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Genome analysis of Chitinivibrio alkaliphilus gen. nov., sp. nov., a novel extremely haloalkaliphilic anaerobic chitinolytic bacterium from the candidate phylum Termite Group 3

Sorokin, Dimitry Y ; Gumerov, Vadim M ; Rakitin, Andrey L ; Beletsky, Alexey V ; Damsté, J. S. Sinninghe ; Muyzer, Gerard ; Mardanov, Andrey V ; Ravin, Nikolai V

Environmental microbiology, 2014-06, Vol.16 (6), p.1549-1565 [Periódico revisado por pares]

Oxford: Blackwell Science

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  • Título:
    Genome analysis of Chitinivibrio alkaliphilus gen. nov., sp. nov., a novel extremely haloalkaliphilic anaerobic chitinolytic bacterium from the candidate phylum Termite Group 3
  • Autor: Sorokin, Dimitry Y ; Gumerov, Vadim M ; Rakitin, Andrey L ; Beletsky, Alexey V ; Damsté, J. S. Sinninghe ; Muyzer, Gerard ; Mardanov, Andrey V ; Ravin, Nikolai V
  • Assuntos: Adenosine triphosphatase ; adenosinetriphosphatase ; Anaerobiosis ; Animals ; Bacteria ; Base Sequence ; chitin ; Chitin - metabolism ; fermentation ; Fibrobacteres - classification ; Fibrobacteres - cytology ; Fibrobacteres - genetics ; genes ; Genome, Bacterial ; Genomes ; Hydrogen-Ion Concentration ; Isoptera ; Isoptera - microbiology ; Molecular Typing ; Phylogenetics ; Phylogeny ; proteome ; ribosomal proteins ; ribosomal RNA ; RNA, Ribosomal, 16S - genetics ; Sequence Analysis, DNA ; transporters
  • É parte de: Environmental microbiology, 2014-06, Vol.16 (6), p.1549-1565
  • Notas: http://dx.doi.org/10.1111/1462-2920.12284
    ark:/67375/WNG-8ST8BM2C-C
    istex:189733F5E695B358068BF8FE913C9EAB33E54DC0
    Russian Foundation for Basic Research - No. 12-04-31945; No. 13-04-00049
    Russian Academy of Science
    European Research Council - No. 322551
    Fig. S1. Cell morphology of anaerobic haloalkaliphilic chitinolytic bacterial isolates from hypersaline soda habitats. Fig. S2. Chitin degradation at pH 10 and 2 M Na+ in a culture of extreme natronophile ACht1 from soda lakes. Amorphous chitin degradation starts and proceeds almost to completion entirely in the solid phase by cells attached to chitin globules. It is evident from the appearance of trenches in the chitin layer and its gradual clearing. At the same time, no cells are visible in the culture supernatant. They appear only after substantial chitin hydrolysis and visible cell turbidity becomes evident after homogenization of the culture. When all chitin is hydrolysed, the biomass lyses very rapidly. Fig. S3. Influence of pH and salt concentration on endochitinase activity of whole cells of strain ACht1. Enzyme activities were measured with 4-MU-β-D-N,N′,N″-triacetylchitotriose in 1 M carbonate buffers with pH 6 to 11 (A) or in pH 9.0 carbonate buffer with molarity from 0.1 to 3 M (B). Activities are shown in relative units proportional to the amounts of liberated 4-MU. The cells were grown at pH 10 with 2 M total Na+. Fig. S4. Genomic organization of the loci encoding the two ACht1 hydrogenases and schematic representation of modular structures of the corresponding proteins. The H cluster domain in HfsB deviates from the consensus pattern. Table S1. Fatty acid composition of the membrane polar lipids of strain ACht1 grown at pH 10, 2 M Na+ and 30°C. Table S2. Accumulation of fermentation products by ACht strains after complete chitin degradation at 2 M Na+ and pH 10. Table S3. Hydrolytic activities of cell extract of C. alkaliphilus ACht1 towards different polysaccharides. Table S4. Central metabolic pathways of C. alkaliphilus. Table S5. A list of known 16S rRNA clones previously assigned to the candidate phylum TG3. Table S6. Ribosomal proteins of C. alkaliphilus ACht1 used for constructing the tree on Fig. 3B.
    ArticleID:EMI12284
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    SourceType-Scholarly Journals-1
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  • Descrição: Anaerobic enrichments from hypersaline soda lakes with chitin as substrate yielded five closely related anaerobic haloalkaliphilic isolates growing on insoluble chitin by fermentation at pH 10 and salinities up to 3.5 M. The chitinolytic activity was exclusively cell associated. To better understand the biology and evolutionary history of this novel bacterial lineage, the genome of the type strain ACht1 was sequenced. Analysis of the 2.6 Mb draft genome revealed enzymes of chitin‐degradation pathways, including secreted cell‐bound chitinases. The reconstructed central metabolism revealed pathways enabling the fermentation of polysaccharides, while it lacks the genes needed for aerobic or anaerobic respiration. The Rnf‐type complex, oxaloacetate decarboxylase and sodium‐transporting V‐type adenosine triphosphatase were identified among putative membrane‐bound ion pumps. According to 16S ribosomal RNA analysis, the isolates belong to the candidate phylum Termite Group 3, representing its first culturable members. Phylogenetic analysis using ribosomal proteins and taxonomic distribution analysis of the whole proteome supported a class‐level classification of ACht1 most probably affiliated to the phylum Fibribacteres. Based on phylogenetic, phenotypic and genomic analyses, the novel bacteria are proposed to be classified as Chitinivibrio alkaliphilus gen. nov., sp. nov., within a novel class Chitinivibrione.
  • Editor: Oxford: Blackwell Science
  • Idioma: Inglês;Russo
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