Celeribacter marinus sp. nov., isolated from coastal seawater

Genome Analysis of Celeribacter sp. PS-C1 Isolated from Sekinchan Beach in Selangor, Malaysia, Reveals Its β-Glucosidase and Licheninase Activities

A halophilic marine bacterial strain, PS-C1, was isolated from Sekinchan beach in Selangor, Malaysia. The 16S rRNA gene sequence analysis indicated that strain PS-C1 was associated with the genus Celeribacter. To date, there have been no reports on enzymes from the genus Celeribacter. The present study reports on the cellular features of Celeribacter sp. PS-C1, its annotated genome sequence, and comparative genome analyses of Celeribacter glycoside hydrolase (GH) enzymes. The genome of strain PS-C1 has a size of 3.87 Mbp and a G+C content of 59.10%, and contains 3739 protein-coding genes. Detailed analysis using the Carbohydrate-Active enZYmes (CAZy) database revealed that Celeribacter genomes harboured at least 12 putative genes encoding industrially important GHs that are grouped as cellulases, β-glucanases, hemicellulases, and starch-degrading enzymes. Herein, the potential applications of these enzymes are discussed. Furthermore, the activities of two types of GHs (β-glucosidase and licheninase) in strain PS-C1 were demonstrated. These findings suggest that strain PS-C1 could be a reservoir of novel GH enzymes for lignocellulosic biomass degradation.

Celeribacter litoreus sp. nov., isolated from intertidal sediment

A Gram-negative, aerobic, non-flagellated and rod-shaped bacterium, strain ASW11-22^T, was isolated from an intertidal sediment collected from a coastal area of Qingdao, PR China. The strain grew at 15-40 °C (optimum, 37 °C), at pH 6.0-9.0 (optimum, pH 7.0) and with 0.5-10 % (w/v) NaCl (optimum, 1.0 %). It hydrolysed gelatin and aesculin but did not reduce nitrate to nitrite. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain ASW11-22^T belonged to the genus Celeribacter, showing the highest sequence similarity to the type strains of Celeribacter halophilus MCCC 1A06432^T (98.20 %) and Celeribacter ethanolicus NH195^T (97.84 %). The genomic DNA G+C content was 59.1 mol%. The major cellular fatty acid (>10 %) of the strain was summed feature 8 (C_18 : 1 ω7c and/or C_18 : 1 ω6c) and its main polar lipids were phosphatidylglycerol and one unidentified aminolipid. The sole respiratory quinone of strain ASW11-22^T was ubiquinone-10. On the basis of the polyphasic evidence presented in this paper, strain ASW11-22^T represents a novel Celeribacter species, for which the name Celeribacter litoreus sp. nov. is proposed. The type strain is ASW11-22^T (=KCTC 82495^T=MCCC 1K05584^T).

Mle046 Is a Marine Mesophilic MHETase-Like Enzyme

Accumulation of plastics in the oceans presents a major threat to diverse ecosystems. The introduction of biodegradable plastics into the market aims to alleviate the ecological burden caused by recalcitrant plastics. Poly (butylene adipate-co-terephthalate) (PBAT) is a biodegradable commercial plastic that can be biodegraded similarly to polyethylene terephthalate (PET) by PETase-like enzymes and MHETases. The role of MHETases is to hydrolyze the intermediate degradation product of PET, mono-2-hydroxyethyl terephthalate (MHET) to its monomers. We recently identified a homolog of the MHETase of the PET-degrading bacterium Ideonella sakaiensis, Mle046, from a marine microbial consortium. In this consortium, Mle046 was highly expressed when a PBAT-based blend film (PF) was supplied as the sole carbon source. In this study, we recombinantly expressed and biochemically characterized Mle046 under different conditions. Mle046 degrades MHET but also 4-(4-hydroxybutoxycarbonyl) benzoic acid (Bte), the intermediate of PF degradation. Mle046 is a mesophilic enzyme adapted to marine conditions, which rapidly degrades MHET to terephthalate and ethylene glycol at temperatures between 20 and 40°C. Mle046 degradation rates were similar for Bte and MHET. Despite its mesophilic tendency, Mle046 retains a considerable amount of activity at temperatures ranging from 10 to 60°C. In addition, Mle046 is active at a range of pH values from 6.5 to 9. These characteristics make Mle046 a promising candidate for biotechnological applications related to plastic recycling.

Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria

The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.

Effects of Hydraulic Retention Time and Influent Nitrate-N Concentration on Nitrogen Removal and the Microbial Community of an Aerobic Denitrification Reactor Treating Recirculating Marine Aquaculture System Effluent

The effects of hydraulic retention time (HRT) and influent nitrate-N concentration on nitrogen removal and the microbial community composition of an aerobic denitrification reactor treating recirculating marine aquaculture system effluent were evaluated. Results showed that over 98% of nitrogen was removed and ammonia-N and nitrite-N levels were below 1 mg/L when influent nitrate-N was below 150 mg/L and HRT over 5 h. The maximum nitrogen removal efficiency and nitrogen removal rate were observed at HRT of 6 or 7 h when influent nitrate-N was 150 mg/L. High-throughput DNA sequencing analysis revealed that the microbial phyla Proteobacteria and Bacteroidetes were predominant in the reactor, with an average relative total abundance above 70%. The relative abundance of denitrifying bacteria of genera Halomonas and Denitratisoma within the reactor decreased with increasing influent nitrate-N concentrations. Our results show the presence of an aerobically denitrifying microbial consortium with both expected and unexpected members, many of them relatively new to science. Our findings provide insights into the biological workings and inform the design and operation of denitrifying reactors for marine aquaculture systems.

Celeribacter naphthalenivorans sp. nov., a naphthalene-degrading bacterium from tidal flat sediment

A Gram-stain-negative, aerobic and moderately halophilic bacterium, designated strain EMB201T, was isolated from tidal flat sediment of the South Sea in Korea. Cells were motile rods with a single polar flagellum and had catalase- and oxidase-positive activities. Growth of strain EMB201T was observed at 15–37 °C (optimum, 30 °C), at pH 5.0–9.5 (optimum, pH 7.0–7.5) and in the presence of 1–7 % (w/v) NaCl (optimum, 2–3 %). Strain EMB201T contained ubiquinone-10 as the sole isoprenoid quinone and summed feature 8 (comprising C18 : 1ω7c/ω6c), C18 : 0ω7c 11-methyl and C10 : 0 3-OH as the major fatty acids. Phosphatidylglycerol and an unidentified amino lipid were identified as the major polar lipids and an unidentified phospholipid and three unidentified lipids were detected as minor components. The G+C content of the genomic DNA was approximately 58.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain EMB201T formed a phylogenetic lineage with members of the genus Celeribacter. Strain EMB201T was related most closely to Celeribacter halophilus ZXM137T with a 16S rRNA gene sequence similarity of 98.3 %, and the level of DNA–DNA relatedness between the two strains was 17.0 ± 2.0 %. The combined chemotaxonomic and molecular properties suggest that strain EMB201T represents a novel species of the genus Celeribacter, for which the name Celeribacter naphthalenivorans sp. nov. is proposed. The type strain is EMB201T ( = KACC 18393T = JCM 30679T).

Celeribacter manganoxidans sp. nov., a manganese-oxidizing bacterium isolated from deep-sea sediment of a polymetallic nodule province

A Gram-stain-negative, strictly aerobic, non-motile, rod-shaped, manganese-oxidizing bacterial strain, designated DY2-5T, was isolated from surface sediment of Pacific Clarion-Clipperton Fracture Zone (CCFZ). Growth occurred at 0-37 °C (optimum 28 °C), pH 6.5-9.0 (optimum pH 7.0-7.5) and in the presence of 1-11% (w/v) NaCl (optimum 3-4%). Phylogenetic analysis based on 16S rRNA gene sequences revealed that the novel strain was most closely related to Celeribacter halophilus ZXM137T with 96.13% sequence similarity, and had 16S rRNA gene sequence similarities in the range 93.89-95.87% with other species of the genus Celeribacter. The dominant fatty acids were summed feature 8 (C18:1ω7c and/or C18:1ω6c) and C16:0. The polar lipids of strain DY2-5T comprised phosphatidylglycerol, phosphatidylcholine and two unknown aminolipids. The major respiratory quinone was ubiquinone-10 (Q-10). The DNA G+C content of strain DY2-5T was 64.8 mol%. On the basis of the phenotypic, genotypic and physiological evidence, strain DY2-5T represents a novel species of the genus Celeribacter, for which the name Celeribacter manganoxidans sp. nov. is proposed. The type strain is DY2-5T ( = JCM 19384T = KCTC 32473T).

Celeribacter indicus sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium from deep-sea sediment and reclassification of Huaishuia halophila as Celeribacter halophilus comb. nov

A taxonomic study was carried out on strain P73T, which was isolated from deep-sea sediment of the Indian Ocean by enrichment of polycyclic aromatic hydrocarbons. The strain was able to degrade biphenyl, naphthalene, 2-methylnaphthalene, 2,6-dimethylnaphthalene, acenaphthene, anthracene, phenanthrene, dibenzothiophene, dibenzofuran, fluorene, 4-methyldibenzothiophene and fluoranthene, but not pyrene or chrysene. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain P73T formed a clade with the genera Celeribacter and Huaishuia within the family Rhodobacteraceae , with highest sequence similarity of 96.98 % to Celeribacter neptunius H 14T, followed by Huaishuia halophila ZXM137T (96.42 %). The bacterium was Gram-stain-negative, oxidase- and catalase-positive, rod-shaped and non-motile. Growth was observed at salinities from 0.5 to 12 % and at temperatures from 10 to 41 °C. The principal fatty acids (>10 %) of strain P73T were summed feature 8 (C18 : 1ω7c/ω6c) and C19 : 0ω8c cyclo. The sole respiratory quinone was Q-10. The major lipids were phosphatidylglycerol, one unknown aminolipid, one unknown phospholipid and one unknown lipid; a second unknown phospholipid and one unknown glycolipid were present as minor components. The G+C content of the chromosomal DNA was 66.0 mol%. The combined genotypic and phenotypic data show that strain P73T represents a novel species of the genus Celeribacter , for which the name Celeribacter indicus sp. nov. is proposed. The type strain is P73T ( = MCCC 1A01112T = LMG 27600T = DSM 27257T). Phylogenetic study and existing phenotypic information also show that Huaishuia halophila should be transferred to the genus Celeribacter as Celeribacter halophilus comb. nov. (type strain ZXM137T = MCCC 1A06432T = CGMCC 1.8891T = LMG 24854T).