Publications

4256

A novel Gram-stain-negative, motile and thermo-halophilic rod-shaped bacterium SMD15-11T was isolated from Seokmodo hot spring in Incheon, Republic of Korea. The strain grew at concentrations of 0.5–7% (w/v) NaCl (optimum at 3%), at pH 5.0–9.0 (optimum at 7.0) and in a temperature range of 30–60 °C (optimum at 50 °C). Strain SMD15-11T shared the highest 16S rRNA gene sequence percentage with Hahella chejuensis 96CJ10356T (92.5%). Both the phylogenetic and phylogenomic analyses showed that strain SMD15-11T clustered with Hahellaceae members, demonstrating its close relatedness to the type species of the Hahellaceae family. The genome-relatedness indices between strain SMD15-11T and other type species of the family Hahellaceae were in the ranges of 67.2–69.1% for average nucleotide identity, 59.3–62.8% for average amino acid identity and 15.9–24.8% for digital DNA–DNA hybridization, which were significantly below the cut-off values for the genus delineation. The genome comprised 3,444,746 bp with a G+C content of 60.1 mol%. The polar lipids contained phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, four unidentified phospholipids, two unidentified aminophospholipids and two unidentified lipids. The predominant fatty acids are C16:1  ω9c, C16:0, C18:1  ω9c and summed feature 3, comprising C16:1  ω7c/C16: 1  ω6c. The polyphasic taxonomic properties indicate that the strain represents a novel genus and species in the family Hahellaceae for which the name Thermohahella caldifontis gen. nov., sp. nov. is proposed. The type strain is SMD15-11T (=KCTC 8289T=NBRC 116488T).

An anaerobic, thermophilic methanogen, designated strain LWZ-6T, was isolated from the Shengli oil field, China. The cells of strain LWZ-6T were non-motile cocci, with a diameter of 0.5–1.0 µm, and formed aggregates. They reduced methanol and monomethylamine into methane, using H2 as an electron donor. Dimethylamine, trimethylamine and methanethiol, H2/CO2, formate, acetate, pyruvate, lactate and glucose were not used as energy sources. Strain LWZ-6T required yeast extract, acetate or CO2 as carbon sources. Strain LWZ-6T grew at 35–65 °C (optimum 55 °C), pH 5.0–8.0 (optimum 6.0–6.5) and 0–60 g l−1 NaCl (optimum 9 g l−1). The genome was 1.54 Mbp with a G+C content of 54.42 mol%. Strain LWZ-6T shared 83.54% 16S rRNA gene sequence identity with Infirmifilum lucidum strain 3507LTT in the class Thermoprotei. Phylogenetic analysis based on the 16S rRNA gene, along with phylogenomic analysis, indicated that strain LWZ-6T belonged to the candidate class ‘Candidatus Methanomethylicia’, which lacks cultivated representatives. Based on these findings, a new species within a new genus, Methanosuratincola petrocarbonis gen. nov., sp. nov., is proposed for LWZ-6T (=CCAM 1872T=JCM 39528T). In addition, we propose the Methanosuratincolia class. nov. for candidate class ‘Ca. Methanomethylicia’ represented by Methanosuratincolaceae fam. nov. and Methanosuratincolales ord. nov. within the phylum Thermoproteota.

Citrus greening or Huanglongbing (HLB) is a rapidly spreading disease caused by Candidatus Liberibacter species, which inhabit the phloem of citrus plants. It is primarily transmitted by psyllid insects. Managing HLB is challenging due to the bacterium's phloem-restricted nature, making diagnosis and treatment with antimicrobials difficult. Here in the present study, the bacterial consensus sequences were used for the primer design with In silico approaches and validated by PCR. The study was carried out in the Malwa region of Madhya Pradesh, India, which is known for citrus cultivations and remains affected by the HLB disease. Phylogenetic analysis of 100 Candidatus Liberibacter 16S rRNA sequences from NCBI was conducted using MEGA 6, with Malwa-specific refinement via MAFFT alignment. Eight previously deposited sequences formed the basis for the study. A consensus sequence was derived and used to design region-specific primers with GeneFisher. PCR validation was carried out with standard thermal cycling and gel electrophoresis. Phylogenetic analysis of 100 Candidatus Liberibacter 16S rRNA sequences from NCBI was conducted using Phylogenetic analysis showed high genetic variation among Liberibacter strains, supporting the need for region-specific detection. Eight sequences from the Malwa region were aligned using BioEdit, confirming conserved primer sites. Consensus primers were designed using GeneFisher and optimized for 16S rRNA targets. PCR validation identified 22 positives out of 100 samples, with primer set 2 detecting all target species effectively. The study concludes that primer set 2 enables rapid and accurate detection of HLB-causing bacteria in the Malwa region.

Cyanobacteria biodiversity remains underexplored despite their ecological importance and potential applications. To address this, we investigated two Leptolyngbya-like strains, LEGE 07170 and LEGE 191244, collected from marine tide pools in Portugal and Morocco using polyphasic approach. Phylogenetic analyses indicates that the strains form a distinct clade with strong statistical support in the Oculatellales order. The 16S rRNA gene identity matrix shows that the maximum shared values with the phylogenetically closest genera Gansulinema, Kaiparowitsia, Shahulinema, Aerofilum and Thermoleptolyngbya is consistently below 94.5%. Morphologically, LEGE 07170 and LEGE 191244 are indistinguishable to each other. Both optical and TEM analyses showed vacuole-like structures at the cells cross-walls and this character morphologically distinguishes these strains from their phylogenetically related genera. The 16S–23S ITS secondary structures also differed the LEGE-CC strains from their closest related genera.

Abstract The presence of fastidious phytopathogenic bacteria ‘Candidatus Arsenophonus phytopathogenicus’ and ‘Candidatus Phytoplasma solani’ challenges sugar beet cultivation in Austria. Reptalus artemisiae (Becker, 1865) (referred before as Reptalus quinquecostatus sensu Holzinger et al. 2003) is the principal vector of ‘Ca. P. solani’ to sugar beet in Serbia, while Pentastiridius leporinus is the primary vector of ‘Ca. A. phytopathogenicus’ in western Europe and can also transmit ‘Ca. P. solani’. This study investigates the epidemiology of the associated diseases in Austrian sugar beet fields. An extensive survey in 2024 at 33 locations revealed significant spatial and temporal variability in cixiid populations, with R. artemisiae emerging as the predominant species. Transmission trials and field surveys confirmed R. artemisiae as a vector of ‘Ca. A. phytopathogenicus’ and ‘Ca. P. solani’ 16SrXII-P driving a disease outbreak in Nikitsch. The predominance of R. artemisiae in nearly all monitored fields suggests its significant role in the pathogens’ epidemiology on a broader scale in the Pannonian plain. Spatial and temporal variations in pathogen incidence in Austrian sugar beet mirror patterns in Serbia, driven by R. artemisiae. The co-occurrence of ‘Ca. A. phytopathogenicus’ and ‘Ca. P. solani’ 16SrXII-A and 16SrXII-P and their transmission by two vectors complicate disease management efforts.

Abstract Background Rare species, especially of the marine sedimentary biosphere, have long been overlooked owing to the complexity of sediment microbial communities, their sporadic temporal and patchy spatial abundance, and challenges in cultivating environmental microorganisms. In this study, we combined enrichments, targeted metagenomic sequencing, and extensive data mining to uncover uncultivated members of the archaeal rare biosphere in marine sediments. Results In protein-amended enrichments, we detected the ecologically and metabolically uncharacterized class Candidatus Penumbrarchaeia within the phylum Thermoplasmatota. By screening more than 8000 metagenomic runs and 11,479 published genome assemblies, we expanded the phylogeny of Ca. Penumbrarchaeia by 3 novel orders. All six identified families of this class show low abundance in environmental samples characteristic of rare biosphere members. Members of the class Ca. Penumbrarchaeia were predicted to be involved in organic matter degradation in anoxic, carbon-rich habitats. All Ca. Penumbrarchaeia families contain high numbers of taxon-specific orthologous genes, highlighting their environmental adaptations and habitat specificity. Besides, members of this group exhibit the highest proportion of unknown genes within the entire phylum Thermoplasmatota, suggesting a high degree of functional novelty in this class. Conclusions In this study, we emphasize the necessity of targeted, data-integrative approaches to deepen our understanding of the rare biosphere and uncover the functions and metabolic potential hidden within these understudied taxa.