Phylogenomic evaluation of Mangrovimicrobium sediminis gen. nov. sp. nov., the first nitrogen fixing member of the family Halieaceae adapted to mangrove habitat and reclassification of Halioglobus pacificus to Pseudohaliglobus pacificus comb. nov

The taxonomic position and genomic characteristics of a nitrogen fixing and polymer degrading marine bacterium, strain SAOS 164 isolated from a mangrove sediment sample was investigated. Sequence analysis based on 16S rRNA gene identified it as a member of family Halieaceae with closest similarity to Haliea salexigens DSM 19537T (96.3 %), H. alexandrii LZ-16-2T (96.2 %) and Parahaliea maris HSLHS9T (96.0 %) but was distantly related to the genera Haliea, Parahaliea and Halioglobus in phylogenetic trees. In order to ascertain the exact taxonomic position, phylogeny based on RpoBC proteins, whole genome, core and orthologous genes, and comparative analysis of metabolic potential retrieved the strain in an independent lineage clustering along with the genera Halioglobus, Pseudohalioglobus and Seongchinamella. Further, various genome based delimitation parameters represented by mol % GC content, percentage of conserved proteins (POCP), and amino acid identity (AAI) along with chemotaxonomic markers (i.e. fatty acids and polar lipids) supported the inferences of genome based phylogeny and indicated that the strain SAOS 164 belongs to a novel genus. The genome was mapped to 4.8 Mb in size with 65.1 % DNA mol% G + C content. In-silico genomic investigation and phenotyping revealed diverse metabolite genes/pathways related to polymer hydrolysis, nitrogen fixation, light induced growth, carbohydrate, sulfur, phosphorus and amino acid metabolism, virulence factors, defense mechanism, and stress-responsive elements facilitating survival in the mangrove habitat. Based on polyphasic taxonomic approach including genome analyses, a novel genus Mangrovimicrobium sediminis gen. nov. sp. nov. (=SAOS 164T = MTCC 12907T = KCTC 52755T = JCM 32136T) is proposed. Additionally, the reclassification of Halioglobus pacificus (=DSM 27932T = KCTC 23430T = S1-72T) to Pseudhalioglobus pacificus comb. nov. is also proposed.

Aequoribacter fuscus gen. nov., sp. nov., a new member of the family Halieaceae, isolated from coastal seawater

A Gram-stain-negative, rod-shaped, obligately aerobic, nonflagellated, and chemoheterotrophic bacterium, designated IMCC3088^T, was isolated from coastal seawater of the Yellow Sea. The 16S rRNA gene sequence analysis indicated that this strain belonged to the family Halieaceae which shared the highest sequence similarities with Luminiphilus syltensis NOR5-1B^T (94.5%) and Halioglobus pacificus S1-72^T (94.5%), followed by 92.3-94.3% sequence similarities with other species within the aforementioned family. Phylogenetic analyses demonstrated that strain IMCC3088^T was robustly clustered with Luminiphilus syltensis NOR5-1B^T within the family Halieaceae. However, average amino acid identity (AAI), percentages of conserved proteins (POCP), average nucleotide identity (ANI), and alignment fraction (AF) between strain IMCC3088^T and Luminiphilus syltensis NOR5-1B^T were 54.5%, 47.7%, 68.0%, and 16.5%, respectively, suggesting that they belonged to different genera. Whole-genome sequencing of strain IMCC3088^T revealed a 3.1 Mbp genome size with a DNA G + C content of 51.7 mol%. The genome encoded diverse metabolic pathways including sulfur oxidation, phenol degradation, and proteorhodopsin phototrophy. Mono-unsaturated fatty acids were found to be the predominant cellular fatty acid components in the strain. Phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol were the primarily identified polar lipids, and ubiquinone-8 was identified as a major respiratory quinone. The taxonomic data collected herein suggested that strain IMCC3088^T represented a novel genus and species of the family Halieaceae, for which the name Aequoribacter fuscus gen. nov., sp. nov. is proposed with the type strain (= KACC 15529^T = NBRC 108213^T).

Seongchinamella unica gen. nov., sp. nov., isolated from a tidal mudflat of beach, and transfer of Halioglobus sediminis to Seongchinamella sediminis comb. nov. and Halioglobus lutimaris to Pseudohalioglobus gen. nov. as Pseudohalioglobus lutimaris comb. nov

A Gram-reaction-negative, motile by gliding, rod-shaped bacterium, designated strain GH4-78T, was isolated from the tidal mudflat of a beach in the Republic of Korea. Cells were aerobic, catalase-positive, oxidase-negative and produced cream-coloured colonies. Q-8 was the only isoprenoid quinone. The major fatty acids were summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c), summed feature 3 (C16 : 1  ω6c and/or C16 : 1  ω7c) and C16 : 0. The major polar lipids are phosphatidylethanolamine and phosphatidylglycerol. Results of phylogenetic analyses based on 16S rRNA gene sequences revealed that strain GH4-78T formed a distinct lineage with Halioglobus sediminis (98.2 % sequence similarity). The DNA G+C content was 59.9 mol%. The average nucleotide identity value with the closest relative was 82.90 %. On the basis of the results from phenotypic, chemotaxonomic, phylogenetic and phylogenomic analyses, strain GH4-78T (=KCTC 62383T=DSM 106349T) represents a novel species of a new genus in the family Halieaceae , for which the name Seongchinamella unica gen. nov., sp. nov. is proposed. Moreover, the transfers of Halioglobus sediminis Han et al. 2019 to Seongchinamella sediminis comb. nov. and Halioglobus lutimaris Shi et al. 2018 to Pseudohalioglobus gen. nov. as Pseudohalioglobus lutimaris comb. nov. are also proposed, with the emended description of the genus Halioglobus .

Halioglobus maricola sp. nov., isolated from coastal seawater

A Gram-stain-negative, rod-shaped, aerobic, non-flagellated, chemoheterotrophic bacterium, designated IMCC14385T, was isolated from surface seawater of the East Sea, Republic of Korea. The 16S rRNA gene sequence analysis indicated that IMCC14385T represented a member of the genus Halioglobus sharing 94.6–97.8 % similarities with species of the genus. Whole-genome sequencing of IMCC14385T revealed a genome size of 4.3 Mbp and DNA G+C content of 56.7 mol%. The genome of IMCC14385T shared an average nucleotide identity of 76.6 % and digital DNA–DNA hybridization value of 21.6 % with the genome of Halioglobus japonicus KCTC 23429T. The genome encoded the complete poly-β-hydroxybutyrate biosynthesis pathway. The strain contained summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and C17 : 1 ω8c as the predominant cellular fatty acids as well as ubiquinone-8 (Q-8) as the respiratory quinone. The polar lipids detected in the strain were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, five unidentified phospholipids, an unidentified aminolipid, an unidentified aminophospholipid and four unidentified lipids. On the basis of taxonomic data obtained in this study, it is suggested that IMCC14385T represents a novel species of the genus Halioglobus , for which the name Halioglobus maricola sp. nov. is proposed. The type strain is IMCC14385T (=KCTC 72520T=NBRC 114072T).

Haliea alexandrii sp. nov., isolated from phycosphere microbiota of the toxin-producing dinoflagellate Alexandrium catenella

A Gram-negative, aerobic, non-motile, non-spore-forming and rod-shaped bacterium, named strain LZ-16-2^T, was isolated from the phycosphere microbiota of the paralytic shellfish poisoning toxin-producing marine dinoflagellate Alexandrium catenella LZT09. Strain LZ-16-2^T grew optimally at 28 °C at pH 6.5 and with 3 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence revealed that strain LZ-16-2^T fell within the genus Haliea and was most closely related to Haliea salexigens DSM 19537^T, with which the new isolate exhibited 98.5 % 16S rRNA gene sequence similarity. The major respiratory quinone was Q-8. The predominant cellular fatty acids were C_17 : 1  ω8c, summed feature 3 (C_16 : 1  ω7c and/or C_16 : 1  ω6c), summed feature 8 (C_18 : 1  ω7c and/or C_18 : 1  ω6c), C_17 : 1  ω6c, C_11 : 0 3-OH and C_17 : 0. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The average nucleotide identity and in silico DNA-DNA genome hybridization relatedness values between strain LZ-16-2^T and its closest relative, H. salexigens DSM 19537^T, were 92.8 and 55.1 %, respectively. The DNA G+C content was 61.3 mol%. Differential phenotypic properties and phylogenetic distinctiveness distinguished strain LZ-16-2^T from all other members of the genus Haliea. On the basis of the polyphasic characterization, strain LZ-16-2^T represents a novel species of the genus Haliea, for which the name Haliea alexandrii sp. nov. is proposed. The type strain is LZ-16-2^T (=KCTC 62344^T=CCTCC AB2017229^T).

Halioglobus sediminis sp. nov., isolated from coastal sediment

A novel aerobic, Gram-stain-negative, non-motile and rod-shaped bacterium, designated strain U0301^T, was isolated from a marine sediment sample in Weihai, China. This strain grew optimally at 33 °C, pH 7.5 and in the presence of 2.0-3.0 % (w/v) NaCl. Strain U0301^T shared pairwise 16S rRNA gene sequence similarities of 95.5, 95.4, 95.2 and 95.0 % to Parahaliea aestuarii S2-26^T, Halioglobus pacificus KCTC 23430^T, Halioglobus lutimaris HF004^T and Halioglobus japonicus KCTC 23429^T, respectively. Phylogenetic analysis based on the 16S rRNA gene sequences demonstrated that U0301^T formed a tight phylogenetic lineage with type strains of H. pacificus and H. japonicus. The percentage of conserved protein values of strain U0301^T as compared with H. japonicus KCTC 23429^Tand Parahalieamediterranea 7SM29^T were 62.5 and 58.0 %, respectively. The ANI values of strain U0301^T with H. japonicus KCTC 23429^T and P. mediterranea 7SM29^T were 78.2 and 75.3 %, respectively. Both metrics of genome comparison suggested that strain U0301^T showed higher homology with the genus Halioglobus than the genus Parahaliea. The strain contained ubiquinone 8 as the sole respiratory quinone. The major fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and C17 : 1ω8c. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The DNA G+C content was 61.7 mol%. Considering the phenotypic characteristics, chemotaxonomic data and phylogenetic analysis comprehensively, strain U0301^T should represent a novel species of the genus Halioglobus, for which the name of Halioglobus sediminis sp. nov. is proposed. The type strain is U0301^T (=KCTC 62082^T=MCCC 1H00234^T).

Genetic and Physiological Characteristics of a Novel Marine Propylene-Assimilating Halieaceae Bacterium Isolated from Seawater and the Diversity of Its Alkene and Epoxide Metabolism Genes

The Gram-negative marine propylene-assimilating bacterium, strain PE-TB08W, was isolated from surface seawater. A structural gene analysis using the 16S rRNA gene showed 96, 94, and 95% similarities to Halioglobus species, Haliea sp. ETY-M, and Haliea sp. ETY-NAG, respectively. A phylogenetic tree analysis showed that strain PE-TB08W belonged to the EG19 (Chromatocurvus)-Congregibacter-Haliea cluster within the Halieaceae (formerly Alteromonadaceae) family. Thus, strain PE-TB08W was characterized as a newly isolated Halieaceae bacterium; we suggest that this strain belongs to a new genus. Other bacterial characteristics were investigated and revealed that strain PE-TB08W assimilated propylene, n-butane, 1-butene, propanol, and 1-butanol (C3 and C4 gaseous hydrocarbons and primary alcohols), but not various other alcohols, including methane, ethane, ethylene, propane, and i-butane. The putative alkene monooxygenase (amo) gene in this strain was a soluble methane monooxygenase-type (sMMO) gene that is ubiquitous in alkene-assimilating bacteria for the initial oxidation of alkenes. In addition, two epoxide carboxylase systems containing epoxyalkane, the co-enzyme M transferase (EaCoMT) gene, and the co-enzyme M biosynthesis gene, were found in the upstream region of the sMMO gene cluster. Both of these genes were similar to those in Xanthobacter autotrophicus Py2 and were inductively expressed by propylene. These results have a significant impact on the genetic relationship between terrestrial and marine alkene-assimilating bacteria.