Publications

4634

The interactions between the phloem-limited pathogen ‘Candidatus Liberibacter solanacearum’ haplotype C and carrot (Daucus carota subsp. sativus) were studied at 4, 5, and 9 weeks postinoculation (wpi), by combining dual RNA-Seq results with data on bacterial colonization and observations of the plant phenotype. In the infected plants, genes involved in jasmonate biosynthesis, salicylate signaling, pathogen-associated molecular pattern- and effector-triggered immunity, and production of pathogenesis-related proteins were up-regulated. At 4 wpi, terpenoid synthesis-related genes were up-regulated, presumably as a response to the psyllid feeding, whereas at 5 and 9 wpi, genes involved in both the terpenoid and flavonoid production were down-regulated and phenylpropanoid genes were up-regulated. Chloroplast-related gene expression was down-regulated, in concordance with the observed yellowing of the infected plant leaves. Both the RNA-Seq data and electron microscopy suggested callose accumulation in the infected phloem vessels, likely to impair the transport of photosynthates, while phloem regeneration was suggested by the formation of new sieve cells and the upregulation of cell wall–related gene expression. The ‘Ca. L. solanacearum’ genes involved in replication, transcription, and translation were expressed at high levels at 4 and 5 wpi, whereas, at 9 wpi, the Flp pilus genes were highly expressed, suggesting adherence and reduced mobility of the bacteria. The ‘Ca. L. solanacearum’ genes encoding ATP and C4-dicarboxylate uptake were differentially expressed between the early and late infection stages, suggesting a change in the dependence on different host-derived energy sources. HPE1 effector and salicylate hydroxylase were expressed, presumably to suppress host cell death and salicylic acid-dependent defenses during the infection. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

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.

Two strains of filamentous, colorless sulfur bacteria were isolated from bacterial fouling in the outflow of hydrogen sulfide-containing waters from a coal mine (Thiothrix sp. Ku-5) and on the seashore of the White Sea (Thiothrix sp. AS). Metagenome-assembled genome (MAG) A52 was obtained from a sulfidic spring in the Volgograd region, Russia. Phylogenetic analysis based on the 16S rRNA gene sequences showed that all genomes represented the genus Thiothrix. Based on their average nucleotide identity and digital DNA-DNA hybridization data these new isolates and the MAG represent three species within the genus Thiothrix with the proposed names Thiothrix subterranea sp. nov. Ku-5T, Thiothrix litoralis sp. nov. AST, and “Candidatus Thiothrix anitrata” sp. nov. A52. The complete genome sequences of Thiothrix fructosivorans QT and Thiothrix unzii A1T were determined. Complete genomes of seven Thiothrix isolates, as well as two MAGs, were used for pangenome analysis. The Thiothrix core genome consisted of 1,355 genes, including ones for the glycolysis, the tricarboxylic acid cycle, the aerobic respiratory chain, and the Calvin cycle of carbon fixation. Genes for dissimilatory oxidation of reduced sulfur compounds, namely the branched SOX system (SoxAXBYZ), direct (soeABC) and indirect (aprAB, sat) pathways of sulfite oxidation, sulfur oxidation complex Dsr (dsrABEFHCEMKLJONR), sulfide oxidation systems SQR (sqrA, sqrF), and FCSD (fccAB) were found in the core genome. Genomes differ in the set of genes for dissimilatory reduction of nitrogen compounds, nitrogen fixation, and the presence of various types of RuBisCO.