Sulfitobacter undariae sp. nov., isolated from a brown algae reservoir

Genome-based taxonomic classification of the genus Sulfitobacter along with the proposal of a new genus Parasulfitobacter gen. nov. and exploring the gene clusters associated with sulfur oxidation

BACKGROUND

The genus Sulfitobacter, a member of the family Roseobacteraceae, is widely distributed in the ocean and is believed to play crucial roles in the global sulfur cycle. However, gene clusters associated with sulfur oxidation in genomes of the type strains of this genus have been poorly studied. Furthermore, taxonomic errors have been identified in this genus, potentially leading to significant confusion in ecological and evolutionary interpretations in subsequent studies of the genus Sulfitobacter. This study aims to investigate the taxonomic status of this genus and explore the metabolism associated with sulfur oxidation.

RESULTS

This study suggests that Sulfitobacter algicola does not belong to Sulfitobacter and should be reclassified into a novel genus, for which we propose the name Parasulfitobacter gen. nov., with Parasulfitobacter algicola comb. nov. as the type species. Additionally, enzymes involved in the sulfur oxidation process, such as the sulfur oxidization (Sox) system, the disulfide reductase protein family, and the sulfite dehydrogenase (SoeABC), were identified in almost all Sulfitobacter species. This finding implies that the majority of Sulfitobacter species can oxidize reduced sulfur compounds. Differences in the modular organization of sox gene clusters among Sulfitobacter species were identified, along with the presence of five genes with unknown function located in some of the sox gene clusters. Lastly, this study revealed the presence of the demethylation pathway and the cleavage pathway used by many Sulfitobacter species to degrade dimethylsulfoniopropionate (DMSP). These pathways enable these bacteria to utilize DMSP as important source of sulfur and carbon or as a defence strategy.

CONCLUSIONS

Our findings contribute to interpreting the mechanism by which Sulfitobacter species participate in the global sulfur cycle. The taxonomic rearrangement of S. algicola into the novel genus Parasulfitobacter will prevent confusion in ecological and evolutionary interpretations in future studies of the genus Sulfitobacter.

Growth Substrate and Prophage Induction Collectively Influence Metabolite and Lipid Profiles in a Marine Bacterium

Bacterial growth substrates influence a variety of biological functions, including the biosynthesis and regulation of lipid intermediates. The extent of this rewiring is not well understood nor has it been considered in the context of virally infected cells. Here, we used a one-host-two-temperate phage model system to probe the combined influence of growth substrate and phage infection on host carbon and lipid metabolism. Using untargeted metabolomics and lipidomics, we reported the detection of a suite of metabolites and lipid classes for two Sulfitobacter lysogens provided with three growth substrates of differing complexity and nutrient composition (yeast extract/tryptone [complex], glutamate and acetate). The growth medium led to dramatic differences in the detectable intracellular metabolites, with only 15% of 175 measured metabolites showing overlap across the three growth substrates. Between-strain differences were most evident in the cultures grown on acetate, followed by glutamate then complex medium. Lipid distribution profiles were also distinct between cultures grown on different substrates as well as between the two lysogens grown in the same medium. Five phospholipids, three aminolipid, and one class of unknown lipid-like features were identified. Most (≥94%) of these 75 lipids were quantifiable in all samples. Metabolite and lipid profiles were strongly determined by growth medium composition and modestly by strain type. Because fluctuations in availability and form of carbon substrates and nutrients, as well as virus pressure, are common features of natural systems, the influence of these intersecting factors will undoubtedly be imprinted in the metabolome and lipidome of resident bacteria. IMPORTANCE Community-level metabolomics approaches are increasingly used to characterize natural microbial populations. These approaches typically depend upon temporal snapshots from which the status and function of communities are often inferred. Such inferences are typically drawn from lab-based studies of select model organisms raised under limited growth conditions. To better interpret community-level data, the extent to which ecologically relevant bacteria demonstrate metabolic flexibility requires elucidation. Herein, we used an environmentally relevant model heterotrophic marine bacterium to assess the relationship between growth determinants and metabolome. We also aimed to assess the contribution of phage activity to the host metabolome. Striking differences in primary metabolite and lipid profiles appeared to be driven primarily by growth regime and, secondarily, by phage type. These findings demonstrated the malleable nature of metabolomes and lipidomes and lay the foundation for future studies that relate cellular composition with function in complex environmental microbial communities.

Sulfitobacter aestuariivivens sp. nov., isolated from a tidal flat

A Gram-stain-negative, aerobic, non-flagellated, coccoid, ovoid or rod-shaped bacterial strain, TSTF-M16^T, was isolated from a tidal flat on the Yellow Sea, Republic of Korea. The neighbour-joining phylogenetic tree of 16S rRNA gene sequences showed that strain TSTF-M16^T fell within a clade comprising the type strains of Sulfitobacter species. Strain TSTF-M16^T exhibited 16S rRNA gene sequence similarities of 98.5 and 98.1 % to the type strains of Sulfitobacter mediterraneus and Sulfitobacter sabulilitoris, respectively, and 96.2-97.8 % to the type strains of the other Sulfitobacter species. The average nucleotide identity and digital DNA-DNA hybridization values between the genomic sequences of strain TSTF-M16^T and the type strains of 16 Sulfitobacter species were 70.6-74.2 and 17.9-19.0 %, respectively. The DNA G+C content of strain TSTF-M16^T from genomic sequence data was 59.26 mol%. Strain TSTF-M16^T contained Q-10 as the predominant ubiquinone and C_18 : 1  ω7c as the major fatty acid. The major polar lipids of strain TSTF-M16^T were phosphatidylcholine, phosphatidylglycerol, one unidentified aminolipid and one unidentified lipid. Distinguished phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain TSTF-M16^T is separated from recognized Sulfitobacter species. On the basis of the data presented here, strain TSTF-M16^T is considered to represent a novel species of the genus Sulfitobacter, for which the name Sulfitobacter aestuariivivens sp. nov. is proposed. The type strain is TSTF-M16^T (=KACC 21645^T=NBRC 114501^T).

Sulfitobacter alexandrii sp. nov., a new microalgae growth-promoting bacterium with exopolysaccharides bioflocculanting potential isolated from marine phycosphere

Marine phycosphere harbors unique cross-kingdom associations with enormous ecological significance in aquatic ecosystems as well as relevance for algal biotechnology industry. During our investigating the microbial composition and bioactivity of marine phycosphere microbiota (PM), a novel lightly yellowish and versatile bacterium designated strain AM1-D1^T was isolated from cultivable PM of marine dinoflagellate Alexandrium minutum amtk4 that produces high levels of paralytic shellfish poisoning toxins (PSTs). Strain AM1-D1^T demonstrates notable bioflocculanting bioactivity with bacterial exopolysaccharides (EPS), and microalgae growth-promoting (MGP) potential toward its algal host. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain AM1-D1^T was affiliated to the members of genus Sulfitobacter within the family Rhodobacteraceae, showing the highest sequence similarity of 97.9% with Sulfitobacter noctilucae NB-68^T, and below 97.8% with other type strains. The complete genome of strain AM1-D1^T consisted of a circular 3.84-Mb chromosome and five circular plasmids (185, 95, 15, 205 and 348 Kb, respectively) with the G+C content of 64.6%. Low values obtained by phylogenomic calculations on the average nucleotide identity (ANI, 77.2%), average amino acid identity (AAI, 74.7%) and digital DNA-DNA hybridization (dDDH, 18.6%) unequivocally separated strain AM1-D1^T from its closest relative. The main polar lipids were identified as phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, diphosphatidylglycerol, one unidentified phospholipid and one unidentified lipid. The predominant fatty acids (> 10%) were C_18:1 ω7c, C_19:0 cyclo ω8c and C_16:0. The respiratory quinone was Q-10. The genome of strain AM1-D1^T was predicted to encode series of gene clusters responsible for sulfur oxidation (sox) and utilization of dissolved organic sulfur exometabolites from marine dinoflagellates, taurine (tau) and dimethylsulfoniopropionate (DMSP) (dmd), as well as supplementary vitamin B₁₂ (cob), photosynthesis carotenoids (crt) which are pivotal components during algae-bacteria interactions. Based on the evidences by the polyphasic characterizations, strain AM1-D1^T represents a novel species of the genus Sulfitobacter, for which the name Sulfitobacter alexandrii sp. nov. is proposed. The type strain is AM1-D1^T (= CCTCC 2017277T = KCTC 62491^T).

Sulfitobacter algicola sp. nov., isolated from green algae

A novel Gram-stain-negative, aerobic, non-flagellated, non-motile, oval-rod-shaped and light pink to light tawny-pigmented bacterial strain (designated 1151^T) were isolated from marine green algae obtained from the coastal seawater of Weihai, China. Strain 1151^T was found to grow at 15-37 °C (optimum, 33 °C), pH 7.0-9.5 (optimum, 7.5-8.5) and in the presence of 1-6% (w/v) NaCl (optimum, 3%). Cells were oxidase-positive and catalase-positive. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 1151^T was a member of the genus Sulfitobacter and exhibited the hightest sequence similarity to Sulfitobacter indolifex DSM 14862^T (96.6%), followed by the sequence similarity to Sulfitobacter aestuarii hydD52^T (96.5%) and Sulfitobacter profundi SAORIC-263^T (96.5%). The average nucleotide identity and digital DDH values between strain 1151^T and Sulfitobacter indolifex DSM 14862^T were 69.9% and 20.9%, respectively. The average amino acid identity between strain 1151^T and Sulfitobacter pontiacus DSM 10014^T (type strain of the type species) was 62.3%. Q-10 was detected as the sole respiratory quinone. The dominant cellular fatty acids were sum feature 8 (C_{18: 1}ω7c; 44.1%), C_{20: 1}ω7c (29.7%) and C_{18: 0} (11.7%). The DNA G + C content of strain 1151^T was 51.8 mol%. The polar lipids included phosphatidylglycerol (PG), phosphatidylethanolamine (PE), phosphatidylcholine (PC), and three unidentified lipids (L1, L2 and L3). Based on the phylogenetic and phenotypic characteristics, strain 1151^T is considered to represent a novel species of the genus Sulfitobacter, for which the name Sulfitobacter algicola sp. nov. is proposed. The type strain is 1151^T (= KCTC 72513^T = MCCC 1H00384^T).

Description of Sulfitobacter sediminilitoris sp. nov., isolated from a tidal flat

A Gram-stain-negative bacterial strain, JBTF-M27T, was isolated from a tidal flat from Yellow Sea, Republic of Korea. Neighbor-joining phylogenetic tree of 16S rRNA gene sequences showed that strain JBTF-M27T fell within the clade comprising the type strains of Sulfitobacter species. Strain JBTF-M27T exhibited the highest 16S rRNA gene sequence similarity (98.8%) to the type strain of S. porphyrae. Genomic ANI and dDDH values of strain JBTF-M27T between the type strains of Sulfitobacter species were less than 76.1 and 19.2%, respectively. Mean DNA-DNA relatedness value between strain JBTF-M27T and the type strain of S. porphyrae was 21%. DNA G + C content of strain JBTF-M27T from genome sequence was 57.8% (genomic analysis). Strain JBTF-M27T contained Q-10 as the predominant ubiquinone and C18:1ω7c as the major fatty acid. The major polar lipids of strain JBTF-M27T were phosphatidylcholine, phosphatidylglycerol and one unidentified aminolipid. Distinguished phenotypic properties, along with the phylogenetic and genetic distinctiveness, revealed that strain JBTF-M27T is separated from recognized Sulfitobacter species. On the basis of the data presented, strain JBTF-M27T ( = KACC 21648T = NBRC 114356T) is considered to represent a novel species of the genus Sulfitobacter, for which the name Sulfitobacter sediminilitoris sp. nov. is proposed.

Complete genome of Sulfitobacter sp. BSw21498 isolated from seawater of Arctic Kongsfjorden

The genus Sulfitobacter has been mostly found in marine and hypersaline environments. Members of this genus were observed to be associated with marine microalgae by inducing cell death of algae and degrading of algae-derived dimethylsulfoniopropionate (DMSP). Here we reported the complete genome sequence of strain Sulfitobacter sp. BSw21498 isolated from seawater of Kongsfjorden, an Arctic fjord in Svalbard. The strain contained a circular chromosome of 3,097,372 bp with G+C content of 58.55 mol% and a plasmid of 147,547 bp with G+C content of 56.53 mol%. In particular, a gene for DMSP lyase DddL was found in the genome, rendering Sulfitobacter sp. strain BSw21498 one of the Rhodobacterales bacteria equipped with the potential for DMSP degradation.

Antarcticimicrobium sediminis gen. nov., sp. nov., isolated from Antarctic intertidal sediment, transfer of Ruegeria lutea to Antarcticimicrobium gen. nov. as Antarcticimicrobium luteum comb. nov

A Gram-stain-negative, aerobic, non-flagellated and rod- or ovoid-shaped bacterium, designated as strain S4J41^T, was isolated from Antarctic intertidal sediment. The isolate grew at 0-37 °C and with 0.5-10 % (w/v) NaCl. It reduced nitrate to nitrite and hydrolysed Tween 80 and gelatin. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain S4J41^T constituted a distinct phylogenetic line within the family Rhodobacteraceae and was closely related with some species in the genera Ruegeria, Phaeobacter, Pseudopuniceibacterium, Sulfitobacter, Puniceibacterium and Poseidonocella with 98.6-95.7 % 16S rRNA gene sequence similarities. The major cellular fatty acids were C_16 : 0, summed feature 8 (C_18 : 1  ω7c and/or C_18 : 1  ω6c) and C_18 : 0 and the major polar lipids were phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, phosphatidylethanolamine and one unidentified aminolipid. The sole respiratory quinone was Q-10. The genomic DNA G+C content of strain S4J41^T was 60.3 mol%. Based on the phylogenetic, chemotaxonomic and phenotypic data obtained in this study, strain S4J41^T is considered to represent a novel species in a new genus within the family Rhodobacteraceae, for which the name Antarcticimicrobium sediminis gen. nov., sp. nov. is proposed. The type strain is S4J41^T (=MCCC 1K03508^T=KCTC 62793^T). Moreover, the transfer of Ruegeria lutea Kim et al. 2019 to Antarcticimicrobium gen. nov. as Antarcticimicrobium luteum comb. nov. (type strain 318-1^T=JCM 30927^T=KCTC 72105^T) is also proposed.

Pseudopontivivens aestuariicola gen. nov., sp. nov., a Novel Bacterium of the Class Alphaproteobacteria Isolated from a Tidal Flat

A Gram-stain-negative, non-motile and coccoid, ovoid or rod-shaped bacterial strain, OITF-57^T, which was isolated from a tidal flat sediment in South Korea, was characterized taxonomically. Strain OITF-57^T grew optimally at 25 °C, at pH 7.0-8.0 and in the presence of 2.0% (w/v) NaCl. Strain OITF-57^T exhibited the highest 16S rRNA gene sequence similarity value (94.2%) to the type strain of Pontivivens insulae forming a cluster in the neighbour-joining phylogenetic tree. In the maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences and the phylogenetic tress based on gyrB sequences, strain OITF-57^T formed evolutionary lineages independent of those of other taxa. Strain OITF-57^T contained Q-10 as the predominant ubiquinone and C_18:1 ω7c as the major fatty acid. The major polar lipids of strain OITF-57^T were phosphatidylcholine and phosphatidylglycerol. The DNA G + C content of strain OITF-57^T was 66.0 mol%. The chemotaxonomic data and other differential phenotypic properties made it possible to distinguish strain OITF-57^T from the genus Pontivivens and other phylogenetically related genera. On the basis of the data presented, strain OITF-57^T constitutes a new genus and species within the class Alphaproteobacteria, for which the name Pseudopontivivens aestuariicola gen. nov., sp. nov. is proposed. The type strain is OITF-57^T (= KACC 19570^T = CGMCC 1.13481^T).

Jindonia aestuariivivens gen. nov., sp. nov., isolated from a tidal flat on the south-western sea in Republic of Korea

A Gram-stain-negative, aerobic, non-flagellated, and coccoid, ovoid or rod-shaped bacterium, designated JDTF-65^T, was isolated from a tidal flat on the south-western sea in Republic of Korea. Strain JDTF-65^T grew optimally at 25°C, at pH 7.0-8.0 and in the presence of 2.0% (w/v) NaCl. Strain JDTF-65^T exhibited 16S rRNA gene sequence similarities of 97.1-97.6% to the type strains of 'Aliisedimentitalea scapharcae', Phaeobacter gallaeciensis, Phaeobacter inhibens, Leisingera aquimarina, Tropicibacter litoreus, Sulfitobacter pseudonitzschiae, and Pseudoseohaeicola caenipelagi. Phylogenetic trees based on 16S rRNA gene sequences showed that strain JDTF-65^T forms an independent lineage within the radiation enclosed by the family Rhodobacteraceae. Strain JDTF-65^T contained Q-10 as the predominant ubiquinone and C_18:1 ω7c as the major fatty acid. The major polar lipids of strain JDTF-65^T were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, one unidentified aminolipid, and one unidentified lipid. The DNA G+C content of strain JDTF-65^T was 56.8 mol% and its DNA-DNA relatedness values with the type strains of the phylogenetically related species were 13-27%. Differential phenotypic properties revealed that strain JDTF-65^T is separated from representatives of some phylogenetically related taxa. On the basis of the data presented, strain JDTF-65^T represents a new genus and species within the family Rhodobacteraceae, for which the name Jindonia aestuariivivens gen. nov., sp. nov. is proposed. The type strain of Jindonia aestuariivivens is JDTF-65^T (=KCTC 52564^T =NBRC 112534^T).

Nitropelagius marinus gen. nov., sp. nov., Isolated From Seawater, Je-bu island, South Korea [corrected]

A Gram-stain-negative, non-spore forming, non-motile and aerobic strain, designated JB22(T), was isolated from seawater, Je-bu Island, South Korea. Strain JB22(T) was catalase and oxidase positive. Optimal growth of JB22(T) was observed at 30 °C and pH 7.0. NaCl tolerance range was 1-9 % (w/v) with an optimum of 2.0 % concentration. The phylogenetic analysis based on 16S rRNA gene sequence of strain JB22(T) showed the highest sequence similarity to those of Pelagicola litorisediminis D1-W8(T) (95.8 %), Roseovarius litoreus GSW-M15(T) (95.2 %), Roseovarius aestuarii SMK-122(T) (95.0 %), Donghicola eburmeus SW-277(T) (95.0 %), and Roseovarius halotolerans HJ50(T) (94.9 %). It contained ubiquine-10 as the major respiratory quinone and C18:1 ω7c (69.3 %), :0 (9.9 %), C18:1 ω7c 11-methyl (9.6 %) as the major fatty acid. The polar lipid profile included phosphatidylcholine, phosphatidylglycerol, and unidentified aminolipid. The DNA G+C content of the strain JB22(T) was 47 mol  %. Based on physiological and chemotaxonomic characteristics, strain JB22(T) should be regarded as a new genus of the family Rhodobacteraceae, for which the Nitropelagi marinus gen. nov., sp. nov. is proposed. The type strain is JB22(T) (= KEMB 3001-101(T) = JCM 30822(T)).