Publications

4551

Abstract Members of the genus Acidithiobacillus, now ranked within the class Acidithiobacillia, are model bacteria for the study of chemolithotrophic energy conversion under extreme conditions. Knowledge of the genomic and taxonomic diversity of Acidithiobacillia is still limited. Here, we present a systematic analysis of nearly 100 genomes from the class sampled from a wide range of habitats. Some of these genomes are new and others have been reclassified on the basis of advanced genomic analysis, thus defining 19 Acidithiobacillia lineages ranking at different taxonomic levels. This work provides the most comprehensive classification and pangenomic analysis of this deep-branching class of Proteobacteria to date. The phylogenomic framework obtained illuminates not only the evolutionary past of this lineage, but also the molecular evolution of relevant aerobic respiratory proteins, namely the cytochrome bo3 ubiquinol oxidases.

Abstract Acidobacteriota are widespread and often abundant in marine sediments, yet their metabolic and ecological properties are poorly understood. Here, we examined metabolisms and distributions of Acidobacteriota in marine sediments of Svalbard by functional predictions from metagenome-assembled genomes (MAGs), amplicon sequencing of 16S rRNA and dissimilatory sulfite reductase (dsrB) genes and transcripts, and gene expression analyses of tetrathionate-amended microcosms. Acidobacteriota were the second most abundant dsrB-harboring (averaging 13%) phylum after Desulfobacterota in Svalbard sediments, and represented 4% of dsrB transcripts on average. Meta-analysis of dsrAB datasets also showed Acidobacteriota dsrAB sequences are prominent in marine sediments worldwide, averaging 15% of all sequences analysed, and represent most of the previously unclassified dsrAB in marine sediments. We propose two new Acidobacteriota genera, Candidatus Sulfomarinibacter (class Thermoanaerobaculia, “subdivision 23”) and Ca. Polarisedimenticola (“subdivision 22”), with distinct genetic properties that may explain their distributions in biogeochemically distinct sediments. Ca. Sulfomarinibacter encode flexible respiratory routes, with potential for oxygen, nitrous oxide, metal-oxide, tetrathionate, sulfur and sulfite/sulfate respiration, and possibly sulfur disproportionation. Potential nutrients and energy include cellulose, proteins, cyanophycin, hydrogen, and acetate. A Ca. Polarisedimenticola MAG encodes various enzymes to degrade proteins, and to reduce oxygen, nitrate, sulfur/polysulfide and metal-oxides. 16S rRNA gene and transcript profiling of Svalbard sediments showed Ca. Sulfomarinibacter members were relatively abundant and transcriptionally active in sulfidic fjord sediments, while Ca. Polarisedimenticola members were more relatively abundant in metal-rich fjord sediments. Overall, we reveal various physiological features of uncultured marine Acidobacteriota that indicate fundamental roles in seafloor biogeochemical cycling.

The taxonomic positions of members within the familyPseudonocardiaceaewere assessed based on phylogenomic trees reconstructed using core-proteome and genomeblastdistance phylogeny approaches. The closely clustered genome sequences from the type strains of validly published names within the familyPseudonocardiaceaewere analysed using overall genome-related indices based on average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization values. The familyPseudonocardiaceaeconsists of the type genusPseudonocardia, as well as the generaActinoalloteichus,Actinocrispum,Actinokineospora,Actinomycetospora,Actinophytocola,Actinopolyspora,Actinorectispora,Actinosynnema,Allokutzneria,Allosaccharopolysporagen. nov.,Amycolatopsis,Bounagaea,Crossiella,Gandjariella,Goodfellowiella,Haloactinomyces,Haloechinothrix,Halopolyspora,Halosaccharopolysporagen. nov.,Herbihabitans,Kibdelosporangium,Kutzneria,Labedaea,Lentzea,Longimycelium,Prauserella,Saccharomonospora,Saccharopolyspora,Saccharothrix,Salinifilum,Sciscionella,Streptoalloteichus,Tamaricihabitans,Thermocrispum,ThermotunicaandUmezawaea. The G+C contents of thePseudonocardiaceaegenomes ranged from 66.2 to 74.6 mol% and genome sizes ranged from 3.69 to 12.28 Mbp. Based on the results of phylogenomic analysis, the namesAllosaccharopolyspora corallicomb. nov.,Halosaccharopolyspora lacisalsicomb. nov. andActinoalloteichus caeruleuscomb. nov. are proposed. This study revealed thatActinokineospora mzabensisis a heterotypic synonym ofActinokineospora spheciospongiae,Lentzea desertiis a heterotypic synonym ofLentzea atacamensis,Prauserella endophyticais a heterotypic synonym ofPrauserella coralliicola, andPrauserella flavaandPrauserella sediminisare heterotypic synonyms ofPrauserella salsuginis. This study addresses the nomenclature conundrums ofActinoalloteichus cyanogriseusandStreptomyces caeruleusas well asMicropolyspora internatusandSaccharomonospora viridis.

A wide array of archaea populate Earth’s extreme environments; therefore, they may play important roles in mediating biogeochemical processes such as iron and sulfur cycling. However, our knowledge of archaeal biology and evolution is still limited considering that the majority of the archaeal diversity is uncultured.