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

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.

Functional Insights into the Kelp Microbiome from Metagenome-Assembled Genomes

“…ATP-binding cassette (ABC)-type transporters for amino acids and sugars indicate active transport into bacterial cells ( 33 ). While bacteria in the surrounding seawater also consume kelp-derived DOM ( 26 , 27 ), the microbiome of the giant kelp M. pyrifera was enriched in transport protein genes relative to metagenomes from the surrounding seawater ( 21 ), suggesting the importance of DOM assimilation by kelp surface-associated bacteria. While we cannot infer from genomic content alone that these DOM transport proteins are being expressed, they are good indicators of potential kelp-derived DOM use by members of the kelp microbiome.…”

“…Kelp release ~16% of carbon fixed through photosynthesis into the surrounding seawater as dissolved organic carbon (DOC) ( 24 , 25 ). Bacteria in the surrounding seawater consume kelp-derived DOC ( 26 , 27 ), and cultured bacterial isolates from the kelp surface degrade polysaccharides such as alginate, fucoidan, laminarin, and mannitol ( 28 , 29 ). However, we know little about the metabolic capabilities of kelp-associated bacterial groups in nature.…”

Consuming fresh macroalgae induces specific catabolic pathways, stress reactions and Type IX secretion in marine flavobacterial pioneer degraders

“…were regularly reported on macroalgae [ 87 ], although their role in macroalgae degradation remains unclear. Members of the genus Tenacibaculum were identified as active incorporators of carbon from alginate within natural seawater communities [ 88 ]. The number of CAZymes is highly variable within the genus (between 34 and 102 for the 8 Tenacibaculum genomes available in the CAZy database) but is largely below the 221 CAZymes found in Z. galactanivorans Dsij T [ 20 ].…”

Sargassum Differentially Shapes the Microbiota Composition and Diversity at Coastal Tide Sites and Inland Storage Sites on Caribbean Islands

“…The second most abundant family was the Flavobacteriaceae (Bacteroidetes). Interestingly, utilization of macromolecules such as polysaccharides is a common feature of many members of this family (McBride, 2014;Thomas et al, 2021), and more generally of the Bacteroidetes (McKee et al, 2021). In fact, several genera of the Flavobacteriaceae that were found to possess conserved polysaccharide utilization loci, as defined by Kruger et al (2019), were abundant at tide sites, with the NS5_marine_group, Polaribacter spp., Formosa spp., Dokdonia spp., Gramella spp., Cellulophaga spp., Lutibacter spp., Winogradskyella spp., Cryomorphaceae, Crocinitomicaceae, and Cyclobacteriaceae together making up to 12.9 and 4.3% of the relative abundance in TS-sw and TS-sarg samples, respectively.…”