20]) that permits sequestration of organic matter in the periplasm (e.g. [21]) for subsequent breakdown into monosaccharides

Methods

Results

Conclusion