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ABSTRACTDespite recent genomic studies and increased molecular data, epitheliocystis remains an enigmatic fish disease with no experimental in vitro or in vivo models to aid the advancement of research. In this study, we revert to a classical microscopical approach and screen with the electron microscope the epitheliocystis lesions caused by a Ca. Parilichlamydia sp., infecting mucus cells in Greater amberjack. We report distinct morphological features of this bacterial family, characterised by Intermediate Bodies that closely resemble those of previously described Candidatus similchlamydia, and Elementary Bodies that exhibit morphological similarities to Chlamydia trachomatis. We describe the characteristics of a novel Chlamydial Inclusion Membrane (IM) type, with abundant interdigitations, possibly shaped by fusion of the IM with cytoplasmic vesicles, and moreover discuss the presence of multivesicular bodies in the infected cell. Our observation of immune cells in the infected areas indicates an interaction of macrophages with infected cells, a role for granular cells as pathogens reservoirs and an active phagoptosis process in the nearby areas, overall shedding light on cellular immune processes characterising these infections in fish hosts.

A Gram-negative, facultative anaerobic, rod-shaped, motile with peritrichous flagella, fluorescent bacterium, designated ‘Candidatus Pseudomonas auctus’ sp. nov. JDE115, was isolated from soybean root nodules in Virginia and characterized using a comprehensive integrative methodology. Growth of JDE115 occurred with 0–5.0% (w/v) NaCl (optimum 1%), at pH 6.0–10.0 (optimum pH 7.0), and at 10–40°C (optimum 28°C) in LB broth. Phylogenetic analyses based on the 16S rRNA gene placed the isolate as a member of a novel species within the genus Pseudomonas. Phylogenetic analyses based on whole-genome sequences, 16S rRNA, showed JDE115 having the highest similarity to Pseudomonas glycinae MS586. Average Nucleotide Identity (ANI) analysis also revealed the highest similarity of JDE115 to Pseudomonas glycinae MS586 (94.59%), which is below the 95% threshold for species delineation. Genome-to-genome distance analysis (GGDC, Formula 2) showed a maximum value of 57.10% with the same strain, far below the 70% cutoff. The primary isoprenoid quinone detected in JDE115 was ubiquinone-9 (Q-9) and the DNA G + C content was 60.68 mol%. The whole-cell fatty acid profile was dominated by C16:0, C17:0 cyclo, and the summed features 3 (C16:1ω7c and/or C16:1ω6c) and 8 (C18:1ω7c and/or C18:1ω6c). Additional fatty acids detected included 12:0, 14:0, and 18:0. Based on these phenotypic, chemotaxonomic, and phylogenetic data, strain JDE115 is proposed to represent a new species in the genus Pseudomonas, for which the name ‘Candidatus Pseudomonas auctus’ sp. nov. is proposed.

A Gram-stain-negative, aerobic, non-motile and short rod-shaped bacterium, designated strain SCSIO 64248T, was isolated from the stony coral Fungia sp. collected from South China Sea. Phylogenetic analysis indicated that strain SCSIO 64248T belonged to the family Geminicoccaceae and showed the highest 16S rRNA gene similarities with the types of Marinimicrococcus flavescens (90.5%), Arboricoccus pini (90.2%) and Benzoalithermus flavus (89.8%). The whole genome of strain SCSIO 64248T was 4.9 Mbp with a 68.8mol% G+C content. It shared average amino acid identity (AAI) values of 52–56.2%, which is below the proposed AAI threshold at the genus level and when compared to the known species of Geminicoccaceae. Colonies of strain SCSIO 64248T are circular, pink and convex. It was able to grow in the range of 4–37 °C, at pH 6.0–10.0 and in the presence of up to 8.0% (w/v) NaCl concentration. The major cellular fatty acid (>9%) was summed feature 8, C19 : 0 cyclo ω8c and C16 : 0, and the sole respiratory quinone was Q-10. The polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and an unidentified phospholipid. Data of polyphasic characteristics revealed that strain SCSIO 64248T represented a novel species of a new genus within the family Geminicoccaceae, for which the name Marinivivus gen. nov. is proposed with the type strain of the type species Marinivivus vitaminiproducens SCSIO 64248T (=MCCC 1K08013T=KCTC 92503T).

Sunhemp (Crotalaria juncea L.) is a tropical leguminous crop valued for its multifaceted utility in fiber production, green manuring, and as a raw material in the manufacture of paper and rope. One of the major biotic stresses affecting sunhemp is phyllody disease, caused by a phytoplasma, specifically belonging to the “Candidatus Phytoplasma” spp. These are obligate intracellular pathogens classified under the class Mollicutes, and are primarily transmitted by sap-sucking insect vectors such as leafhoppers, and psyllids. Phyllody-infected plants exhibit a range of morphological abnormalities, including malformed floral structures, chlorosis, stunted growth, and proliferation of axillary shoots, resulting in significant agronomic losses. In the present study, the sunhemp genotype NTPSH 11-02 was subjected to gamma irradiation at doses of 20 kR, 30 kR, 40 kR, and 50 kR to induce genetic variability. The M₂ generation lines derived from these treatments were evaluated under natural field conditions to assess their resistance to phyllody. Out of 44 mutant genotypes, two genotypes, NTPSH 63 and NTPSH 32 exhibited moderate resistance to phyllody, while nine genotypes—NTPSH 24, NTPSH 31, NTPSH 36, NTPSH 39, NTPSH 41, NTPSH 48, NTPSH 53, NTPSH 56, and NTPSH 60 demonstrated a tolerant reaction under natural infestation. Phyllody infection was found to negatively impact key yield-contributing traits, including plant height, number of pods per plant, and 100-seed weight (test weight). A significant reduction in these parameters was observed in infected plants compared to healthy controls, underscoring the detrimental effect of phyllody on overall productivity and crop performance.

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.

A Gram-positive, oval-shaped and non-motile strain, designated MMS21-DH1MA12T, was isolated from riverside soil and subjected to polyphasic taxonomic characterization. Strain MMS21-DH1MA12T grew optimally in tryptic soy agar, forming yellow-coloured, convex and smooth colonies. The optimal growth conditions of the strain were 30 °C, pH 7 and absence of NaCl. Strain MMS21-DH1MA12T shared the highest 16S rRNA gene sequence similarity with Agrococcus sediminis NS18T (97.3%), and then with Diaminobutyricimonas aerilata 6408 J-67T (97.1%) and Mycetocola miduiensis CGMCC 1.11101 T (96.9%), all belonging to the family Microbacteriaceae. Strain MMS21-DH1MA12T had a genome size of 2.4 Mbp and G+C content of 62.6%. The digital DNA–DNA hybridization (dDDH), orthologous average nucleotide identity (orthoANI) and average amino acid identity (AAI) values between strain MMS21-DH1MA12T and related type strains of the genera within the family Microbacteriaceae were no higher than 22.2%, 71.54% and 60.19%, respectively. The dDDH, orthoANI and AAI values of MMS21-DH1MA12T with related taxa were no higher than 22.2%, 71.54% and 61.96%, thus showing a distant relationship of the strain with other members of Microbacteriaceae. It was also notable that the species sharing the highest similarities were different for all three indices. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. The main cellular fatty acids were anteiso-C15 : 1, antesio-C17 : 1 and iso-C15 : 0. The predominant menaquinones were MK-10 and MK-11. The combination of physiological and biochemical properties, as well as chemotaxonomic features, clearly separated strain MMS21-DH1MA12T from related taxa of Microbacteriaceae. It is, thus, evident that MMS21-DH1MA12T represents a novel species in a novel genus, for which the name Humidisolicoccus flavus gen. nov., sp. nov. is proposed (type strain=MMS21-DH1MA12T = KCTC 49751T = LMG 32525T=JCM 37009T).

A strictly anaerobic bacterial strain, designated as AMB_02T, was isolated from a propionate enrichment culture obtained from a high-ammonia biogas digester. The cells were anaerobic and coccoid (0.5 µm), often appearing as diplococci or in a short chain of three to four cells. Growth was observed between 20 and 45 °C (optimum at 37–39 °C), with an initial pH of 6.5–9.0 (optimum pH 8.0–8.5), and the species tolerated up to 0.8 M NH4Cl and 0.5 M NaCl. The major cellular fatty acids were C16 : 0 (31.6%), C14 : 0 (14.6%) and C18 : 0 (13.3%). AMB_02T grew with formate, carbohydrates and aa, including asparagine, histidine, tryptone and tryptophan. Acetate was the major product formed. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain AMB_02T was most closely related to the species Citroniella saccharovorans (92.5%). The genome of strain AMB_02T was 2.5 Mb in length with a G+C content of 34.8 mol%, and 2,354 protein-coding genes were predicted. Furthermore, genes coding for the reductive glycine pathway potentially used for formate metabolism were identified. Comparative genomic analysis of AMB_02T revealed the closest similarity to C. saccharovorans [21.2% digital DNA–DNA hybridization (dDDH) and 77.4% average nt identity (ANI)] and to Parvimonas micra (24.4% dDDH and 76.9% ANI). Based on the phenotypic characteristics and phylogenetic analyses, AMB_02T is regarded as a novel genus, Microaceticoccus, within the family Peptoniphilaceae for which the species name Microaceticoccus formicicus is proposed. The type strain is AMB_02T=DSM 110248T=JCM 39108T.

A Gram-stain-negative, aerobic, rod-shaped bacterial strain, SYSU D60014T, was isolated from a sandy soil sample collected from the Gurbantunggut Desert in Xinjiang, PR China. Colonies of SYSU D60014T were pink-coloured, crystalline, irregular edge with a rough surface. Phylogenetic analyses based on both the 16S rRNA gene and whole-genome sequences assigned strain SYSU D60014T belonged to the family Rhodospirillaceae, formed a distinct lineage and showed 92.5–91.0% similarity to closely related strains. Digital DNA–DNA hybridization, average nucleotide identity and average amino acid identity values between strain SYSU D60014T and members of its related species were 17.2–19.6%, 70.8–74.4% and 48.9–64.5%, respectively. The complete genome of strain SYSU D60014T was 5,100,926 bp with a DNA G+C content of 65.1%. Cells were oxidase-positive and catalase-negative. The strain could grow at 28–40 °C (optimum, 37 °C), pH 5.0–8.0 (optimum, pH 7.0), and in the presence of up to 3% NaCl (optimum, 1–1.5%, w/v) on R2A. The predominant menaquinone was Q-10. The main polar lipids were phosphatidylethanolamine, phosphatidylmethyl ethanolamine, diphosphatidylglycerol, unidentified aminophospholipid, unidentified aminolipid, unidentified phospholipid, four unidentified polar lipids and two unidentified phosphoglycolipids. Major cellular fatty acids were C19 : 0 cyclo ω8c, summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c) and C16 : 0. Based on the results obtained through genotypic and phenotypic analyses, we propose that strain SYSU D60014T represents a novel species and genus within the family Rhodospirillaceae, for which we propose the name Virgifigura deserti gen. nov., sp. nov. (type strain SYSU D60014T=NBRC 112951T=CPCC 101030T).

A Gram-positive, aerobic, non-motile coccoid bacterium, designated strain ZF39T, was isolated from a farm in Quandian Village, Zhengzhou City, Henan Province, China, and subjected to taxonomic characterization. Optimal growth occurred at 32 ℃, pH 7.0 and 0–1% NaCl (w/v). Mannose and glucose were identified as the sugar components in the whole-cell hydrolysates. The strain’s peptidoglycan type was classified as A3γ (ll-Dpm-Gly), and MK-9(H4) was identified as the predominant respiratory quinone. Aminoglycolipid, aminophospholipid, glycolipids, phosphatidylglycerol and phospholipid were detected as the major polar lipids. The predominant cellular fatty acids were anteiso-C15 : 0 (48.7%) and iso-C15 : 0 (20.2%). Phylogenetic analysis based on 16S rRNA gene sequences placed strain ZF39T within the family Propionibacteriaceae. The strain formed a distinct genetic lineage adjacent to the genus Desertihabitans, with 16S rRNA gene sequence similarities of 94.70% to Desertihabitans aurantiacus CPCC 204711T and 94.56% to Desertihabitans brevis KCTC 49116T. The genomic G+C content was 67.7 mol%. Genome comparisons revealed that the average nucleotide identity values between strain ZF39T and D. aurantiacus CPCC 204711T, D. brevis KCTC 49116T, Granulicoccus phenolivorans DSM 17626T were 72.50%, 71.98% and 72.36%, respectively. Moreover, phylogenetic analysis and phenotypic characterization supported the classification of strain ZF39T as a novel species of a new genus within the family Propionibacteriaceae. The name Ammonicoccus fulvus gen. nov., sp. nov. is proposed, with ZF39T (=CGMCC 1.60047T=KCTC 59250T=MCCC 1K08851T) as the type strain.

Bacterial strain SL12-8T was characterized and isolated from the skin microbiota of Pelophylax perezi, the Perez’s frog. Strain SL12-8T stained Gram-negative and formed rod-shaped cells that grew optimally at 25 °C and pH 7.0–7.5. The G+C content of the DNA was 66.2 mol%. Ubiquinone 8 was the respiratory quinone identified in the studied strain and the most closely related taxon. The major fatty acids were summed in feature 3 and summed in feature 8 and C16:0, representing 84% of the total fatty acids. Phylogenetic analyses based on the 16S rRNA gene sequence placed strain SL12-8T within the order Burkholderiales in a distinct lineage. The 16S rRNA gene sequence similarities of strain SL12-8T to that of Rubrivivax albus, Scleromatobacter humisilvae, Piscinibacter aquaticus, Azohydromonas caseinilytica and Aquincola agrisoli were 94.41, 94.08, 93.72, 93.72 and 93.64%, respectively. The draft genome sequence of strain SL12-8T comprises 3,115,197 bases with a 313-fold mapped genome coverage. The assembled genome consists of 53 large contigs with more than 500 bp, and the genome encodes 2,814 putative coding sequences. The analysis of the available genomes from the closest genera showed 124 core genes that reveal a novel genus-level clade including the strain SL12-8T. Analysis of the SL12-8T genome revealed the presence of the beta-lactone and terpene biosynthetic gene clusters. The phylogenomic, phylogenetic, phenotypic and chemotaxonomic data showed that strain SL12-8T (=UCCCB 131T=CECT 30762T) represents the type of a novel species and genus, for which we propose the name Amphibiibacter pelophylacis gen. nov., sp. nov.