Subproject B1 – Comparative (meta-)genomics of marine polysaccharide-degrading bacteria with emphasis on CAZyme and PUL analyses in Bacteroidetes

Responsible: Hanno Teeling, Jens Harder & Rudolf Amann, Max Planck Institute for Marine Microbiology, Bremen

Blooms of marine microalgae can trigger successive blooms of distinct clades of planktonic bacteria. We studied such a succession in great detail in spring 2009 in the North Sea by an integrated -OMICS approach and found that abundant bacterioplankton clades exhibited notably different substrate spectra (Teeling et al., 2012). The succession of clades thus coincided with a succession of degradation functions. This was most pronounced with respect to gene frequencies and expressions of carbohydrate-active enzymes (CAZymes) in Bacteroidetes, indicating a pronounced niche partitioning with respect to the degradation of algal polysaccharides. Since polysaccharide-degrading planktonic bacteria specialize on different polysaccharide subsets they must act together to concertedly degrade algal polysaccharides during blooms events. However, so far the most relevant involved CAZymes are not known and possible CAZyme co-dependencies are largely unexplored. It is also not yet known, whether the succession of CAZymes that we observed follows a predictable pattern during such blooms, and if so, to which extent this pattern depends on the occurrence of specific algal polysaccharides. In Bacteroidetes the genes that encode the machinery for degradation and uptake of distinct polysaccharides are often organized in distinct loci (PULs = polysaccharide utilization loci), but so far neither the diversity of PULs is known nor have the ecologically most relevant PULs been identified, and only few PULs could thus far be linked to particular polysaccharide substrates.

 

Subproject B1 aims at addressing these questions by investigations of bacterial CAZymes and PULs of isolates of Bacteroidetes that are abundant during phytoplankton blooms, as well as of corresponding data from taxonomically classified metagenomes with associated metaproteome and metatranscriptome data. In brief, the research program comprises (i) assessment of the PUL universe during North Sea spring blooms via sequence analysis of a large number of isolates and series of taxonomically classified metagenomes and subsequent identification of the most relevant CAZymes and PULs using gene frequency and expression data, (ii) identification of representative isolates for detailed studies, and (iii) comparative CAZyme and PUL repertoire analysis in order to elucidate distinct ecophysiological glyan-niches of North Sea Bacteroidetes. These objectives involve (a) assistance of subproject Z in -OMICS analyses and integration of data from all subprojects, (b) joint proteogenomic analyses of selected isolates in collaboration with A1, (c) identification of the most relevant but as yet uncharacterized CAZymes and accessory proteins for downstream processing in A2, A3, and EN, including assistance of A3 and EN in the bioinformatic classification of proteins for polysaccharide binding and uptake and PULs for functional analysis.

 

Consensus pattern of a laminarin PUL, containing the typical SusCD gene pair and GH16, GH17 and GH30 family genes. This consensus pattern was derived from laminarin PULs in Cellulophaga sp. Hel1_12, Nonlabens sp. Hel1_56, Sediminibacter sp. Hel1_10, Polaribacter sp. He1_88, and Flavobactericeae bacterium sp. MAR2010_118.