Functional characterization of polysaccharide utilization loci in the marine <i>Bacteroidetes</i> ‘<i>Gramella forsetii</i>’ KT0803

Kabisch, Antje; Otto, Andreas; König, Sten; Becher, Dörte; Albrecht, Dirk; Schüler, Margarete; Teeling, Hanno; Amann, Rudolf; Schweder, Thomas

doi:10.1038/ismej.2014.4

Cited by 183 publications

(176 citation statements)

References 49 publications

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“…TBDR are important for microbial competition in the ocean, as cells with TBDR were observed to outcompete other microbes lacking TBDR in the presence of labile HMW-DOM released after a phytoplankton bloom in the North Sea (Teeling et al, 2012) and were also overexpressed in marine communities following HMW-DOM additions (McCarren et al, 2010). TBDR have been identified as important components of algal glycan utilization in Gramella forsetti, a widespread marine flavobacterium pivotal to remineralization of complex organic matter (Kabisch et al, 2014). However, it is unknown whether TBDR also assist in protein acquisition by marine microbes.…”

Section: Discussionmentioning

confidence: 99%

Diverse, uncultivated bacteria and archaea underlying the cycling of dissolved protein in the ocean

et al. 2016

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Dissolved organic nitrogen (DON) supports a significant amount of heterotrophic production in the ocean. Yet, to date, the identity and diversity of microbial groups that transform DON are not well understood. To better understand the organisms responsible for transforming high molecular weight (HMW)-DON in the upper ocean, isotopically labeled protein extract from Micromonas pusilla, a eukaryotic member of the resident phytoplankton community, was added as substrate to euphotic zone water from the central California Current system. Carbon and nitrogen remineralization rates from the added proteins ranged from 0.002 to 0.35 μmol C l − 1 per day and 0.03 to 0.27 nmol N l − 1 per day. DNA stable-isotope probing (DNA-SIP) coupled with high-throughput sequencing of 16S rRNA genes linked the activity of 77 uncultivated freeliving and particle-associated bacterial and archaeal taxa to the utilization of Micromonas protein extract. The high-throughput DNA-SIP method was sensitive in detecting isotopic assimilation by individual operational taxonomic units (OTUs), as substrate assimilation was observed after only 24 h. Many uncultivated free-living microbial taxa are newly implicated in the cycling of dissolved proteins affiliated with the Verrucomicrobia, Planctomycetes, Actinobacteria and Marine Group II (MGII) Euryarchaeota. In addition, a particle-associated community actively cycling DON was discovered, dominated by uncultivated organisms affiliated with MGII, Flavobacteria, Planctomycetes, Verrucomicrobia and Bdellovibrionaceae. The number of taxa assimilating protein correlated with genomic representation of TonB-dependent receptor (TBDR)-encoding genes, suggesting a possible role of TBDR in utilization of dissolved proteins by marine microbes. Our results significantly expand the known microbial diversity mediating the cycling of dissolved proteins in the ocean.

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Section: Discussionmentioning

confidence: 99%

Diverse, uncultivated bacteria and archaea underlying the cycling of dissolved protein in the ocean

et al. 2016

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“…Studies have shown that Bacteroidetes bacteria are common in marine environments (791), abundant in organic particle-rich coastal waters (108,113,130,611,791), responsive to algal and jellyfish blooms (272,537,756,(791)(792)(793), copiotrophic (252), and prone to leading a surface-associated life (12,17,246,272,574,607) supported by the extracellular degradation of complex biopolymers such as polysaccharides and proteins (194,791,(794)(795)(796)(797). These bacteria harbor a large number of genes for adhesive exopolysaccharides, adhesion proteins, proteases, peptidases, glycoside hydrolases, and lipases, and several genes for biopolymer degradation are coregulated with the genes for TonBdependent transport systems (794,795,(798)(799)(800)(801)(802).…”

Section: Marine Bacteroidetesmentioning

confidence: 99%

Microbial Surface Colonization and Biofilm Development in Marine Environments

Dang

Lovell

2016

Microbiol Mol Biol Rev

870

636

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SUMMARYBiotic and abiotic surfaces in marine waters are rapidly colonized by microorganisms. Surface colonization and subsequent biofilm formation and development provide numerous advantages to these organisms and support critical ecological and biogeochemical functions in the changing marine environment. Microbial surface association also contributes to deleterious effects such as biofouling, biocorrosion, and the persistence and transmission of harmful or pathogenic microorganisms and their genetic determinants. The processes and mechanisms of colonization as well as key players among the surface-associated microbiota have been studied for several decades. Accumulating evidence indicates that specific cell-surface, cell-cell, and interpopulation interactions shape the composition, structure, spatiotemporal dynamics, and functions of surface-associated microbial communities. Several key microbial processes and mechanisms, including (i) surface, population, and community sensing and signaling, (ii) intraspecies and interspecies communication and interaction, and (iii) the regulatory balance between cooperation and competition, have been identified as critical for the microbial surface association lifestyle. In this review, recent progress in the study of marine microbial surface colonization and biofilm development is synthesized and discussed. Major gaps in our knowledge remain. We pose questions for targeted investigation of surface-specific community-level microbial features, answers to which would advance our understanding of surface-associated microbial community ecology and the biogeochemical functions of these communities at levels from molecular mechanistic details through systems biological integration.

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“…Previous genome analysis has revealed that in Bacteroidetes, the polysaccharide degradation genes, including those encoding carbohydrate-active enzymes (CAZymes) and transporters, are frequently carried in large operons or regulon structures called PUL; these structures have been reported in many Bacteroidetes, from commensal bacteria of the human intestine to marine organisms (32,34,36,37). In short, PUL are clusters of coregulated genes or transcriptional units for polysaccharide degradation and related transportation.…”

mentioning

confidence: 99%

“…Detailed analyses of the genome structures of Algibacter species and their relationships with algal polysaccharides are rare. Also, in marine Bacteroidetes, many strains have been sequenced with draft or complete genomes, but only for a few strains in the family Flavobacteriaceae, including Zobellia galactanivorans (30,31), Gramella forsetii KT0803 (32,33), Formosa agariphila KMM 3901 T (34), and Polaribacter sp. strains…”

mentioning

confidence: 99%

Isolation and Complete Genome Sequence of Algibacter alginolytica sp. nov., a Novel Seaweed-Degrading Bacteroidetes Bacterium with Diverse Putative Polysaccharide Utilization Loci

Sun

Zhang

et al. 2016

Appl Environ Microbiol

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eThe members of the phylum Bacteroidetes are recognized as some of the most important specialists for the degradation of polysaccharides. However, in contrast to research on Bacteroidetes in the human gut, research on polysaccharide degradation by marine Bacteroidetes is still rare. The genus Algibacter belongs to the Flavobacteriaceae family of the Bacteroidetes, and most species in this genus are isolated from or near the habitat of algae, indicating a preference for the complex polysaccharides of algae. In this work, a novel brown-seaweed-degrading strain designated HZ22 was isolated from the surface of a brown seaweed (Laminaria japonica). On the basis of its physiological, chemotaxonomic, and genotypic characteristics, it is proposed that strain HZ22 represents a novel species in the genus Algibacter with the proposed name Algibacter alginolytica sp. nov. The genome of strain HZ22, the type strain of this species, harbors 3,371 coding sequences (CDSs) and 255 carbohydrate-active enzymes (CAZymes), including 104 glycoside hydrolases (GHs) and 18 polysaccharide lyases (PLs); this appears to be the highest proportion of CAZymes (ϳ7.5%) among the reported strains in the class Flavobacteria. Seventeen polysaccharide utilization loci (PUL) are predicted to be specific for marine polysaccharides, especially algal polysaccharides from red, green, and brown seaweeds. In particular, PUL N is predicted to be specific for alginate. Taking these findings together with the results of assays of crude alginate lyases, we prove that strain HZ22 T can completely degrade alginate. This work reveals that strain HZ22 T has good potential for the degradation of algal polysaccharides and that the structure and related mechanism of PUL in strain HZ22T are worth further research. Members of the phylum Bacteroidetes, formerly also known as the Cytophaga-Flavobacteria-Bacteroides cluster, constitute one of the major groups of marine heterotrophic bacterioplankton (1, 2). They have been found in various marine habitats, including coastal sediments (3), coastal waters (4, 5), hydrothermal vents (6, 7), and open ocean waters (8-10). In previous studies, marine Bacteroidetes have been reported as important contributors to the utilization of biopolymers such as polysaccharides and proteins (2,(11)(12)(13)(14). As a result, marine Bacteroidetes are assumed to play an important role in the degradation of algae. Marine phytoplankton have been estimated to be responsible for about 50% of global net primary production (15). Polysaccharides constitute a substantial fraction of the primary production from marine phytoplankton. Algae can be an important source of polysaccharides. Brown seaweeds, a traditional and plentiful mariculture product in East Asia, make up a large proportion of the total biomass of algae and synthesize a wide variety of compounds, such as alginate, fucoidan, laminarin, and mannitol (16). Among these compounds, alginate has been assumed to be a potential source for bioethanol production (17-19).The genus Algibacter belongs...

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Functional characterization of polysaccharide utilization loci in the marine Bacteroidetes ‘Gramella forsetii’ KT0803

Cited by 183 publications

References 49 publications

Diverse, uncultivated bacteria and archaea underlying the cycling of dissolved protein in the ocean

Diverse, uncultivated bacteria and archaea underlying the cycling of dissolved protein in the ocean

Microbial Surface Colonization and Biofilm Development in Marine Environments

Isolation and Complete Genome Sequence of Algibacter alginolytica sp. nov., a Novel Seaweed-Degrading Bacteroidetes Bacterium with Diverse Putative Polysaccharide Utilization Loci

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