Publications

4366

Black abalone Haliotis cracherodii from California, USA, and Baja California, Mexico, have faced massive population declines for more than 30 yr. The main factors contributing to these declines have been overfishing, pollution, climate change, and lethal diseases, such as withering syndrome, caused by the intracellular bacterium Candidatus Xenohaliotis californiensis (CXc). In recent years, the presence of an associated bacteriophage, pCXc, infecting CXc was detected and reported in some abalone species from California and Baja California. In the present study, 199 black abalone fecal samples from 14 sites along the Baja California coast were analyzed for the presence of CXc and pCXc DNA. The overall prevalence of bacteria and phage-infected bacteria was 44 and 38%, respectively. We found significant differences in the relationship between the prevalence and the mean lengths of abalone throughout the study area. This result is probably due to differences in the size-frequency distribution between sampling zones. The only site where we found a relationship between prevalence and length was in Isla Todos Santos. We did not see a relationship between abalone density and the prevalence of the bacteria and the phage. Additionally, we found a positive but non-significant correlation in prevalence between CXc and pCXc. This study is the first to detect the presence of pCXc DNA in wild populations of black abalone of Baja California.

Candidatus phytoplasma affects a wide range of host plants. In recent years, the severity and distribution of the disease have increase many fold. The present study isolated the pathogen from leaves (chlorosis), dried branches, and the other tissues of the infected tree. Acacia trees (n=15) showing severe yellowing and desiccation in the landscape areas of Şanlıurfa province were sampled from the buds (V-shaped) in three different parts of the branches, backward from the top of the branches during the flowering period, and from the middle veins of the leaves on the same branch during the leafing period. Samples were initially amplified using the universal primer pair R16F1/R16R0 and subsequently subjected to nested PCR with the primer pair R16F2n/R2. The results indicated that, on average, 2 out of 15 buds collected from the apical parts of the branches, 11 out of 15 from the middle, and 6 out of 15 from the basal parts were infected with ‘Candidatus Phytoplasma australasia’. Moreover, all samples collected from the midribs of these 15 trees were found to be infected with Ca. P. australasia.

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.