Publications

4372

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.

ABSTRACT The functional roles of bacterial symbionts associated with microalgae remain understudied despite the importance of microalgae in biotechnology and environmental microbiology. 16S rRNA gene sequencing was conducted to analyze bacterial communities associated with two microalgae optimized for growth with flue gas containing 5%–10% CO 2 . Two dominant bacteria with no taxonomic classification beyond the class level (Paceibacteria) were discovered repeatedly in the most productive algal cultures. Long-read metagenomic sequencing was conducted to yield high-quality metagenomes, from which two novel species were discovered under the Seqcode (seqco.de/r:ywe1blo2), Phycocordibacter aenigmaticus gen. nov. sp. nov. and Minusculum obligatum gen. nov. sp. nov. The genus Phycocordibacter gen. nov. was proposed as the nomenclatural type of the family Phycocordibacteraceae fam. nov. and the order Phycocordibacterales ord. nov. Both bacteria possessed features typical of Patescibacteria such as reduced genomes (<800 kbp), lack of complete glycolysis and tricarboxylic acid (TCA) cycle pathways, and inability to synthesize amino acids. Instead, they rely on the reductive pentose phosphate pathway (Calvin cycle) for essential biosynthesis and redox balance. P. aenigmaticus may also rely on elemental sulfur oxidation ( sdo ), partial nitrite reduction ( nirK ), and sulfur-related amino acid metabolism (SAMe → SAH). Both bacteria were found in high relative abundance in cultures of Tetradesmus obliquus HTB1 (freshwater) and Nannochloropsis oceanica IMET1 (marine), suggesting a tight association with microalgae in various environments. The absence of full metabolic pathways for energy production suggests extreme metabolic limitations and obligate symbiosis, most likely with other bacteria associated with the microalgae. IMPORTANCE To our knowledge, this is the first report of Patescibacteria as dominant bacteria associated with microalgae or within a biologically mediated carbon capture system. Two novel Patescibacteria were found in two ecologically distinct microalgal cultures (one freshwater strain and one marine) regardless of whether the cultures were bubbled with air, 5% CO 2 , or 10% CO 2 . This unexpected and unprecedented dominance led to long-read sequencing and the assembly of high-quality metagenomes for both Patescibacteria, as well as five other bacteria in the system. The discovery of two novel species belonging to two novel genera, one novel family, and one novel order has enabled us to fill in gaps of a major, uncharacterized branch within the bacterial tree of life. Additionally, the extreme gene loss found in both Patescibacteria, Phycocordibacter aenigmaticus and Minusculum obligatum , contributes knowledge to a rapidly advancing body of research on the scavenging metabolic nature of this enigmatic and largely unclassified phylum.

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.

AbstractPurple sulfur bacteria (PSB) of the family Chromatiaceae (Gammaproteobacteria) can perform chemo‐ and photo‐lithoautotrophy (through anoxygenic photosynthesis) in anoxic layers of freshwater stratified (including meromictic) lakes. This group has been extensively studied via physiological and ecological approaches, albeit their genomics has lagged behind. Here, we monitored a small, shallow, karstic lake, Lagunillo de Cardenillas, that developed a pink coloration throughout the whole water column and prevailed for ca. 2 years across seasons of the limnological cycle. Combining the study of physical/chemical parameters, amplicon sequencing, metagenomics, genomics, and microscopy, we observed this phenomenon was caused by blooms of a novel Thiocapsa species, which represented ca. 40% of the total microbial biomass of the lake's water column during the autumn/winter mixing period, and ca. 36% in the anoxic layers during spring/summer stratification. The dominance of this microbe was attributed to the high sulfur concentrations and biogeochemical features of the lake combined with various genomic footprints/abilities of this microbe to utilize different nutrient sources under anoxic and oxic/microaerophilic conditions. The latter included nitrogen (cyanate and ethanolamine hydrolysis, N fixation, dissimilatory nitrate reduction, ammonia assimilation, denitrification), carbon (anoxygenic photosynthesis and the presence of α‐carboxysomes and type IA RuBisCOs) and sulfur (dimethylsulfide [DMS] and thiosulfate oxidation, dimethylsulfoxide [DMSO] reduction). In addition, this novel species possessed genes for gas vesicle formation, anoxic/oxic respiration pathways, hydrogenases, oxic stress response, and a CRISPR‐Cas array. Thus, its extensive genomic repertoire helped explain its versatility and success in colonizing both the anoxic layers and the oxic/anoxic interphase in this lake.