Publications

4475

Abstract Thi.o.ha.lo.rhab.dal'es N.L. fem. n. Thiohalorhabdus , the type genus of the order; L. fem. pl. n. suff. ‐ ales ending to denote an order; N.L. fem. pl. n. Thiohalorhabdales , order of the genus Thiohalorhabdus . According to the phylogenomic analysis, the order Thiohalorhabdales forms a deeply branching phylogenetic lineage at the base of the Gammaproteobacteria . It consists of a single family Thiohalorhabdaceae and genus Thiohalorhabdus . The cultured members of the order are extremely halophilic, facultatively anaerobic (denitrifying), chemolithoautotrophic, sulfur‐oxidizing bacteria from hypersaline habitats with neutral pH. Type genus : Thiohalorhabdus Sorokin et al. 2008 VP . Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the order Thiohalorhabdales is: correct name (last update, February 2025) * . LPSN classification: Bacteria / Pseudomonadati / Pseudomonadota / Gammaproteobacteria / Thiohalorhabdales The order Thiohalorhabdales can also be recovered in the Genome Taxonomy Database (GTDB) as o__Thiohalorhabdales (version v220) ** . GTDB classification: d__Bacteria / p__Pseudomonadota / c__Gammaproteobacteria / o__Thiohalorhabdales * Meier‐Kolthoff et al. ( 2022 ). Nucleic Acids Res , 50 , D801 – D807 ; DOI: 10.1093/nar/gkab902 ** Parks et al. ( 2022 ). Nucleic Acids Res , 50 , D785 – D794 ; DOI: 10.1093/nar/gkab776

Abstract Thi.o.ha.lo.rhab.da.ce'ae N.L. fem. n. Thiohalorhabdus , the type genus of the family; L. fem. pl. n. suff.‐ aceae , ending to denote a family; N.L. fem. pl. n. Thiohalorhabdaceae , the Thiohalorhabdus family. The family Thiohalorhabdaceae incorporates facultatively anaerobic, chemolithoautotrophic, sulfur‐oxidizing bacteria from hypersaline habitats. They are extreme halophiles utilizing reduced sulfur compounds as energy sources with either O 2 or nitrate as the electron acceptor and assimilating CO 2 via the Calvin–Benson–Bassham cycle. The family is a member of the order Thiohalorhabdales in the Gammaproteobacteria, and it consists of a single genus Thiohalorhabdus . The family‐level status was established by phylogenomic analysis based on the Genome Taxonomy DataBase classification. DNA G  +  C content (%) : 68.9 (genome of the type strain). Type genus : Thiohalorhabdus Sorokin et al. 2008 VP . Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the family Thiohalorhabdaceae is: correct name (last update, February 2025) * . LPSN classification: Bacteria / Pseudomonadati / Pseudomonadota / Gammaproteobacteria / Thiohalorhabdales / Thiohalorhabdaceae The family Thiohalorhabdaceae can also be recovered in the Genome Taxonomy Database (GTDB) as f__Thiohalorhabdaceae (version v220) ** . GTDB classification: d__Bacteria / p__Pseudomonadota / c__Gammaproteobacteria / o__Thiohalorhabdales / f__Thiohalorhabdaceae * Meier‐Kolthoff et al. ( 2022 ). Nucleic Acids Res , 50 , D801 – D807 ; DOI: 10.1093/nar/gkab902 ** Parks et al. ( 2022 ). Nucleic Acids Res , 50 , D785 – D794 ; DOI: 10.1093/nar/gkab776

Abstract Thi.o.ha.lo.bac.ter.a.ce'ae N.L. masc. n. Thiohalobacter , the type genus of the family, ‐ aceae ending to denote a family; N.L. fem. pl. n. Thiohalobacteraceae the Thiohalobacter family. The family Thiohalobacteraceae consists of aerobic, chemolithoautotrophic, sulfur‐oxidizing bacteria from hypersaline salt lakes. They are moderately halophilic aerobic, bacteria utilizing reduced sulfur compounds as the energy source and assimilating CO 2 via the Calvin–Benson–Bassham cycle. The family is a member of the order Thiohalobacterales within the Gammaproteobacteria and consists of a single genus Thiohalobacter . The family‐level status was established by phylogenomic analysis based on the Genome Taxonomy DataBase classification. DNA G + C content (%) : 64.2 (genome sequence). Type genus : Thiohalobacter Sorokin et al. 2010 VP . Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the family Thiohalobacteraceae is: correct name (last update, February 2025) * . LPSN classification: Bacteria / Pseudomonadati / Pseudomonadota / Gammaproteobacteria / Thiohalobacterales / Thiohalobacteraceae The family Thiohalobacteraceae can also be recovered in the Genome Taxonomy Database (GTDB) as f__Thiohalobacteraceae (version v220) ** . GTDB classification: d__Bacteria / p__Pseudomonadota / c__Gammaproteobacteria / o__Thiohalobacterales / f__Thiohalobacteraceae * Meier‐Kolthoff et al. ( 2022 ). Nucleic Acids Res , 50 , D801 – D807 ; DOI: 10.1093/nar/gkab902 ** Parks et al. ( 2022 ). Nucleic Acids Res , 50 , D785 – D794 ; DOI: 10.1093/nar/gkab776

Abstract Understanding vector dispersal capacity is key to assessing the risk of spread of vector borne pathogens. For flying vectors, flight performance is associated with primary and secondary pathogen spread. However, because pathogens induce changes in vector physiology, pathogen status in the vector may impact vector dispersal. In this work, by using flight mills, we assessed the flight performance of Bactericera cockerellithat were infected or not by the plant pathogenic bacterium ‘CandidatusLiberibacter solanacearum’ (CLso), the causal agent of potato zebra chip disease and vein greening in tomato. Bactericera cockerelliperformed short and long-distance flights, but CLso infection status affected the propensity to engage in long flights. CLso-free insects engaged in long flights significantly more often (57%) compared to CLso infected insects (25%). Average distance dispersed for long flyers was 185.33 m for CLso-free insects and 122.99 m for insects infected with CLso. However, distance dispersed was not statistically different by pathogen status of the vector. Maximal flight capacity recorded was 980 m. Overall, our data suggest that CLso reduces the propensity to engage in long distance flights. Our results can be utilized to fine-tune strategies to mitigate CLso establishment in new areas.

AbstractMany marine sponges host highly diverse microbiomes that contribute to various aspects of host health. Although the putative function of individual groups of sponge symbionts has been increasingly described, the extreme diversity has generally precluded in‐depth characterization of entire microbiomes, including identification of syntrophic partnerships. The Indo‐Pacific sponge Ianthella basta is emerging as a model organism for symbiosis research, hosting only three dominant symbionts: a Thaumarchaeotum, a Gammaproteobacterium, and an Alphaproteobacterium and a range of other low abundance or transitory taxa. Here, we retrieved metagenome assembled genomes (MAGs) representing >90% of I. basta's microbial community, facilitating the metabolic reconstruction of the sponge's near complete microbiome. Through this analysis, we identified metabolic complementarity between microbes, including vitamin sharing, described the importance of low abundance symbionts, and characterized a novel microbe–host attachment mechanism in the Alphaproteobacterium. We further identified putative viral sequences, highlighting the role viruses can play in maintaining symbioses in I. basta through the horizontal transfer of eukaryotic‐like proteins, and complemented this data with metaproteomics to identify active metabolic pathways in bacteria, archaea, and viruses. This data provide the framework to adopt I. basta as a model organism for studying host–microbe interactions and provide a basis for in‐depth physiological experiments.

Abstract Thiovulum spp. (Campylobacterota) are large sulfur bacteria that form veil-like structures in aquatic environments. The sulfidic Movile Cave (Romania), sealed from the atmosphere for ~5 million years, has several aqueous chambers, some with low atmospheric O2 (~7%). The cave’s surface-water microbial community is dominated by bacteria we identified as Thiovulum. We show that this strain, and others from subsurface environments, are phylogenetically distinct from marine Thiovulum. We assembled a closed genome of the Movile strain and confirmed its metabolism using RNAseq. We compared the genome of this strain and one we assembled from public data from the sulfidic Frasassi caves to four marine genomes, including Candidatus Thiovulum karukerense and Ca. T. imperiosus, whose genomes we sequenced. Despite great spatial and temporal separation, the genomes of the Movile and Frasassi Thiovulum were highly similar, differing greatly from the very diverse marine strains. We concluded that cave Thiovulum represent a new species, named here Candidatus Thiovulum stygium. Based on their genomes, cave Thiovulum can switch between aerobic and anaerobic sulfide oxidation using O2 and NO3- as electron acceptors, the latter likely via dissimilatory nitrate reduction to ammonia. Thus, Thiovulum is likely important to both S and N cycles in sulfidic caves. Electron microscopy analysis suggests that at least some of the short peritrichous structures typical of Thiovulum are type IV pili, for which genes were found in all strains. These pili may play a role in veil formation, by connecting adjacent cells, and in the motility of these exceptionally fast swimmers.

Abstract Anaerobic ammon ium oxidizing (anammox) bacteria oxidize ammonium and reduce nitrite, producing N2, and could play a major role in energy-optimized wastewater treatment. However, sensitivity to various environmental conditions and slow growth currently hinder their wide application. Here, we attempted to determine online the effect of environmental stresses on anammox bacteria by using an overnight batch activity test with whole cells, in which anammox activity was calculated by quantifying N2 production via headspace-pressure monitoring. A planktonic mixed culture dominated by “Candidatus Kuenenia stuttgartiensis” strain CSTR1 was cultivated in a 30-L semi-continuous stirring tank reactor. In overnight resting-cell anammox activity tests, oxygen caused strong inhibition of anammox activity, which was reversed by sodium sulfite (30 µM). The tested antibiotics sulfamethoxazole, kanamycin, and ciprofloxacin elicited their effect on a dose-dependent manner; however, strain CSTR1 was highly resistant to sulfamethoxazole. Anammox activity was improved by activated carbon and Fe2O3. Protein expression analysis from resting cells after anammox activity stimulation revealed that NapC/NirT family cytochrome c (KsCSTR_12840), hydrazine synthase, hydrazine dehydrogenase, hydroxylamine oxidase, and nitrate:nitrite oxidoreductase were upregulated, while a putative hydroxylamine oxidoreductase HAO (KsCSTR_49490) was downregulated. These findings contribute to the growing knowledge on anammox bacteria physiology, eventually leading to the control of anammox bacteria growth and activity in real-world application. Key Points • Sulfite additions can reverse oxygen inhibition of the anammox process • Anammox activity was improved by activated carbon and ferric oxide • Sulfamethoxazole marginally affected anammox activity Graphical abstract

AbstractOur knowledge of ciliate endosymbiont diversity greatly expanded over the past decades due to the development of characterization methods for uncultivable bacteria. Chlamydia‐like bacteria have been described as symbionts of free‐living amoebae and other phylogenetically diverse eukaryotic hosts. In the present work, a systematic survey of the bacterial diversity associated with the ciliate Euplotes octocarinatus strain Zam5b‐1 was performed, using metagenomic screening as well as classical full‐cycle rRNA approach, and a novel chlamydial symbiont was characterized. The metagenomic screening revealed 16S rRNA gene sequences from Polynucleobacter necessarius, three previously reported accessory symbionts, and a novel chlamydia‐like bacterium. Following the full‐cycle rRNA approach, we obtained the full‐length 16S rRNA gene sequence of this chlamydia‐like bacterium and developed probes for diagnostic fluorescence in situ hybridizations. The phylogenetic analysis of the 16S rRNA gene sequences unambiguously places the new bacterium in the family Rhabdochlamydiaceae. This is the first report of chlamydia‐like bacterium being found in Euplotes. Based on the obtained data, the bacterium is proposed as a new candidate genus and species: “Candidatus Euplotechlamydia quinta.”