Phenotypic and Genomic Properties of Chitinispirillum alkaliphilum gen. nov., sp. nov., A Haloalkaliphilic Anaerobic Chitinolytic Bacterium Representing a Novel Class in the Phylum Fibrobacteres

Abstract

Anaerobic enrichment from sediments of hypersaline alkaline lakes in Wadi el Natrun (Egypt) with chitin resulted in the isolation of a fermentative haloalkaliphilic bacterium, strain ACht6-1, growing exclusively with insoluble chitin as the substrate in a sodium carbonate-based medium at pH 8.5–10.5 and total Na+ concentrations from 0.4 to 1.75 M. The isolate had a Gram-negative cell wall and formed lipid cysts in old cultures. The chitinolytic activity was associated with cells. Analysis of the 4.4 Mb draft genome identified pathways for chitin utilization, particularly, secreted chitinases linked to the cell surface, as well as genes for the hydrolysis of other polysaccharides and fermentation of sugars, while the genes needed for aerobic and anaerobic respiration were absent. Adaptation to a haloalkaliphilic lifestyle was reflected by the gene repertoire encoding sodium rather than proton-dependent membrane-bound ion pumps, including the Rnf-type complex, oxaloacetate decarboxylase, V-type ATPase, and pyrophosphatase. The phylogenetic analysis using 16S rRNA gene and ribosomal proteins indicated that ACht6-1 forms a novel deep lineage at the class level within the bacterial candidate division TG3. Based on phylogenetic, phenotypic and genomic analyses, the novel chitinolytic bacterium is described as Chitinispirillum alkaliphilum gen. nov., sp. nov., within a novel class Chitinispirillia that could be included into the phylum Fibrobacteres.

Response of Microbial Community Function to Fluctuating Geochemical Conditions within a Legacy Radioactive Waste Trench Environment

“…S2 in the supplemental material). In addition, numerous facultative and strict anaerobes can degrade chitin and/or chitobiose ( 43 – 45 ), which lessens the likelihood of the alternative hypothesis that chitin depletion could be derived from the intrinsic lack of chitobiase in anaerobes.…”

Symbiosis between nanohaloarchaeon and haloarchaeon is based on utilization of different polysaccharides

“…Nanohalobium. Complete hydrolysis of insoluble chitin to its monomer usually occurs via action of two types of hydrolytic enzymes: endochitinases, which digest chitin microfibrils at internal sites to form chitodextrins, and N,N ′-diacetylchitobiose and exochitodextrinases, which further break down chitodextrin oligomers at their termini to produce the monosaccharide (8). The second phase of hydrolysis typically occurs in the periplasm or cytoplasm, and there are only a few indications that chitinitrophic halo(natrono)archaea are able to perform this process outside the cell (10).…”

Differential polysaccharide utilization is the basis for a nanohaloarchaeon : haloarchaeon symbiosis

“…These arthropods have chitinous exoskeletons and reach considerable biomass (up to 50 g m -2 ), making chitin one of the most abundant biopolymers in these ecosystems 2-4 . Halophilic fermentative bacteria are known to play a role in chitin mineralization in hypersaline habitats worldwide 5-7 , and more recently it was shown that haloarchaea also take part in the primary degradation of polymeric organic matter in many of the same habitats 8-11 . Here we reveal the role of haloarchaea as chitinotrophic hosts for nanohaloarchaea, the extremely halophilic members of the DPANN superphylum 12-15 .…”