Polysaccharide utilization loci of North Sea <i>Flavobacteriia</i> as basis for using SusC/D-protein expression for predicting major phytoplankton glycans

Kappelmann, Lennart; Krüger, Karen; Hehemann, Jan Hendrik; Harder, Jens; Markert, Stephanie; Unfried, Frank; Becher, Dörte; Shapiro, Nicole; Schweder, Thomas; Amann, Rudolf; Teeling, Hanno

doi:10.1038/s41396-018-0242-6

Cited by 149 publications

(234 citation statements)

References 76 publications

(110 reference statements)

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“…We combined 16S rRNA gene analyses, metagenomics, and metaproteomics. In this comprehensive and integrated approach, the individual methods and their respective advantages complemented each other, as previously demonstrated in several marine ecology studies (15)(16)(17). This procedure provided a detailed picture of taxonomy, function, and protein abundance in our samples.…”

Section: Actino-bacteriamentioning

confidence: 62%

“…Knowledge on dominant genera, as obtained from 16S rRNA analyses, allowed us to assign metaproteomics-derived protein functions specifically to individual genera. This approach has been successfully applied previously (15)(16)(17). Assignment of protein functions to taxonomic groups is crucial when analyzing metabolic processes in microbial communities, since thousands of taxa contribute proteins with overlapping functions in an environmental sample.…”

Section: Discussionmentioning

confidence: 99%

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Individual Physiological Adaptations Enable Selected Bacterial Taxa To Prevail during Long-Term Incubations

Herlemann

Markert

Meeske

et al. 2019

Appl Environ Microbiol

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Enclosure experiments are frequently used to investigate the impact of changing environmental conditions on microbial assemblages. Yet, how the incubation itself challenges complex bacterial communities is thus far unknown. In this study, metaproteomic profiling, 16S rRNA gene analyses, and cell counts were combined to evaluate bacterial communities derived from marine, mesohaline, and oligohaline conditions after long-term batch incubations. Early in the experiment, the three bacterial communities were highly diverse and differed significantly in their compositions. Manipulation of the enclosures with terrigenous dissolved organic carbon resulted in notable differences compared to the control enclosures at this early phase of the experiment. However, after 55 days, bacterial communities in the manipulated and the control enclosures under marine and mesohaline conditions were all dominated by gammaproteobacterium Spongiibacter. In the oligohaline enclosures, actinobacterial cluster I of the hgc group (hgc-I) remained abundant in the late phase of the incubation. Metaproteome analyses suggested that the ability to use outer membrane-based internal energy stores, in addition to the previously described grazing resistance, may enable the gammaproteobacterium Spongiibacter to prevail in long-time incubations. Under oligohaline conditions, the utilization of external recalcitrant carbon appeared to be more important (hgc-I). Enclosure experiments with complex natural microbial communities are important tools to investigate the effects of manipulations. However, species-specific properties, such as individual carbon storage strategies, can cause manipulation-independent effects and need to be considered when interpreting results from enclosures. IMPORTANCE In microbial ecology, enclosure studies are often used to investigate the effect of single environmental factors on complex bacterial communities. However, in addition to the manipulation, unintended effects ("bottle effect") may occur due to the enclosure itself. In this study, we analyzed the bacterial communities that originated from three different salinities of the Baltic Sea, comparing their compositions and physiological activities both at the early stage and after 55 days of incubation. Our results suggested that internal carbon storage strategies impact the success of certain bacterial species, independent of the experimental manipulation. Thus, while enclosure experiments remain valid tools in environmental research, microbial community composition shifts must be critically followed. This investigation of the metaproteome during long-term batch enclosures expanded our current understanding of the so-called "bottle effect," which is well known to occur during enclosure experiments.

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Section: Actino-bacteriamentioning

confidence: 62%

Section: Discussionmentioning

confidence: 99%

Individual Physiological Adaptations Enable Selected Bacterial Taxa To Prevail during Long-Term Incubations

Herlemann

Markert

Meeske

et al. 2019

Appl Environ Microbiol

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“…GH92 family genes were also detected in bacterioplankton metagenome datasets during four consecutive years of North Sea spring blooms (Teeling et al ., ), as well as in the open Atlantic (Bennke et al ., ). Recently we could show that homologues of SusC‐ and SusD‐like proteins from predicted bacterial β‐mannan PULs are expressed during North Sea spring phytoplankton blooms (Kappelmann et al ., ). All of these results suggest substantial levels of substrate‐driven selection of marine bacteria by both α‐ and β‐mannose‐rich algal polysaccharides.…”

Section: Introductionmentioning

confidence: 97%

“…CAZymes in Flavobacteriia are often encoded in polysaccharide utilization loci, or PULs (Sonnenburg et al, 2010). These PULs usually contain tandem genes of SusD-like surface glycan-binding proteins and TonB-dependent receptors (TBDR) as well as glycan-specific CAZymes (e.g., Kappelmann et al, 2018). Accessory genes, such as transcriptional regulators, transporter genes and sulfatases, are also often encoded by PULs.…”

Section: Introductionmentioning

confidence: 99%

Alpha‐ and beta‐mannan utilization by marine Bacteroidetes

Chen

Robb

Unfried

et al. 2018

Environmental Microbiology

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Summary Marine microscopic algae carry out about half of the global carbon dioxide fixation into organic matter. They provide organic substrates for marine microbes such as members of the Bacteroidetes that degrade algal polysaccharides using carbohydrate‐active enzymes (CAZymes). In Bacteroidetes genomes CAZyme encoding genes are mostly grouped in distinct regions termed polysaccharide utilization loci (PULs). While some studies have shown involvement of PULs in the degradation of algal polysaccharides, the specific substrates are for the most part still unknown. We investigated four marine Bacteroidetes isolated from the southern North Sea that harbour putative mannan‐specific PULs. These PULs are similarly organized as PULs in human gut Bacteroides that digest α‐ and β‐mannans from yeasts and plants respectively. Using proteomics and defined growth experiments with polysaccharides as sole carbon sources we could show that the investigated marine Bacteroidetes express the predicted functional proteins required for α‐ and β‐mannan degradation. Our data suggest that algal mannans play an as yet unknown important role in the marine carbon cycle, and that biochemical principles established for gut or terrestrial microbes also apply to marine bacteria, even though their PULs are evolutionarily distant.

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“…Revisiting the PTS classification. In the last few years, a huge mass of omics data has accumulated (81), and microfluidic approaches have been developed to rapidly identify the substrates targeted by (meta)genomic loci (82). Meanwhile, an increasing number of tridimensional transporter structures have been solved (83), and the panel of biochemical methods for transporter characterization has been extended, as described in the present paper.…”

Section: Discussionmentioning

confidence: 99%

Harvesting of Prebiotic Fructooligosaccharides by Nonbeneficial Human Gut Bacteria

Wang

Tauzin

Laville

et al. 2020

mSphere

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Prebiotic oligosaccharides, such as fructooligosaccharides, are increasingly being used to modulate the composition and activity of the gut microbiota. However, carbohydrate utilization analyses and metagenomic studies recently revealed the ability of deleterious and uncultured human gut bacterial species to metabolize these functional foods. Moreover, because of the difficulties of functionally profiling transmembrane proteins, only a few prebiotic transporters have been biochemically characterized to date, while carbohydrate binding and transport are the first and thus crucial steps in their metabolization. Here, we describe the molecular mechanism of a phosphotransferase system, highlighted as a dietary and pathology biomarker in the human gut microbiome. This transporter is encoded by a metagenomic locus that is highly conserved in several human gut Firmicutes, including Dorea species. We developed a generic strategy to deeply analyze, in vitro and in cellulo, the specificity and functionality of recombinant transporters in Escherichia coli, combining carbohydrate utilization locus and host genome engineering and quantification of the binding, transport, and growth rates with analysis of phosphorylated carbohydrates by mass spectrometry. We demonstrated that the Dorea fructooligosaccharide transporter is specific for kestose, whether for binding, transport, or phosphorylation. This constitutes the biochemical proof of effective phosphorylation of glycosides with a degree of polymerization of more than 2, extending the known functional diversity of phosphotransferase systems. Based on these new findings, we revisited the classification of these carbohydrate transporters.IMPORTANCE Prebiotics are increasingly used as food supplements, especially in infant formulas, to modify the functioning and composition of the microbiota. However, little is currently known about the mechanisms of prebiotic recognition and transport by gut bacteria, while these steps are crucial in their metabolism. In this study, we established a new strategy to profile the specificity of oligosaccharide transporters, combining microbiomics, genetic locus and strain engineering, and state-of-the art metabolomics. We revisited the transporter classification database and proposed a new way to classify these membrane proteins based on their structural and mechanistic similarities. Based on these developments, we identified and characterized, at the molecular level, a fructooligosaccharide transporting phosphotransferase system, which constitutes a biomarker of diet and gut pathology. The deciphering of this prebiotic metabolization mechanism by a nonbeneficial bacterium highlights the controversial use of prebiotics, especially in the context of chronic gut diseases.

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Polysaccharide utilization loci of North Sea Flavobacteriia as basis for using SusC/D-protein expression for predicting major phytoplankton glycans

Cited by 149 publications

References 76 publications

Individual Physiological Adaptations Enable Selected Bacterial Taxa To Prevail during Long-Term Incubations

Individual Physiological Adaptations Enable Selected Bacterial Taxa To Prevail during Long-Term Incubations

Alpha‐ and beta‐mannan utilization by marine Bacteroidetes

Harvesting of Prebiotic Fructooligosaccharides by Nonbeneficial Human Gut Bacteria

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