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

Abstract

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.

Molecular investigation of Australian termites and their gut symbionts

“…The ingroup comprised the two complete reference genomes representing the Fibrobacteres (Suen et al, 2011) and TG3 (Sorokin et al, 2014) lineages and eight population genomes obtained in this study (Table 5.1). We evaluated the monophyly of these genomes using an outgroup consisting of 2358 genomes from 33 phyla.…”

“…However, it likely belongs to the TG3 lineage, and more specifically in the termite cluster proximate to isolate ACht6-1 (Figure 5.1; Sorokin et al (2012)). Sorokin et al, (2014) proposed the class Chitinivibrionia to accommodate C. alkaliphilus ACht1, which now becomes the second recognised class within the Fibrobacteres due to its amalgamation with TG3 (Figure 5.1). We have provisionally included MC_77 in the class Chitinivibrionia, however, given the depth of the relationship with C. alkaliphilus (Figure 5.1…”

“…Candidate phylum TG3 (Termite group 3) is often phylogenetically associated with the Fibrobacteres based on comparative analyses of the 16S rRNA gene Hongoh et al, 2006;Warnecke et al, 2007;Sorokin et al, 2014). TG3 was initially detected in environmental surveys of termite guts , but was later found to be present in a diverse range of habitats (Hongoh et al, 2006).…”

“…TG3 was initially detected in environmental surveys of termite guts , but was later found to be present in a diverse range of habitats (Hongoh et al, 2006). Recently, the first isolates for TG3 have been described (Sorokin et al, 2012), one of which has been named Chitinivibrio alkaliphilus and its genome sequenced (Sorokin et al, 2014). C. alkaliphilus is a haloalkaliphilic anaerobic chitinutilising bacterium isolated from soda lake sediments.…”

“…C. alkaliphilus is a haloalkaliphilic anaerobic chitinutilising bacterium isolated from soda lake sediments. There have been conflicting views as to whether TG3 should be merged with the Fibrobacteres or retained as a separate phylum (Sorokin et al, 2014).…”