Algibacter onchidii sp. nov., a symbiotic bacterium isolated from a marine invertebrate

A novel symbiotic bacterium, designated strain XY-114^T, was isolated from the cerata of an Onchidium marine invertebrate species collected in the South China Sea. Strain XY-114^T was an aerobic, Gram-stain-negative, non-motile and short rod-shaped bacterium (0.5-0.8 µm wide and 1.0-1.5 µm long) without flagellum. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain XY-114^T belonged to the genus Algibacter with the highest similarity of 97.2 % to the closest phylogenetic relative Algibacter aestuarii KYW371^T. Cells grew at 15-37 °C (optimum, 30 °C), at pH 5.5-9.0 (optimum 7.0-8.0) and at NaCl concentrations of 0.5-5.0 % (w/v; optimum 1.5-3.0 %). The major fatty acids (>10 %) were summed feature 3 (comprising C_16 : 1  ω7c and/or C_16 : 1  ω6c), iso-C_15 : 0, iso-C_15 : 1 G and iso-C_17 : 0 3-OH. The predominant polar lipid was phosphatidylethanolamine. The predominant respiratory quinone was MK-6. Flexirubin-type pigments were absent. The genome size of strain XY-114^T was 3.4 Mbp, with 34.9 mol% of DNA G+C content. The average nucleotide identity, digital DNA-DNA hybridization and amino acid identity values between strain XY-114^T and A. aestuarii KYW371^T were 74.5 %, 17.0±1.8 % and 73.9 %. Characterization based on phylogenetic, phenotypic, chemotaxonomic and genomic evidence demonstrated that strain XY-114^T represents a novel species of the genus Algibacter, for which the name Algibacter onchidii sp. nov. is proposed. The type strain is XY-114^T (=KCTC 72217^T=MCCC 1K03606^T).

Phylogenomic Analyses of a Clade Within the Family Flavobacteriaceae Suggest Taxonomic Reassignments of Species of the Genera Algibacter, Hyunsoonleella, Jejuia, and Flavivirga, and the Proposal of Pseudalgibacter gen. nov. and Pseudalgibacter alginicilyticus comb. nov

The family Flavobacteriaceae forms a major branch within the phylum Bacteroidetes. Whole-genome sequence-based analysis could significantly improve the accuracy of taxonomic assignments. In this study, phylogenomic analyses were carried out to revisit the taxonomic status of a clade of the family Flavobacteriaceae. Taking genome-based phylogeny as the primary guideline and average amino acid identity and phenotypic information as supplements, the following taxonomic proposals were put forward: Arenitalea lutea should be reclassified into the genus Algibacter; Algibacter aquaticus should be reclassified into the genus Flavivirga; Jejuia pallidilutea and Algibacter aestuarii should be reclassified into the genus Hyunsoonleella; Algibacter alginicilyticus should be reclassified into the novel genus Pseudalgibacter gen. nov. This study builds up a solid framework for taxonomic decisions of a clade of the family Flavobacteriaceae and will contribute to further insights into the evolution of this family.

Reclassification of Algibacter wandonensis as a Later Heterotypic Synonym of Algibacter lectus Based on Whole-Genome Sequence Analysis

The genus Algibacter belongs to the family Flavobacteriaceae of the Bacteroidetes, and all members of this genus were isolated from marine environments. Among the Algibacter species, two members, Algibacter lectus KMM 3902^T and Algibacter wandonensis WS-MY22^T, were isolated from green algae and sediment around a brown algae respectively. The 16S rRNA gene sequences of these two type strains possess 99.4% sequence similarity. In this study, further studies were undertaken to clarify the taxonomic assignments of the two species. Whole-genome sequence analysis showed that the similarities for other phylogenetic markers are also very high (i.e. 99.9% for gyrB, 99.6% for recA and 99.9% for rpoD). Average nucleotide identity, average amino acids identity and digital DNA-DNA hybridization value between A. lectus KMM 3902^T and A. wandonensis WS-MY22^T are 98.3%, 98.6% and 89.4% respectively, all clearly exceed suggested species delineation thresholds. Furthermore, phylogenetic trees based on sequences of 16S rRNA gene and up-to-date bacterial core gene set (UBCG) consisting of 92 genes provided additional evidence that A. lectus KMM 3902^T and A. wandonensis WS-MY22^T are very closely related. In addition, a review of their profiles indicated that A. lectus KMM 3902^T and A. wandonensis WS-MY22^T did not present pronounced differences at phenotypic and chemotaxonomic levels. Based on these evidence, we propose that A. wandonensis should be reclassified as later heterotypic synonyms of A. lectus.

Mesohalobacter halotolerans gen. nov., sp. nov., isolated from a marine solar saltern

A Gram-stain-negative, non-motile, fine rod or short filament shaped, jacinth pigmented bacterium, designated strain WDS2C27^T, was isolated from a marine solar saltern in Wendeng, Weihai, PR China (37°31'5″ N, 122°1'47″ E). Growth of WDS2C27^T occurred at 20-42 °C (optimum 37 °C) and pH 6.5-8.5 (optimal pH 7.0-8.0). Optimal growth occurred in modified marine broth containing 6 % (w/v) NaCl. The major polar lipids in WDS2C27^T were phosphatidylethanolamine, two unidentified aminolipids and one unidentified lipid. The major respiratory quinone of WDS2C27^T was MK-6. The dominant fatty acids were iso-C_15 : 0 and anteiso-C_15 : 0. The DNA G+C content was 35.0 mol%. The nucleotide sequence of the 16S rRNA gene indicated that the most closely related strain was Psychroflexus planctonicus X15M-8^T (92.0 % over 1452 bp). WDS2C27^T showed 60.7 % average amino acid identity, 55.6 % percentage of conserved proteins, 75.0 % average nucleotide identity and 13.1 % digital DNA-DNA hybridization identity with the type species of the genus Psychroflexus, Psychroflexus torquis ATCC 700755^T. The phenotypic and genotypic properties and phylogenetic inference indicated that WDS2C27^T could be assigned to a novel species within a novel genus, for which the name Mesohalobacter halotolerans gen. nov., sp. nov. is proposed. Strain WDS2C27^T (=MCCC 1H00133^T=KCTC 52044^T) is the type strain.

Algibacter pacificus sp. nov., isolated from a deep-sea seamount

The Gram-stain-negative, rod-shaped, yellow-pigmented and facultative anaerobic bacterial strain, designated H164T, was isolated from seawater collected from the Caroline Seamounts in the Pacific Ocean. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain H164T was related to the genus Algibacter and had highest 16S rRNA gene sequence similarity to Algibacter wandonensis WS-MY22T (97.4 %). The major cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C15 : 1 G, iso-C15 : 0 3-OH and iso-C17 : 0 3-OH. The predominant menaquinone was MK-6. The polar lipid profile contained phosphatidylethanolamine, one unidentified aminolipid and two unidentified lipids. The genomic DNA G+C content of strain H164T was 33.2 mol%. The values of in silico DNA–DNA hybridization (isDDH) and average nucleotide identity (ANI) between strain H164T and A. wandonensis KCTC 32381T were 26.10 and 81.88 %. The isDDH and ANI values between strain H164T and Algibacter lectus DSM 15365T were 25.40 and 81.79 %. Combined data from phenotypic, phylogenetic, isDDH and ANI analyses demonstrated that strain H164T represents a novel species of the genus Algibacter , for which we propose the name Algibacter pacificus sp. nov. (type strain H164T=KCTC 72432T=CGMCC 1.17117T).

Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes

Although considerable progress has been made in recent years regarding the classification of bacteria assigned to the phylum Bacteroidetes, there remains a need to further clarify taxonomic relationships within a diverse assemblage that includes organisms of clinical, piscicultural, and ecological importance. Bacteroidetes classification has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees and a limited number of phenotypic features. Here, draft genome sequences of a greatly enlarged collection of genomes of more than 1,000 Bacteroidetes 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 proposed long ago such as Bacteroides, Cytophaga, and Flavobacterium 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. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which can be considered valuable taxonomic markers. We detected many incongruities when comparing the results of the present study with existing classifications, which appear to be caused by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. The few significant incongruities found between 16S rRNA gene and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences and the impediment in using ordinary bootstrapping in phylogenomic studies, particularly when combined with too narrow gene selections. While a significant degree of phylogenetic conservation was detected in all phenotypic characters investigated, the overall fit to the tree varied considerably, which is one of the probable causes of misclassifications in the past, much like the use of plesiomorphic character states as diagnostic features.

Thalassorhabdus aurantiaca gen. nov., sp. nov., a new member of the family Flavobacteriaceae isolated from seawater in South Korea

A novel Gram-negative, orange pigmented, strictly aerobic bacterium, designated strain IP9^T, was isolated from seawater at the sea shore of Incheon Eulwang-ri beach, South Korea. Cells of strain IP9^T were observed to be straight or slightly curved rods and colonies to be round and convex. Strain IP9^T was found to be catalase and oxidase positive, and non-motile. Growth was observed in the temperature range of 10-37 °C (optimum at 30 °C), pH range of 6-10 (optimum at pH 7-8) and salt concentration range of 0-7% (w/v) NaCl (optimum at 0-1%). On the basis of 16S rRNA gene sequence similarity and phylogenetic analysis, strain IP9^T was found to be related to the members of the family Flavobacteriaceae, being closely related to Hwangdonia seohaensis KCTC 32177^T (95.3% sequence similarity). The DNA G + C content of the novel strain was determined to be 39.1 mol%. The major polar lipids were found to be phosphatidylethanolamine, three unidentified aminoglycolipids and two unidentified glycolipids. The major fatty acids (> 10%) were identified as iso-C_15:0 and iso-C_17:0 3-OH. The predominant quinone was found to be menaquinone 6 (MK-6). Based on the biochemical, phylogenetic and physiological data, we conclude that strain IP9^T (= KCTC 52523^T = JCM 31732^T) represents the type species of a novel genus of the family Flavobacteriaceae for which the name Thalassorhabdus aurantiaca gen. nov., sp. nov. is proposed.