Publications

4039

Phylogenetic analysis of the genus Aureimonas, utilizing both 16S rRNA gene sequences and comprehensive whole-genome data, revealed its polyphyletic nature, necessitating a revision to accommodate phylogenetically distinct species. Based on established threshold values for genus demarcation – specifically, 16S rRNA gene similarity, Average Amino Acid Identity and Percentage of Conserved Proteins – a notably substantial divergence was observed within the genus Aureimonas, and the division of Aureimonas into four distinct genera is strongly supported. To address this, we propose the establishment of four new genera: Dennerimonas gen. nov., Mesocryomonas gen. nov., Rathsackimonas gen. nov. and Plantimonas gen. nov. These classifications accommodate species that are significantly divergent from the type species of Aureimonas, thereby more accurately reflecting their distinct evolutionary lineages. Additionally, Aureimonas glaciistagni is proposed to be reclassified within the genus Jiella as Jiella glaciistagni comb. nov. based on phylogenetic evidence indicating a closer evolutionary relationship to Jiella species than to other members of Aureimonas. Our analysis, which included assessments of 16S rRNA gene similarity, Average Nucleotide Identity, and digital DNA–DNA hybridization values exceeding species delineation thresholds, further supports the reclassification of Jeongeupella Jiang et al. 2024 as a later heterotypic synonym of Antarcticirhabdus Du et al. 2023.

Marine heterotrophic bacteria in coastal waters respond to the influx of carbon from natural and anthropogenic sources. We identified two nearly identical, (99.9% average nucleotide identity; 100% amino acid identity; same DNA G + C content of 52.3 mol%) high-quality (≥99% CheckM completeness and ≤ 1.3% contamination) draft metagenome-assembled genomes (MAGs; SJ0813 and SJ0972) from seawater microbiomes of a southern island of Singapore that is in a protected marine park. The MAGs were only assigned to the Cellvibrionaceae family according to Genome Taxonomy Database. Overall genome related indices to Pseudomaricurvus alkylphenolicus KU41GT as the closest phylogenetic relative revealed no more than 70.45% average nucleotide identity (ANIcutoff < 95%), below the 50% percentage of conserved proteins (POCPcutoff = 43.54%) for genera cutoff and low digital DNA–DNA hybridization values (DDH = 20.6 and 20.8%). The major respiratory quinone is predicted to be ubiquinone-9 from the annotation of 3-demethylubiquinone-9 3-methyltransferase (ubiG, K00568) involved in the last step of the ubiquinone biosynthesis pathway (M00117), which differed from the ubiquinone-8 utilized by known members of Cellvibrionaceae. Both MAGs contained a complete pathway for dissimilatory nitrate reduction to ammonia, which increases bioavailability of nitrogen in seawater. An identical choline dehydrogenase found in both MAGs have a low amino-acid identity (≤64.47%) compared to existing GMC family oxidoreductases, expanding on the diversity of this family of enzymes. The MAGs meet nearly all the minimum requirements but lack a 16S rRNA gene of sufficient length required for the proposed novel genus and species under SeqCode. Nevertheless, phylogenetic trees based on core-genome and RpoB as an alternative phylogenetic marker are congruent with the taxon standing as a monophyletic clade to other taxa of the order Cellvibrionales. Taken together, the MAGs (SJ0813 and SJ0972) represent an uncultured, undescribed genus and species in which we tentatively propose the name Candidatus Pelagadaptatus aseana gen. nov., sp. nov. and strain SJ0813TS (=BAABNI000000000.1TS) as type sequence. Phylogenetic inference from core-genome and RpoB phylogenetic trees placed Umboniibacter marinipuniceus KMM 3891T outside Cellvibrionaceae. We, therefore, propose the transfer of the genus Umboniibacter from the family Cellvibrionaceae to a new family Umboniibacteraceae according to the International Code of Nomenclature of Prokaryotes.

Surveys for exotic plant pests conducted during July and August of 2023 and 2024 across 20 vineyards in 12 counties throughout Minnesota, USA, revealed that less than 2% of the approximatively 3000 vines inspected (Vitis spp., hybrid grape varieties) exhibited symptoms suggestive of phytoplasma yellows disease. Observed symptoms included yellowing of leaf lamina, downward rolling of leaf margins, and necrosis of leaf margins. To investigate a potential association between these symptoms and phytoplasmas, two symptomatic plants were selected in August of 2024 from two distinct vineyards for further analysis. Petiole tissue DNA extracts were initially tested using a phytoplasma-specific real-time PCR assay (Hodgetts et al. 2009), which confirmed the presence of phytoplasma DNA in both symptomatic plants. Subsequently, the samples underwent semi-nested PCR amplification targeting the phytoplasma 16S rRNA gene, using primers P1/16S-SR followed by P1A/16S-SR (Deng and Hiruki 1991; Lee et al. 2004). The resulting amplicons were cloned and sequenced. No amplicon was produced from an asymptomatic grapevine DNA sample included as a test control. Analysis of the 16S rRNA gene sequences revealed that each plant was infected by one of two distinct phytoplasma strains, designated MN450 and MN466. Representative sequences obtained from the two samples exhibiting interoperon heterogeneity were deposited in the GenBank database under accession numbers: PQ889195 (rrnA) and PQ889196 (rrnB) for strain MN450, and PQ889197 (rrnA) and PQ889198 (rrnB), for strain MN466. Sequence analysis using the online phytoplasma classification tool iPhyClassifier (Zhao et al. 2009) showed that the 16S rRNA gene sequences from MN450 shared 1491/1495 bp (99.73%) and 1492/1495 bp (99.80%) identity (rrnA and rrnB, respectively) with that of the ‘'Ca. Phytoplasma pruni' rrnA’ reference strain (GenBank JQ044393), identifying MN450 as a ‘'Ca. Phytoplasma pruni' rrnA’-related strain and possibly representing a new subgroup within the 16Sr group III. For MN466, the 16S rRNA gene sequences shared 1471/1482 bp (99.26%) and 1469/1482 bp (99.12%) identity (rrnA and rrnB, respectively) with that of the ‘Ca. Phytoplasma asteris’ reference strain (GenBank M30790), and identifying the phytoplasma as a ‘Ca. P. asteris’-related strain belonging to subgroup 16SrI-A. To further characterize the two phytoplasma strains, the secY gene was PCR amplified from the DNA extracts as described by Lee et al. (2010). The obtained amplicons were cloned and sequenced, and representative secY gene sequences were deposited in GenBank under accession numbers PQ899621 (MN450) and PQ899622 (MN466). BLASTn searches against the NCBI core nucleotide database revealed that the secY gene sequence for MN450 exhibited 100% identity (1614/1614 bp) with ‘Ca. P. pruni’ (GenBank KM268860). Similarly, the sequence for MN466 showed 100% identity (1287/1287 bp) with ‘Ca. P. asteris’ (GenBank CP000061). In North America, grapevine yellows disease associated with strains related to 'Ca. P. asteris' and 'Ca. P. pruni' has previously been reported in various states and referred to as North American grapevine yellows (NAGY) by Davis et al. (2015). To our knowledge, this is the first report of NAGY in Minnesota, confirming that the two phytoplasma species detected are consistently associated with the disease in U.S. vineyards. While further research is needed to evaluate the potential impacts of NAGY in Minnesota, this study highlights the broader distribution of the disease across the United States.

AbstractThe severe Asiatic form of huanglongbing (HLB), caused by “Candidatus Liberibacter asiaticus” (CLas), threatens global citrus production via the citrus psyllid, Diaphorina citri. Culturing challenges of CLas necessitate reducing D. citri populations for disease management. CLas boosts the fecundity of CLas‐positive (CLas+) D. citri and fosters its own proliferation by modulating the insect host's juvenile hormone (JH), but the intricate endocrine regulatory mechanisms remain elusive. Here, it is reported that the D. citri ecdysis‐triggering hormone (DcETH) and its receptor DcETHR play pivotal roles in the reciprocal benefits between CLas and D. citri within the ovaries, influencing energy metabolism and reproductive development in host insects; miR‐210, negatively regulates DcETHR expression, contributing to this symbiotic interaction. CLas infection reduces 20‐hydroxyecdysone (20E) levels and stimulates DcETH release, elevating JH production via DcETHR, enhancing fecundity and CLas proliferation. Furthermore, circulating JH levels suppress 20E production in CLas+ ovaries. Collectively, the orchestrated functional interplay involving 20E, ETH, and JH increases energy metabolism and promotes the fecundity of CLas+ D. citri and CLas proliferation. These insights not only broaden the knowledge of how plant pathogens manipulate the reproductive behavior of insect hosts but also offer novel targets and strategies for combatting HLB and D. citri.

Marine sediments are vast, underexplored habitats and represent one of the largest carbon deposits on our planet. Microbial communities drive nutrient cycling in these sediments, but the full extent of their taxonomic and metabolic diversity remains to be explored. Here, we analysed shallow coastal and deep subseafloor sediment cores from 0.01 to nearly 600 metres below the seafloor, in the Western Pacific Region. Applying metagenomics, we identified several taxonomic clusters across all samples, which mainly aligned with depth and sediment type. Inferring functional patterns provided insights into possible ecological roles of the main microbial taxa. These included Chloroflexota, the most abundant phylum across all samples, whereby the classes Dehalococcoida and Anaerolineae dominated deep-subsurface and most shallow coastal sediments, respectively. Thermoproteota and Asgardarchaeota were the most abundant phyla among Archaea, contributing to high relative abundances of Archaea reaching over 50% in some samples. We recovered high-quality metagenome-assembled genomes for all main prokaryotic lineages and proposed names for three phyla, i.e. Tangaroaeota phyl. nov. (former RBG-13-66-14), Ryujiniota phyl. nov. (former UBA6262) and Spongiamicota phyl. nov. (former UBA8248). Metabolic capabilities across all samples ranged from aerobic respiration and photosynthesis in the shallowest sediment layers to heterotrophic carbon utilization, sulphate reduction and methanogenesis in deeper anoxic sediments. We also identified taxa with the potential to be involved in nitrogen and sulphur cycling and heterotrophic carbon utilization. In summary, this study contributes to our understanding of the taxonomic and functional diversity in benthic prokaryotic communities across marine sediments in the Western Pacific Region.

An anaerobic isolate, designated me31T, was isolated from pit mud in Yibin, Sichuan Province, PR China. Phylogenetic results based on 16S rRNA gene sequence showed that strain me31T belongs to the family Dysgonomonadaceae, and the most closely related isolated relatives were Seramator thermalis SYSU GA16112T (93.65%) and Proteiniphilum propionicum JNU-WLY501T (93.22%). The DNA G+C content was 44.26 mol%. The ANI and AAI values between strain me31T and the closely related strains were 69.25–71.18% and 69.59–71.15%, respectively. Cells of strain me31T were Gram-stain-negative, rod-shaped and non-motile. Growth of strain me31T was observed at 25–37 °C, pH 6.0–8.0 and a salt tolerance range of 0–1.0% (w/v). The predominant respiratory quinone was MK-9. The major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and C17 : 0 2OH. The polar lipids of strain me31T were found to consist of phosphatidylethanolamine, three unidentified phospholipids, three unidentified phosphoglycolipids, one unidentified phosphoglycolipid, one unidentified lipid, two unidentified glycolipids and one aminophosphoglycolipid. According to the results of morphological, physiological, biochemical, chemotaxonomic, genotypic and phylogenetic analysis, strain me31T represents a novel species of a novel genus of the family Dysgonomonadaceae, for which the name Limibacterium fermenti gen. nov., sp. nov. is proposed. The type strain is me31T (=GDMCC 1.4237T=KCTC 25756T=WMCC 10035T).

A taxonomic study was conducted on four bacterial strains isolated from the soil of a coking plant. Phylogenetic analysis showed that the four strains belonged to three families: Comamonadaceae, Micrococcaceae and Roseiarcaceae. Identification of the 16S rRNA gene exhibited that their sequence similarities were between 94.96 and 98.98% when compared to known and validly nominated species. Their genomes ranged from 3.4 to 7.2 Mb, with DNA G+C molar contents varying from 62.3 to 67.2%. The average nucleotide identities ranged from 71.4 to 92.3%, and digital DNA–DNA hybridization values were 19.7–47.0% when comparing them with closely related type species, supporting the classification of these four strains. Functional analysis demonstrated that strain H3Y2-7T was robustly resistant to chromate (VI) and arsenite (III) and was able to grow on aromatic compounds including naphthalene as carbon sources even in the presence of chromate (VI). These features reflect its ability to treat combined pollutants and adapt to a polluted environment. Based on the analysis of polyphasic taxonomy, we propose the four bacterial strains representing novel species, namely Curvibacter soli sp. nov. (type strain H39-3-26T=JCM 36178T=CGMCC 1.61344T), Extensimonas soli sp. nov. (type strain H3M7-6T=JCM 36176T=CGMCC 1.61336T), Pseudarthrobacter naphthalenicus sp. nov. (type strain H3Y2-7T=JCM 36482T=CGMCC 1.61323T) and Terripilifer ovatus gen. nov., sp. nov. (type strain H3SJ34-1T=JCM 36465T=CGMCC 1.61333T).

‘Candidatus Liberibacter asiaticus’ (CLas), the agent associated with the Huanglongbing (HLB) citrus disease, is commonly detected using quantitative polymerase chain reaction (qPCR) with hydrolysis probes. Internal standards are typically included in the qPCR assays to reduce the risk of false negatives caused by inhibitors. When the internal standard is detected but CLas is not, it is generally assumed that the pathogen is absent from the tested sample. However, our study shows that trace amounts of CLas may go undetected if the internal standard is either overly abundant or too dissimilar to CLas. To overcome these limitations, we developed a synthetic internal standard (IS) that uses the same primer as the CLas target sequence, along with three to four downstream nucleotides, but with a unique internal sequence derived from smooth hammerhead shark (Sphyrna zygaena; IS-SHK). This sequence matches the G/C content and melting temperature of the CLas target and was specifically selected to minimize potential interference from other nucleic acid materials in citrus samples. To minimize competition between the IS-SHK standard and the CLas target, an average of only 21 molecules of IS-SHK standard is added to each qPCR reaction. Therefore, when IS-SHK standard is detected at expected levels and CLas is not, the absence of CLas is confirmed rather than inhibition of the detection. Conversely, the absence of both IS-SHK standard and CLas suggests the presence of a qPCR inhibitor, warranting retesting of the sample.