Abstract
Gene clusters rich in carbohydrate-active enzymes within Flavobacteriia genera provide a competitiveness for their hosts to degrade diatom-derived polysaccharides. One such widely distributed polysaccharide is glucuronomannan, a main cell wall component of diatoms. A conserved gene cluster putatively degrading glucuronomannan was found previously among various flavobacterial taxa in marine metagenomes. Here, we aimed to visualize two glycoside hydrolase family 92 genes coding for α-mannosidases with fluorescently-labeled polynucleotide probes using direct-geneFISH. Reliable in situ localization of single-copy genes was achieved with an efficiency up to 74% not only in the flavobacterial strains Polaribacter Hel1_33_49 and Formosa Hel1_33_131 but also in planktonic samples from the North Sea. In combination with high-resolution microscopy, direct-geneFISH gave visual evidence of the contrasting lifestyles of closely related Polaribacter species in those samples and allowed for the determination of gene distribution among attached and free-living cells. We also detected highly similar GH92 genes in yet unidentified taxa by broadening probe specificities, enabling a visualization of the functional trait in subpopulations across the borders of species and genera. Such a quantitative insight into the niche separation of flavobacterial taxa complements our understanding of the ecology of polysaccharide-degrading bacteria beyond omics-based techniques on a single-cell level.
Highlights
Glucuronomannan is a universal polysaccharide found in diatom cell walls
A preceding analysis of genomic data obtained from sampling campaigns in the German Bight in 2010–2012 indicated that the gene sequences of susCDlike tandem pairs retrieved from GH92- and sulfatase-rich PULs, clustered together based on their amino acid sequence similarity [10]
A more detailed analysis revealed that these PULs were taxonomically linked to representative strains and metagenome-assembled genome (MAG) of the genera Formosa and Polaribacter [10], and to MAGs affiliated to Aurantivirga and Algibacter (Fig. 1, Supplementary Fig. 1)
Summary
Glucuronomannan is a universal polysaccharide found in diatom cell walls. Since diatoms are a major polysaccharide source and contribute substantially to the marine food web by attributing to 40% of primary production [5,6,7], it can be assumed that glucuronomannan is widely distributed wherever diatoms are found. Marine bacteria are adapted to its degradation and, especially Bacteroidetes, can digest substrates rich in sulphated αmannose using complementary carbohydrate active enzymes (CAZymes), such as glycoside hydrolases (GHs) of family 92 [8]. The GH92 family codes for exo-acting α-mannosidases and far, catalytic activity has been detected on α-1,2-, α-1,3-, α-1,4- and α1,6-linked mannose [9]. A co-evolution along with diverse cell wall components of algae seems plausible and would explain the many GH92 variants. Extensive analysis of metagenome and metaproteome data retrieved from bacterioplankton seawater samples revealed conserved GH92-rich polysaccharide utilization loci (PULs) that contain sulfatases and cluster for their SusC-like
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