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Physiology, functional genomics and proteomics of Verruconatronum alginilyticum gen. nov., sp. nov., a first haloalkaliphilic representative of the phylum Verrucomicrobiota from soda habitats

ABSTRACT: Despite cultivation of many representatives of rich bacterial communities inhabiting alkaline soda lakes, members of the bacterial phylum Verrucomicrobiota have so far been detected only by molecular techniques. Here, we used alginate as a selective substrate to enrich and isolate two strains of haloalkaliphilic Verrucomicrobiota. The isolates share identical 16S rRNA gene sequences and represent a new genus, and, together with metagenome assembled genomes, a new family within Opitutales. Cells of strains AB-alg1T (from soda lakes) and AB-alg4 (from soda soils) are small motile cocci forming submerged colonies in soft alginate agar. They are saccharolytic heterotrophs growing aerobically on polysaccharides (alginate, starch and inulin) and sugars (glucose, fructose, mannose, sucrose, melezitose, maltose and cellobiose). They also grow anaerobically by fermentation of alginate and D-mannose and by coupling incomplete denitrification to oxidation of alginate. Both isolates are obligately alkaliphilic and moderately salt-tolerant. The dominant membrane phospholipids include phosphatidylcholine and cardiolipin. The genome of AB-alg1T features polysaccharide lyases of the PL6, 7, 15, 17, 38, and 39 families for depolymerization of alginate. On the basis of phenotypic and distinct phylogeny, we propose classification of strains AB-alg1T (JCM 35393T=UQM 41574T) and AB-alg4 as Verruconatronum alginilyticum gen. nov., sp. nov. within a new family Verruconatronumaceae.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Marc Strous

LAB HEAD: Marc Strous

PROVIDER: PXD071159 | Pride | 2026-04-17

REPOSITORIES: Pride

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Source:

			Action	DRS
	AB-alg1_alginate_400ng.mzML	Mzml
	AB-alg1_alginate_400ng.raw	Raw
	AB-alg1_mannose_400ng.mzML	Mzml
	AB-alg1_mannose_400ng.raw	Raw
	AB-alg1_sucrose_400ng.mzML	Mzml

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Project description:Haloalkaliphilic microorganisms are double extremophiles functioning optimally at high salinity and pH. Their typical habitats are soda lakes, representing geologically ancient ecosystems which are still widespread on Earth and supposedly harbor relict microbial communities. We compared metabolic features and their genomic determinants in two strains of a single natronophilic species Dethiobacter alkaliphilus, the only cultured representative of “Dethiobacteria” class within Bacillota phylum. The strains of D. alkaliphilus were previously isolated from geographically remote Mongolian and Kenyan soda lakes. The type strain AHT1T was described as a facultatively chemolithoautotrophic sulfidogen reducing or disproportionating sulfur or thiosulfate, while strain Z-1002 was isolated as a chemolithoautotrophic iron reducer. Here, we uncovered iron reducing ability of strain AHT1T, as well as the capability of strain Z-1002 for thiosulfate reduction and anaerobic Fe(II) oxidation. Key catabolic processes sustaining the growth of both strains appeared to fit the geochemical settings of two contrasting natural alkaline environments, sulfur-enriched soda lakes and iron-enriched serpentinites. This assumption was supported by meta-analysis of publicly available Dethiobacterial metagenomes, as well as by the enrichment of a novel phylotype from a deep subsurface non-serpentinizing slightly alkaline water after its amendment with an Fe(III) mineral. Genome analysis of D. alkaliphilus strains revealed that the most probable determinants of iron and sulfur redox transformations in the organism are multiheme c-type cytochromes. Their phylogeny reconstruction showed that sulfur and thiosulfate respiration is most probably provided by evolutionary early forms of unconventional octaheme tetrathionate and sulfite reductases sharing a root with structurally similar group of OmhA/OcwA Fe(III)-reductases. Large sets of other multihemes are likely to provide Fe(III) reduction in both strains. Also, several different, yet phylogenetically related, determinants of anaerobic Fe(II) oxidation were identified in Z-1002 genome, and the oxidation process was further experimentally proven. Considering these results and phylogenetic relatedness of D. alkaliphilus’s sulfur reductases with Fe(III) reducing cytochromes, but not with archetypal bacterial sulfur/thiosulfate reductases, we suggest that sustaining high variation of multiheme cytochromes is an effective adaptive strategy to occupy geochemically contrasting alkaline anaerobic environments. We further propose that sulfur-enriched soda lakes are secondary habitats for D. alkaliphilus comparing to Fe-rich serpentinites, and discuss the evolutionary traits which might occur in prokaryotes on a crucial junction of the biosphere’s history, when intensification of the sulfur cycle outweighed the global significance of the iron cycle.

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Physiology, functional genomics and proteomics of Verruconatronum alginilyticum gen. nov., sp. nov., a first haloalkaliphilic representative of the phylum Verrucomicrobiota from soda habitats

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