FGB1 and WSC3 are in planta-induced beta-glucan-binding fungal lectins with different functions

In the root endophyte Serendipita indica, several lectin-like members of the expanded multigene family of WSC proteins are transcriptionally induced in planta and are potentially involved in beta-glucan remodeling at the fungal cell wall. Using biochemical and cytological approaches we show that one of these lectins, SiWSC3 with three WSC domains, is an integral fungal cell wall component that binds to long-chain beta 1-3-glucan but has no affinity for shorter beta 1-3- or beta 1-6-linked glucose oligomers. Comparative analysis with the previously identified beta-glucan-binding lectin SiFGB1 demonstrated that whereas SiWSC3 does not require beta 1-6-linked glucose for efficient binding to branched beta 1-3-glucan, SiFGB1 does. In contrast to SiFGB1, the multivalent SiWSC3 lectin can efficiently agglutinate fungal cells and is additionally induced during fungus-fungus confrontation, suggesting different functions for these two beta-glucan-binding lectins. Our results highlight the importance of the beta-glucan cell wall component in plant-fungus interactions and the potential of beta-glucan-binding lectins as specific detection tools for fungi in vivo

Ion-exchange purification and structural characterization of five sulfated fucoidans from brown algae

Fucoidans are a diverse class of sulfated polysaccharides integral to the cell wall of brown algae, and due to their various bioactivities, they are potential drugs. Standardized work with fucoidans is required for structure-function studies, but remains challenging since available fucoidan preparations are often contaminated with other algal compounds. Additionally, fucoidans are structurally diverse depending on species and season, urging the need for standardized purification protocols. Here, we use ion-exchange chromatography to purify different fucoidans and found a high structural diversity between fucoidans. Ion-exchange chromatography efficiently removes the polysaccharides alginate and laminarin and other contaminants such as proteins and phlorotannins across a broad range of fucoidans from major brown algal orders including Ectocarpales, Laminariales and Fucales. By monomer composition, linkage analysis and NMR characterization, we identified galacturonic acid, glucuronic acid and O-acetylation as new structural features of certain fucoidans and provided a novel structure of fucoidan from Durvillaea potatorum with alpha-1,3-linked fucose backbone and beta-1,6 and beta-1,3 galactose branches. This study emphasizes the use of standardized ion-exchange chromatography to obtain defined fucoidans for subsequent molecular studies

Enigmatic persistence of dissolved organic matter in the ocean

Marine dissolved organic matter (DOM) contains more carbon than the combined stocks of Earth’s biota. Organisms in the ocean continuously release a myriad of molecules that become food for microheterotrophs, but, for unknown reasons, a residual fraction persists as DOM for millennia. In this Perspective, we discuss and compare two concepts that could explain this persistence. The long-standing ‘intrinsic recalcitrance’ paradigm attributes DOM stability to inherent molecular properties. In the ‘emergent recalcitrance’ concept, DOM is continuously transformed by marine microheterotrophs, with recalcitrance emerging on an ecosystems level. Both concepts are consistent with observations in the modern ocean, but they imply very different responses of the DOM pool to climate-related changes. To better understand DOM persistence, we propose a new overarching research strategy — the ecology of molecules — that integrates the concepts of intrinsic and emergent recalcitrance with the ecological and environmental context

Glycoside hydrolase from the GH76 family indicates that marine Salegentibacter sp. Hel_I_6 consumes alpha-mannan from fungi

Microbial glycan degradation is essential to global carbon cycling. The marine bacterium Salegentibacter sp. Hel_I_6 (Bacteroidota) isolated from seawater off Helgoland island (North Sea) contains an α-mannan inducible gene cluster with a GH76 family endo-α-1,6-mannanase (ShGH76). This cluster is related to genetic loci employed by human gut bacteria to digest fungal α-mannan. Metagenomes from the Hel_I_6 isolation site revealed increasing GH76 gene frequencies in free-living bacteria during microalgae blooms, suggesting degradation of α-1,6-mannans from fungi. Recombinant ShGH76 protein activity assays with yeast α-mannan and synthetic oligomannans showed endo-α-1,6-mannanase activity. Resolved structures of apo-ShGH76 (2.0 Å) and of mutants co-crystalized with fungal mannan-mimicking α-1,6-mannotetrose (1.90 Å) and α-1,6-mannotriose (1.47 Å) retained the canonical (α/α)6 fold, despite low identities with sequences of known GH76 structures (GH76s from gut bacteria: <27%). The apo-form active site differed from those known from gut bacteria, and co-crystallizations revealed a kinked oligomannan conformation. Co-crystallizations also revealed precise molecular-scale interactions of ShGH76 with fungal mannan-mimicking oligomannans, indicating adaptation to this particular type of substrate. Our data hence suggest presence of yet unknown fungal α-1,6-mannans in marine ecosystems, in particular during microalgal blooms

Single cell fluorescence imaging of glycan uptake by intestinal bacteria

Microbes in the intestines of mammals degrade dietary glycans for energy and growth. The pathways required for polysaccharide utilization are functionally diverse; moreover, they are unequally dispersed between bacterial genomes. Hence, assigning metabolic phenotypes to genotypes remains a challenge in microbiome research. Here we demonstrate that glycan uptake in gut bacteria can be visualized with fluorescent glycan conjugates (FGCs) using epifluorescence microscopy. Yeast α-mannan and rhamnogalacturonan-II, two structurally distinct glycans from the cell walls of yeast and plants, respectively, were fluorescently labeled and fed to Bacteroides thetaiotaomicron VPI-5482. Wild-type cells rapidly consumed the FGCs and became fluorescent; whereas, strains that had deleted pathways for glycan degradation and transport were non-fluorescent. Uptake of FGCs, therefore, is direct evidence of genetic function and provides a direct method to assess specific glycan metabolism in intestinal bacteria at the single cell level

Low-Level Resource Partitioning Supports Coexistence Among Functionally Redundant Bacteria During Successional Dynamics

Members of microbial communities can substantially overlap in substrate use. However, what enables functionally redundant microorganisms to coassemble or even stably coexist remains poorly understood. Here, we show that during unstable successional dynamics on complex, natural organic matter, functionally redundant bacteria can coexist by partitioning low-concentration substrates even though they compete for one simple, dominant substrate. We allowed ocean microbial communities to self-assemble on leachates of the brown seaweed Fucus vesiculosus and then analyzed the competition among 10 taxonomically diverse isolates representing two distinct stages of the succession. All, but two isolates, exhibited an average of 90% ± 6% pairwise overlap in resource use, and functional redundancy of isolates from the same assembly stage was higher than that from between assembly stages, leading us to construct a simpler four-isolate community with two isolates from each of the early and late stages. We found that, although the short-term dynamics of the four-isolate communities in F. vesiculosus leachate was dependent on initial isolate ratios, in the long term, the four isolates stably coexist in F. vesiculosus leachate, albeit with some strains at low abundance. We therefore explored the potential for nonredundant substrate use by genomic content analysis and RNA expression patterns. This analysis revealed that the four isolates mainly differed in peripheral metabolic pathways, such as the ability to degrade pyrimidine, leucine, and tyrosine, as well as aromatic substrates. These results highlight the importance of fine-scale differences in metabolic strategies for supporting the frequently observed coexistence of large numbers of rare organisms in natural microbiomes

Lattice instabilities of cubic NiTi from first principles

The phonon dispersion relation of NiTi in the simple cubic B2 structure is computed using first-principles density-functional perturbation theory with pseudopotentials and a plane-wave basis set. Lattice instabilities are observed to occur across nearly the entire Brillouin zone, excluding three interpenetrating tubes of stability along the (001) directions and small spheres of stability centered at R. The strongest instability is that of the doubly degenerate M5' mode. The atomic displacements of one of the eigenvectors of this mode generate a good approximation to the observed B19' ground-state structure.Comment: 11 pages, 3 figure

A vast icefish breeding colony discovered in the Antarctic

A breeding colony of notothenioid icefish (Neopagetopsis ionah, Nybelin 1947) of globally unprecedented extent has been discovered in the southern Weddell Sea, Antarctica. The colony was estimated to cover at least similar to 240 km(2) of the eastern flank of the Filchner Trough, comprised of fish nests at a density of 0.26 nests per square meter, representing an estimated total of -60 million active nests and associated fish biomass of >60,000 tonnes. The majority of nests were each occupied by 1 adult fish guarding 1,735 eggs (+/- 433 SD). Bottom water temperatures measured across the nesting colony were up to 2 degrees C warmer than the surrounding bottom waters, indicating a spatial correlation between the modified Warm Deep Water (mWDW) upflow onto the Weddell Shelf and the active nesting area. Historical and concurrently collected seal movement data indicate that this concentrated fish biomass may be utilized by predators such as Weddell seals (Leptonychotes weddellii, Lesson 1826). Numerous degraded fish carcasses within and near the nesting colony suggest that, in death as well as life, these fish provide input for local food webs and influence local biogeochemical processing. To our knowledge, the area surveyed harbors the most spatially expansive continuous fish breeding colony discovered to date globally at any depth, as well as an exceptionally high Antarctic seafloor biomass. This discovery provides support for the establishment of a regional marine protected area in the Southern Ocean under the Convention on the Conservation of Antarctic Marine Living Resources (CCAMLR) umbrella