Nioella sediminis sp. nov., isolated from surface sediment and emended description of the genus Nioella

Abyssibius alkaniclasticus gen. nov., sp. nov., a novel member of the family Rhodobacteraceae, isolated from the Mariana Trench

A Gram-stain-negative bacterium with rod-shaped or irregular cells approximately 0.5-0.9×2.0-3.8 µm in size, designated as 960558^T, was isolated from sediment sampled in the Mariana Trench. Strain 960558^T grows at 4-37 °C (optimum, 28 °C), pH 6-7 (optimum, pH 7) and in the presence of 1-5 % (w/v) NaCl (optimum, 3 %). Strain 960558^T utilizes tetradecane or hexadecane as a sole carbon and energy source, respectively. Phylogenetic trees based on 16S rRNA gene sequences and phylogenomic reconstruction revealed a close phylogenetic relationship between strain 960558^T and members of the family Rhodobacteraceae by forming a separate branch within the type species of closely related genera. The validly published species that is most closely related to strain 960558^T is Planktotalea lamellibrachiae JAM 119^T, which has the highest 16S rRNA gene sequence similarity (93.47 %). Ubiquinone 10 is the predominant ubiquinone, while C_16 : 0, 11-methyl C_18 : 1  ω7c and C_18 : 1  ω7c and/or C_18 : 1  ω6c are the predominant fatty acids (>10 %). Additionally, phosphatidylglycerol, glycolipids, diphosphatidylglycerol, unidentified polar lipids and unidentified aminolipids are the major polar lipids. The DNA G+C content of strain 960558^T is 61 %. Average nucleotide identity and digital DNA-DNA hybridization results of strain 960558^T with other type strains are <70.2 and 22.1 %, respectively. Based on its phylogenetic, chemotaxonomic and other phenotypic properties, strain 960558^T is considered to represent a novel genus and species within the family Rhodobacteraceae, for which the name Abyssibius alkaniclasticus gen. nov., sp. nov. is proposed. The type strain of Abyssibius alkaniclasticus is 960558^T (=KCTC 82619^T=MCCC 1K04727^T).

Harenicola maris gen. nov., sp. nov. isolated from the Sea of Japan shallow sediments

A Gram-negative, non-motile bacterium КMM 3653^T was isolated from a sediment sample from the Sea of Japan seashore, Russia. On the basis of the 16S rRNA gene sequence analysis the strain КMM 3653^T was positioned within the family Rhodobacteraceae (class Alphaproteobacteria) forming a distinct lineage with the highest gene sequence similarities to the members of the genera Pacificibacter (95.2-94.7%) and Nioella (95.1-94.5%), respectively. According to the phylogenomic tree based on 400 conserved protein sequences, strain КMM 3653^T was placed in the cluster comprising Vannielia litorea, Nioella nitratireducens, Litoreibacter albidus and Pseudoruegeria aquimaris as a separate lineage adjacent to V. litorea KCTC 32083^T. The average nucleotide identity values between strain КMM 3653^T and V. litorea KCTC 32083^T, N. nitratireducens KCTC 32417^T, L. albidus KMM 3851^T, and P. aquimaris CECT 7680^T were 71.1, 70.3, 69.6, and 71.0%, respectively. Strain КMM 3653^T contained Q-10 as the predominant ubiquinone and C_18:1ω7c as the major fatty acid followed by C_16:0. The polar lipids were phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified phospholipid, two unidentified aminolipids, and five unidentified lipids. The DNA G+C content of 61.8% was calculated from the genome sequence. Based on the phylogenetic evidence and distinctive phenotypic characteristics, we proposed strain KMM 3653^T (= KCTC 82575^T) to be classified as a novel genus and species Harenicola maris gen. nov., sp. nov.

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).

A genomic view of trophic and metabolic diversity in clade-specific Lamellodysidea sponge microbiomes

BACKGROUND

Marine sponges and their microbiomes contribute significantly to carbon and nutrient cycling in global reefs, processing and remineralizing dissolved and particulate organic matter. Lamellodysidea herbacea sponges obtain additional energy from abundant photosynthetic Hormoscilla cyanobacterial symbionts, which also produce polybrominated diphenyl ethers (PBDEs) chemically similar to anthropogenic pollutants of environmental concern. Potential contributions of non-Hormoscilla bacteria to Lamellodysidea microbiome metabolism and the synthesis and degradation of additional secondary metabolites are currently unknown.

RESULTS

This study has determined relative abundance, taxonomic novelty, metabolic capacities, and secondary metabolite potential in 21 previously uncharacterized, uncultured Lamellodysidea-associated microbial populations by reconstructing near-complete metagenome-assembled genomes (MAGs) to complement 16S rRNA gene amplicon studies. Microbial community compositions aligned with sponge host subgroup phylogeny in 16 samples from four host clades collected from multiple sites in Guam over a 3-year period, including representatives of Alphaproteobacteria, Gammaproteobacteria, Oligoflexia, and Bacteroidetes as well as Cyanobacteria (Hormoscilla). Unexpectedly, microbiomes from one host clade also included Cyanobacteria from the prolific secondary metabolite-producer genus Prochloron, a common tunicate symbiont. Two novel Alphaproteobacteria MAGs encoded pathways diagnostic for methylotrophic metabolism as well as type III secretion systems, and have been provisionally assigned to a new order, designated Candidatus Methylospongiales. MAGs from other taxonomic groups encoded light-driven energy production pathways using not only chlorophyll, but also bacteriochlorophyll and proteorhodopsin. Diverse heterotrophic capabilities favoring aerobic versus anaerobic conditions included pathways for degrading chitin, eukaryotic extracellular matrix polymers, phosphonates, dimethylsulfoniopropionate, trimethylamine, and benzoate. Genetic evidence identified an aerobic catabolic pathway for halogenated aromatics that may enable endogenous PBDEs to be used as a carbon and energy source.

CONCLUSIONS

The reconstruction of high-quality MAGs from all microbial taxa comprising greater than 0.1% of the sponge microbiome enabled species-specific assignment of unique metabolic features that could not have been predicted from taxonomic data alone. This information will promote more representative models of marine invertebrate microbiome contributions to host bioenergetics, the identification of potential new sponge parasites and pathogens based on conserved metabolic and physiological markers, and a better understanding of biosynthetic and degradative pathways for secondary metabolites and halogenated compounds in sponge-associated microbiota. Video Abstract.

Nioella ostreopsis sp. nov., isolated from toxic dinoflagellate, Ostreopsis lenticularis

A novel short-rod-shaped bacterial strain with poly-β-hydroxybutyric acid granules inside, designated as Z7-4^T, was isolated from a culture of a marine dinoflagellate with palytoxin-producing capacity, Ostreopsis lenticularis OS06, collected from the East China Sea. Cells of Z7-4^T were Gram-stain-negative, non-motile, strictly aerobic, 0.9-1.2 µm wide and 2.0-3.9 µm long. Growth occurred in 1-4 % (w/v) NaCl, at 15-37 °C and at pH 5.0-10.0, with optimum growth in 3.5 % (w/v) NaCl, at 30 °C and at pH 7.0. Analysis of 16S rRNA gene sequence revealed that Z7-4^T shared the highest 16S rRNA gene sequence similarities with Nioella aestuarii JCM 30752^T (98.8 %), followed by Nioella sediminis KCTC 42144^T (98.6 %) and Nioella nitratireducens KCTC 32417^T (96.9 %). Phylogenetic analysis based on nearly complete 16S rRNA gene sequences revealed that Z7-4^T clearly represented a member of the genus Nioella within the family Rhodobacteraceae. The respiratory quinone of Z7-4^T was identified as Q-10. Polar lipids of Z7-4^T were phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, three unidentified aminophospholipids and one unidentified phospholipid. The major fatty acids were summed feature 8 (C_18 : 1ω7c and/or C_18 : 1ω6c) and C_16 : 0. The DNA G+C content of Z7-4^T was 63.0 mol%. DNA-DNA hybridization values of the isolate against the closely related type strains were far below the 70 % limit for species delineation. The average nucleotide identity and in silico DNA-DNA genome hybridization relatedness between Z7-4^T and the closely related members of the genus Nioella, N. sediminis KCTC 42144^T and N. nitratireducens KCTC 32417^T, were 91.1 and 46.3 %, and 79.3 and 19.4 %, respectively. On the basis of the results of polyphasic analysis, Z7-4^T is proposed to represent a novel species of the genus Nioella, for which the name Nioella ostreopsis sp. nov. is proposed. The type strain of Nioella ostreopsis is Z7-4^T (=KCTC 62459^T=CCTCC AB 2017231^T).

Cobaviruses - a new globally distributed phage group infecting Rhodobacteraceae in marine ecosystems

Bacteriophages are widely considered to influence bacterial communities, however most phages are still unknown or not studied well enough to understand their ecological roles. We have isolated two phages infecting Lentibacter sp. SH36, affiliated with the marine Roseobacter group, and retrieved similar phage genomes from publicly available metagenomics databases. Phylogenetic analysis placed the new phages within the Cobavirus group, in the here newly proposed genus Siovirus and subfamily Riovirinae of the Podoviridae. Gene composition and presence of direct terminal repeats in cultivated cobaviruses point toward a genome replication and packaging strategy similar to the T7 phage. Investigation of the genomes suggests that viral lysis of the cell proceeds via the canonical holin-endolysin pathway. Cobaviral hosts include members of the genera Lentibacter, Sulfitobacter and Celeribacter of the Roseobacter group within the family Rhodobacteraceae (Alphaproteobacteria). Screening more than 5,000 marine metagenomes, we found cobaviruses worldwide from temperate to tropical waters, in the euphotic zone, mainly in bays and estuaries, but also in the open ocean. The presence of cobaviruses in protist metagenomes as well as the phylogenetic neighborhood of cobaviruses in glutaredoxin and ribonucleotide reductase trees suggest that cobaviruses could infect bacteria associated with phototrophic or grazing protists. With this study, we expand the understanding of the phylogeny, classification, genomic organization, biogeography and ecology of this phage group infecting marine Rhodobacteraceae.

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).

Nioella aestuarii sp. nov., of the family Rhodobacteraceae, isolated from tidal flat

A bacterium, designated strain MME-018^T, was isolated from a tidal flat of the Muui-do in the Republic of Korea and identified within the family Rhodobacteraceae. The 16S rRNA gene sequence of the isolate showed the highest similarity to that of Nioella sediminis JS7-11^T (98.9 %), followed by Nioella nitratireducens SSW136^T (97.1 %). In phylogenetic analyses, these taxa formed a clade at neighbour-joining, maximum-likelihood, and maximum-parsimony algorithms, in which it was separated from other genus belonging to the family Rhodobacteraceae. Ubiquinone-10 (Q-10) was the major respiratory quinone. Major polar lipids included phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, two unidentified phospholipids, and an unidentified lipid. Major fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) C16 : 0, cyclo C19 : 0ω8c, and 11-methyl C18 : 1ω7c. Genomic DNA G+C content was 61 mol%. Cells were Gram-stain negative, non-motile, aerobic, and rod-shaped. This strain grew in 1‒4 % (w/v) NaCl, at 4-40 °C and pH 6.0‒8.0, with optimal growth in 2 % (w/v) NaCl, at 25‒30 °C and pH 7.0. DNA-DNA hybridization values between strain MME-018^T and Nioella sediminis KCTC 42144^T and Nioella nitratireducens KCTC 32417^T were 17±3 and 13±1 %, respectively. On the basis of polyphasic taxonomic analysis, strain MME-018^T is proposed to represent a novel species of the genus Nioella, for which the name Nioellaaestuarii sp. nov. The type strain of Nioellaaestuarii is MME-018^T (=KCCM 43135^T=JCM 30752^T).