Isotopic tracing reveals single-cell assimilation of a macroalgal polysaccharide by a few marine Flavobacteria and Gammaproteobacteria

François Thomas,Ting-Di Wu,Cédric Leroux,Gwenn Tanguy,Nolwen Le Duff,Aurélie Cébron,Erwan Legeay,Jean-Luc Guerquin-Kern,Stéphane Uroz,Pascal Riera

doi:10.1038/s41396-021-00987-x

Abstract

Algal polysaccharides constitute a diverse and abundant reservoir of organic matter for marine heterotrophic bacteria, central to the oceanic carbon cycle. We investigated the uptake of alginate, a major brown macroalgal polysaccharide, by microbial communities from kelp-dominated coastal habitats. Congruent with cell growth and rapid substrate utilization, alginate amendments induced a decrease in bacterial diversity and a marked compositional shift towards copiotrophic bacteria. We traced 13C derived from alginate into specific bacterial incorporators and quantified the uptake activity at the single-cell level, using halogen in situ hybridization coupled to nanoscale secondary ion mass spectrometry (HISH-SIMS) and DNA stable isotope probing (DNA-SIP). Cell-specific alginate uptake was observed for Gammaproteobacteria and Flavobacteriales, with carbon assimilation rates ranging from 0.14 to 27.50 fg C µm−3 h−1. DNA-SIP revealed that only a few initially rare Flavobacteriaceae and Alteromonadales taxa incorporated 13C from alginate into their biomass, accounting for most of the carbon assimilation based on bulk isotopic measurements. Functional screening of metagenomic libraries gave insights into the genes of alginolytic Alteromonadales active in situ. These results highlight the high degree of niche specialization in heterotrophic communities and help constraining the quantitative role of polysaccharide-degrading bacteria in coastal ecosystems.

Highlights

By recycling a large proportion of the available organic matter, heterotrophic bacteria control the oceanic fluxes of carbon and energy [1]
Two-days incubation strongly decreased the richness (Chao1 index) and diversity (Shannon and Simpson index) of the seawater bacterial community compared to its initial state (Figure S1A)
The community was more diverse in alginate-amended microcosms compared to unamended controls (Welch’s t-test, p = 0.002 and p = 0.021 for Shannon and Simpson, respectively), one of the microcosms amended with 13C-enriched alginate was an outlier with low diversity

Summary

Introduction

By recycling a large proportion of the available organic matter, heterotrophic bacteria control the oceanic fluxes of carbon and energy [1]. The dissolved fraction is the largest reservoir of oceanic organic matter, with a global estimate of 662 Pg dissolved organic carbon (DOC) [2, 3]. Brown macroalgae of the order Laminariales, collectively known as kelps, can release up to 25% of the fixed carbon as exudates, contributing ~1.3 kg C m−2 y−1 to the DOC pool [7, 8]. This significantly impacts coastal ecosystems, where kelp forests locally increase DOC concentrations and sustain distinct microbial communities [9].

Methods

Results

Conclusion