Rhodophyticola porphyridii gen. nov., sp. nov., isolated from a red alga, Porphyridium marinum

Long-Read Sequencing Unlocks New Insights into the Amphidinium carterae Microbiome

Dinoflagellates are one of the largest groups of marine microalgae and exhibit diverse trophic strategies. Some dinoflagellates can produce secondary metabolites that are known to be toxic, which can lead to ecologically harmful blooms. Amphidinium carterae is one species of dinoflagellate that produces toxic compounds and is used as a model for dinoflagellate studies. The impact of the microbiome on A. carterae growth and metabolite synthesis is not yet fully understood, nor is the impact of bacterial data on sequencing and assembly. An antibiotic cocktail was previously shown to eliminate 16S amplification from the dinoflagellate culture. Even with drastically reduced bacterial numbers during antibiotic treatment, bacterial sequences were still present. In this experiment, we used novel Nanopore long-read sequencing techniques on A. carterae cultures to assemble 15 full bacterial genomes ranging from 2.9 to 6.0 Mb and found that the use of antibiotics decreased the percentage of reads mapping back to bacteria. We also identified shifts in the microbiome composition and identified a potentially deleterious bacterial species arising in the absence of the antibiotic treatment. Multiple antibiotic resistance genes were identified, as well as evidence that the bacterial population does not contribute to toxic secondary metabolite synthesis.

Fontisubflavum oceani gen. nov., sp. nov., isolated from the deep-sea cold seep water of South China Sea

In this study, we report a Gram-stain-negative, rod-shaped, atrichous and aerobic bacterial strain named CSW1921T, which was isolated from the deep-sea water of a cold seep in South China Sea. Growth of strain CSW1921T occurred at 10.0-35.0 °C (optimum, 30 °C), pH 5.0-10.0 (optimum, pH 8.0-9.0) and with 0-9.0 % (w/v) NaCl (optimum, 1.0-2.0 %). Phylogenetic tree analysis based on 16S rRNA gene sequence or the genomic sequence indicated that strain CSW1921T belonged to the family Rhodobacteraceae and was closely related to Rhodophyticola porphyridii MA-7-27T (97.5 % sequence similarity). Genomic analysis indicated that strain CSW1921T contains a circular chromosome of 3 592 879 bp with G+C content of 60.5 mol%. The predominant respiratory quinone of CSW1921T was ubiquinone-10. The polar lipids of CSW1921T contained phosphatidylglycerol, three unidentified aminolipids, two unidentified phospholipids and two unidentified lipids. The major fatty acids of strain CSW1921T contained C16 : 0, C18 : 1 ω7c 11-methyl and summed feature 8 (C18 : 1 ω7c). The average nucleotide identity, DNA-DNA hybridization and average amino acid identity values between strain CSW1921T and members of its related species were 68.02-69.08 %, 12.7-12.9 % and 46.87-48.08 %, respectively, which were lower than the recommended threshold values for bacterial species or genus delineation. Phylogenetic, physiological, biochemical and morphological analyses suggested that strain CSW1921T represents a novel genus and a novel species of the family Rhodobacteraceae, and the name Fontisubflavum oceani gen. nov., sp. nov. is proposed with the type strain CSW1921T (=MCCC 1K08371T=KCTC 92834T).

Alkalicoccobacillus porphyridii sp. nov., isolated from a marine red alga, reclassification of Shouchella plakortidis and Shouchella gibsonii as Alkalicoccobacillus plakortidis comb. nov. and Alkalicoccobacillus gibsonii comb. nov., and emended description of the genus Alkalicoccobacillus Joshi et al. 2022

A Gram-stain-positive alkali-tolerant and strictly aerobic bacterium, designated strain P16T, was isolated from a marine red alga, Porphyridium cruentum, in the Yellow Sea, Republic of Korea. Cells were motile rods with peritrichous flagella and exhibited catalase and oxidase activities. The optimal growth of strain P16T was observed to occur at 30 °C and pH 8.0 and in the presence of 2.0 % (w/v) NaCl. Menaquinone-7 was identified as the sole respiratory quinone. Strain P16T contained anteiso-C15 : 0, iso-C15 : 0, iso-C14 : 0 and iso-C16 : 0, and diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine as major cellular fatty acids and polar lipids, respectively. The G+C content of strain P16T was 40.8 mol%. Strain P16T was most closely related to Shouchella plakortidis P203T, Shouchella gibsonii DSM 8722T and Alkalicoccobacillus murimartini LMG 21005T with 98.1, 98.1 and 98.0 % 16S rRNA gene sequence similarities, respectively. Phylogenetic analyses based on 16S rRNA gene and genome sequences revealed that strain P16T, S, plakortidis, S. gibsonii and A. murimartini formed a single phylogenetic lineage cluster, and genomic relatedness analyses showed that they are different species. Based on phylogenetic, phenotypic, chemotaxonomic and molecular features, strain P16T represents a novel species of the genus Alkalicoccobacillus, for which the name Alkalicoccobacillus porphyridii sp. nov. is proposed. The type strain is P16T (=KACC 19520T=JCM 32931T). In addition, S. plakortidis and S. gibsonii are reclassified as Alkalicoccobacillus plakortidis comb. nov. (type strain P203T=DSM 19153T=NCIMB 14288T) and Alkalicoccobacillus gibsonii comb. nov. (type strain PN-109T=ATCC 700164T=DSM 8722T=KCCM 41407T), respectively.

A Possible Aquatic Origin of the Thiaminase TenA of the Human Gut Symbiont Bacteroides thetaiotaomicron

TenA thiamin-degrading enzymes are commonly found in prokaryotes, plants, fungi and algae and are involved in the thiamin salvage pathway. The gut symbiont Bacteroides thetaiotaomicron (Bt) produces a TenA protein (BtTenA) which is packaged into its extracellular vesicles. An alignment of BtTenA protein sequence with proteins from different databases using the basic local alignment search tool (BLAST) and the generation of a phylogenetic tree revealed that BtTenA is related to TenA-like proteins not only found in a small number of intestinal bacterial species but also in some aquatic bacteria, aquatic invertebrates, and freshwater fish. This is, to our knowledge, the first report describing the presence of TenA-encoding genes in the genome of members of the animal kingdom. By searching metagenomic databases of diverse host-associated microbial communities, we found that BtTenA homologues were mostly represented in biofilms present on the surface of macroalgae found in Australian coral reefs. We also confirmed the ability of a recombinant BtTenA to degrade thiamin. Our study shows that BttenA-like genes which encode a novel sub-class of TenA proteins are sparingly distributed across two kingdoms of life, a feature of accessory genes known for their ability to spread between species through horizontal gene transfer.

Algicella marina gen. nov., sp. nov., a novel marine bacterium isolated from a Pacific red alga

A novel Gram-staining negative, strictly aerobic, rod-shaped, and non-motile bacterium, designated strain 9Alg 56^T, was isolated from the red alga Tichocarpus crinitus. The phylogenetic analysis based on 16S rRNA gene sequences placed the novel strain within the family Rhodobacteraceae, the order Rhodobacterales, the class Alphaproteobacteria, the phylum Pseudomonadota. The nearest neighbors of the new strain were Pontivivens insulae KCTC 42458^T, Oceanibium sediminis KCTC 62076^T, Halovulum dunhuangense YYQ-30^T and Monaibacterium marinum C7^T with 16S rRNA gene sequence similarity of 94.7, 94.4%, 93.1 and 92.7%, respectively. The AAI/ANI/dDDH values between 9Alg 56^T and the five species of the closest genera (Pontivivens, Oceanibium, Halovulum, Monaibacterium, and 'Oceanomicrobium') were 58.63-63.91%/ 75.91-77.37%/ 19.3-20.4%. The prevalent fatty acids of strain 9Alg 56^T were C_18:1 ω7c, C_18:0 and C_14:0 3-OH. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, phosphatidic acid, phosphatidylcholine, and two unidentified lipids. The DNA G+C content of strain 9Alg 56^T was 61.5 mol%. A combination of the genotypic and phenotypic data showed that the algal isolate represents a novel genus and species, for which the name Algicella marina gen. nov., sp. nov. is proposed. The type strain is 9Alg 56^T (= KCTC 72005^T = KMM 6775^T).

Mesobacterium pallidum gen. nov., sp. nov., Heliomarina baculiformis gen. nov., sp. nov. and Oricola indica sp. nov., three novel Alphaproteobacteria members isolated from deep-sea water in the southwest Indian ridge

Three Gram-staining-negative, aerobic and rod-shaped strains, designated as T40-1T, T40-3T and JL-62T, were isolated from the deep-sea water in the southwest Indian ridge. For strain T40-1T, growth occurred at 15–37 °C (optimum, 28 °C), pH 6.0–9.0 (optimum, pH 7.5) and in the presence of 0.5–5.0 % NaCl (w/v; optimum, 2.0 %). Strain T40-3T could grow at 15–40 °C (optimum, 28 °C), with 0.5–11.0 % NaCl (optimum, 2.0 %, w/v) at pH 6.0–9.5 (optimum, 8.0). The temperature, pH and salinity ranges for growth of strain JL-62T were 15–40 °C (optimum, 30 °C), pH 5.5–9.0 (optimum, pH 7.5–8.0) and 0.5–9.0 % NaCl (w/v; optimum, 4.0 %). Ubiquinone-10 was the sole ubiquinone in all strains, the major fatty acids (>20 %) were summed feature 8 (C18 : 1  ω7c / C18 : 1  ω6c). The major polar lipids of strains T40-1T and T40-3T were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine and diphosphatidylglycerol. Strain JL-62T contained phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and sulfoquinovosyldiacylglycerol as major polar lipids. Phylogenetic trees based on 16S rRNA gene and core-genomic sequences revealed affiliation of strains T40-1Tand T40-3T to the family Roseobacteraceae and formed two independent clades from other Roseobacteraceae genera, and those two strains had average nucleotide identities of 62.0–72.0 % to their phylogenetically related species which fell into to the genus boundary range, indicating that they represent two novel genera. While strain JL-62T represents a novel species in the genus Oricola belonging to the family Phyllobacteriaceae , which was supported by overall genomic relatedness index calculations. The DNA G+C contents of strains T40-1T, T40-3T and JL-62T were 66.5, 60.1 and 62.1 mol %, respectively. Based on the polyphasic taxonomic data, strains T40-1T (=MCCC M24557T=KCTC 82975T) and T40-3T (=MCCC 1K05135T=KCTC 82976T) are classified as representing two novel genera belonging to the family Roseobacteraceae with the names Mesobacterium pallidum gen. nov., sp. nov. and Heliomarina baculiformis gen. nov., sp. nov. are proposed, and strain JL-62T (=MCCC M24579T=KCTC 82974T) is proposed to represent a novel species within the genus Oricola with the name Oricola indica sp. nov. is proposed.

Genetic and phylogenetic analysis of dissimilatory iodate-reducing bacteria identifies potential niches across the world's oceans

Iodine is oxidized and reduced as part of a biogeochemical cycle that is especially pronounced in the oceans, where the element naturally concentrates. The use of oxidized iodine in the form of iodate (IO3-) as an electron acceptor by microorganisms is poorly understood. Here, we outline genetic, physiological, and ecological models for dissimilatory IO3- reduction to iodide (I-) by a novel estuarine bacterium, Denitromonas sp. IR-12. Our results show that dissimilatory iodate reduction (DIR) by strain IR-12 is molybdenum-dependent and requires an IO3- reductase (idrA) and likely other genes in a mobile cluster with a conserved association across known and predicted DIR microorganisms (DIRM). Based on genetic and physiological data, we propose a model where three molecules of IO3- are likely reduced to three molecules of hypoiodous acid (HIO), which rapidly disproportionate into one molecule of IO3- and two molecules of iodide (I-), in a respiratory pathway that provides an energy yield equivalent to that of nitrate or perchlorate respiration. Consistent with the ecological niche expected of such a metabolism, idrA is enriched in the metagenome sequence databases of marine sites with a specific biogeochemical signature (high concentrations of nitrate and phosphate) and diminished oxygen. Taken together, these data suggest that DIRM help explain the disequilibrium of the IO3-:I- concentration ratio above oxygen-minimum zones and support a widespread iodine redox cycle mediated by microbiology.

Muriiphilus fusiformis gen. nov., sp. nov., a novel non-marine bacterium belonging to the Roseobacter group, and reclassification of Maritimibacter lacisalsi (Zhong et al. 2015) as Muriicola lacisalsi gen. nov., comb. nov

An aerobic, Gram-stain-negative, non-sporulating, flagellated and spindle-like bacterium, designated HY14^T, was isolated from a pickle-processing factory wastewater sample. The isolate chemoheterotrophically grew at 4-42 °C (optimum, 35 °C) and pH 5.5-9.0 (optimum, pH 6.0-6.5). Salt was required for growth (0.5-12 % NaCl, w/v). A deep brown and water-soluble uncharacterized pigment was produced when grown in certain media. The predominant fatty acids (>5 %) included C_16 : 0, C_18 : 1  ω7c, 11-methyl C_18 : 1  ω7c and C_19 : 0 cyclo ω8c. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, two unidentified aminolipids, two unidentified phospholipids, two unidentified glycolipids and five unknown lipids. The major isoprenoid quinone was ubiquinone-10. Pairwise alignment based on 16S rRNA gene sequences indicated that strain HY14^T had the highest sequence similarity to genera Maritimibacter (95.61-96.05 %) and Boseongicola (95.82 %). Phylogenetic analysis based on core genome illustrated that strain HY14^T formed a monophyletic lineage with members of the genus Maritimibacter in the clade of the Roseobacter group in the family Rhodobacteraeceae. The core-gene average amino acid identity used to define bacterial genera by a threshold of 60-80 % was calculated to be 68.56-76.5 % between HY14^T and closely related taxa. Several genomic characteristics, such as carrying two RuBisCO-mediated pathways and different osmoprotectant transport pathways, exhibited the genotypic discrepancies of strain HY14^T. Based on the polyphasic taxonomic characterization, strain HY14^T is considered to represent a novel species of a novel genus belonging to the family Rhodobacteraeceae, for which the name Muriiphilus fusiformis gen. nov., sp. nov. is proposed. The type strain is HY14^T (=CGMCC 1.15973^T=KCTC 52499^T). Maritimibacter lacisalsi (Zhong et al. 2015) is considered to diverge from Maritimibacter alkaliphilus at the genus level, and should be reassigned as a novel genus, for which the name Muriicola lacisalsi gen. nov., comb. nov. is proposed.

Mesobaculum littorinae gen. nov., sp. nov., a novel bacterium isolated from a sea snail Littorina scabra

Members within the family Rhodbacteraceae are morphologically and genetically highly diverse, and originate mostly from coastal marine environments. In this study, a novel species of this family, designated M0103^T, was isolated from the surface of a sea snail Littorina scabra. Strain M0103^T is Gram-stain-negative, halophilic, non-motile and non-Bacteriochlorophyll a-producing bacterium. Several phenotypic characteristics of the isolate were similar to other species within this family, such as the sole respiratory quinone Q-10 and major fatty acid components C_18 : 1  ω7c, C_18 : 0 and C_16 : 0. Strain M0103^T contains a diphosphatidylglycerol, a phosphatidylglycerol, a phosphatidylcholine, a phosphatidy ethanolamine, a phosphatidylinositol, five unidentified phospholipids and four unidentified polar lipids. Based on the 16S rRNA gene sequence analysis, this isolate showed the closest phylogenetic relationship with 'Palleronia pontilimi' GH1-23^T (95.1 %). Values of average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) of genome sequences were of 70.1-76.4 % and 18.3-20.9 % between the isolate and 24 closely related type strains. Analysis the 4.0 Mb genome of strain M0103^T revealed several putative genes associated with cellular stress resistance, which may play protective roles for the isolate in the adaptation to a marine environment. Phylogenetic, phenotypic and chemotaxonomic analyses suggested that strain M0103^T represents a novel genus and novel species of the family Rhodobacteraceae, for which the name Mesobaculum littorinae gen. nov., sp. nov. is proposed. The type strain is M0103^T (=MCCC 1K03619^T=KCTC 62358^T).

Alterinioella nitratireducens gen. nov., sp. nov., Isolated from Seawater in the West Pacific Ocean

A novel Gram-negative, nonspore forming, nonmotile, and short-rod-shaped aerobic bacterium, designated DY48A3-103^T, was isolated from a seawater sample collected from the West Pacific Ocean. Strain DY48A3-103^T showed oxidase-positive and catalase-positive activities. Growth was observed at 10-37 °C (optimum 30 °C), at pH 6.5-9.5 (optimum 8.0) and in 1-11% NaCl (optimum 3%, w/v). 16S rRNA gene sequence analysis exhibited 96.3%, 96.1%, 96.0%, and 94.9% sequence similarity to the type strains Rhodophyticola porphyridii MA-7-27^T, Nioella sediminis JS7-11^T, N. nitratireducens SSW136^T, and Jannaschia helgolandensis DSM 14858^T, respectively. Strain DY48A3-103^T and the type strains of phylogenetically related species have 61.7-75.4% AAI values, which fell into to the genus boundary range (60-80% AAI). Phylogenetic trees based on the 16S rRNA gene sequences and the genome sequences of strain DY48A3-103^T revealed that it was affiliated to the members of the family Rhodobacteraceae. The G+C content was 65.4%. The sole isoprenoid quinone was Q-10. The predominant polar lipids were phosphatidylcholine and phosphatidylglycerol. Major fatty acids were summed feature 8 (comprising C_18:1ω7c and/or C_18:1ω6c), C_19:0 cyclo ω8c, and C_16:0. On the basis of the phenotypic, chemotaxonomic, and genomic properties, strain DY48A3-103t is proposed to represent a novel genus and a novel species, Alterinioella nitratireducens gen. nov., sp. nov., in the family Rhodobacteraceae. The type strain is DY48A3-103^T (= KCTC 72738^T = MCCC 1K04322^T).

Maribacter algicola sp. nov., isolated from a marine red alga, Porphyridium marinum, and transfer of Maripseudobacter aurantiacus Chen et al. 2017 to the genus Maribacter as Maribacter aurantiacus comb. nov

A Gram-stain-negative, strictly aerobic and moderately halophilic bacterial strain, designated strain PoM-212^T, was isolated from a marine alga, Porphyridium marinum, in the Republic of Korea. Cells were catalase- and oxidase-positive rods with gliding motility without flagellum. Growth was observed at 20-40 °C (optimum, 30 °C) and pH 5.0-8.5 (pH 5.0-5.5) and in the presence of 0.5-5 % (w/v) NaCl (2-3 %). Strain PoM-212^T contained iso-C_15 : 1, iso-C_15 : 0, iso-C_17 : 0 3-OH and summed feature 3 (comprising C_16 : 1ω7c and/or C_16 : 1ω6c) as major fatty acids and menaquinone-6 as the sole isoprenoid quinone. Phosphatidylethanolamine, three unidentified aminolipids and two unidentified polar lipids were detected as major polar lipids. The G+C content of the genomic DNA was 41.0 mol%. Strain PoM-212^T was most closely related to Maribacter lutimaris KJ4^T, Maripseudobacter aurantiacus CDA4^T and Maribacter flavus C3^T with 97.2, 97.2 and 97.0 % 16S rRNA gene sequence similarities, respectively, and it formed a distinct phylogenetic lineage from them within the genus Maribacter. Maripseudobacter aurantiacus formed a close phylogenetic lineage with Maribacter flavus with 99.7 % 16S rRNA gene sequence similarity, but their digital DNA-DNA hybridization value was 67.4 %. On the basis of its phenotypic, chemotaxonomic and molecular properties, strain PoM-212^T represents a novel species of the genus Maribacter, for which the name Maribacter algicola sp. nov. is proposed. The type strain is PoM-212^T (=KACC 19789^T=JCM 32941^T). The transfer of Maripseudobacter aurantiacus to the genus Maribacter as Maribacter aurantiacus comb. nov. is also proposed (type strain CDA4^T=KCTC 52409^T=MCCC 1K03210^T).