Neptuniibacter halophilus sp. nov., isolated from a salt pan, and emended description of the genus Neptuniibacter

Identification of putative coral pathogens in endangered Caribbean staghorn coral using machine learning

Coral diseases contribute to the rapid decline in coral reefs worldwide, and yet coral bacterial pathogens have proved difficult to identify because 16S rRNA gene surveys typically identify tens to hundreds of disease-associate bacteria as putative pathogens. An example is white band disease (WBD), which has killed up to 95% of the now-endangered Caribbean Acropora corals since 1979, yet the pathogen is still unknown. The 16S rRNA gene surveys have identified hundreds of WBD-associated bacterial amplicon sequencing variants (ASVs) from at least nine bacterial families with little consensus across studies. We conducted a multi-year, multi-site 16S rRNA gene sequencing comparison of 269 healthy and 143 WBD-infected Acropora cervicornis and used machine learning modelling to accurately predict disease outcomes and identify the top ASVs contributing to disease. Our ensemble ML models accurately predicted disease with greater than 97% accuracy and identified 19 disease-associated ASVs and five healthy-associated ASVs that were consistently differentially abundant across sampling periods. Using a tank-based transmission experiment, we tested whether the 19 disease-associated ASVs met the assumption of a pathogen and identified two pathogenic candidate ASVs-ASV25 Cysteiniphilum litorale and ASV8 Vibrio sp. to target for future isolation, cultivation, and confirmation of Henle-Koch's postulate via transmission assays.

Genome taxonomy of the genus Neptuniibacter and proposal of Neptuniibacter victor sp. nov. isolated from sea cucumber larvae

A Gram-staining-negative, oxidase-positive, strictly aerobic rod-shaped bacterium, designated strain PT1T, was isolated from the laboratory-reared larvae of the sea cucumber Apostichopus japonicus. A phylogenetic analysis based on the 16S rRNA gene nucleotide sequences revealed that PT1T was closely related to Neptuniibacter marinus ATR 1.1T (= CECT 8938T = DSM 100783T) and Neptuniibacter caesariensis MED92T (= CECT 7075T = CCUG 52065T) showing 98.2% and 98.1% sequence similarity, respectively. However, the average nucleotide identity (ANI) and in silico DNA-DNA hybridization (DDH) values among these three strains were 72.0%-74.8% and 18.3%-19.5% among related Neptuniibacter species, which were below 95% and 70%, respectively, confirming the novel status of PT1T. The average amino acid identity (AAI) values of PT1T showing 74-77% among those strains indicated PT1T is a new species in the genus Neptuniibacter. Based on the genome-based taxonomic approach, Neptuniibacter victor sp. nov. is proposed for PT1T. The type strain is PT1T (JCM 35563T = LMG 32868T).

Colonization of Non-biodegradable and Biodegradable Plastics by Marine Microorganisms

Plastics are ubiquitous in the oceans and constitute suitable matrices for bacterial attachment and growth. Understanding biofouling mechanisms is a key issue to assessing the ecological impacts and fate of plastics in marine environment. In this study, we investigated the different steps of plastic colonization of polyolefin-based plastics, on the first one hand, including conventional low-density polyethylene (PE), additivated PE with pro-oxidant (OXO), and artificially aged OXO (AA-OXO); and of a polyester, poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV), on the other hand. We combined measurements of physical surface properties of polymers (hydrophobicity and roughness) with microbiological characterization of the biofilm (cell counts, taxonomic composition, and heterotrophic activity) using a wide range of techniques, with some of them used for the first time on plastics. Our experimental setup using aquariums with natural circulating seawater during 6 weeks allowed us to characterize the successive phases of primo-colonization, growing, and maturation of the biofilms. We highlighted different trends between polymer types with distinct surface properties and composition, the biodegradable AA-OXO and PHBV presenting higher colonization by active and specific bacteria compared to non-biodegradable polymers (PE and OXO). Succession of bacterial population occurred during the three colonization phases, with hydrocarbonoclastic bacteria being highly abundant on all plastic types. This study brings original data that provide new insights on the colonization of non-biodegradable and biodegradable polymers by marine microorganisms.

Draft Genome Sequences of Neptuniibacter sp. Strains LFT 1.8 and ATR 1.1

We present the draft genomes of two strains previously identified as Neptuniibacter sp. LFT 1.8 (= CECT 8936 = DSM 100781) and ATR 1.1 (= CECT 8938 = DSM 100783) isolated from larvae of great scallops ( Pecten maximus ) and seawater, respectively. Both strains surely constitute two novel species in this genus, with putative applications for aromatic compound degradation.

Neptuniibacter pectenicola sp. nov. and Neptuniibacter marinus sp. nov., two novel species isolated from a Great scallop (Pecten maximus) hatchery in Norway and emended description of the genus Neptuniibacter

Nine isolates obtained from a great scallop hatchery in Norway were characterized using a polyphasic approach. Strains were Gram-negative, aerobic and motile rods with oxidative metabolism. Phylogenetic analysis based on the sequences of 16S rRNA and rpoB genes showed that these strains formed two different groups associated with members of the genus Neptuniibacter. DNA-DNA hybridization (DDH) and Average Nucleotide Identity (ANI) demonstrated that the isolates constituted two novel species of this genus, which can be phenotypically differentiated from their closest relatives. The names Neptuniibacter marinus sp. nov. and Neptuniibacter pectenicola sp. nov are proposed, with ATR 1.1^T (=CECT 8938^T=DSM 100783^T) and LFT 1.8^T (=CECT 8936^T=DSM 100781^T) as respective type strains.

Motiliproteus sediminis gen. nov., sp. nov., isolated from coastal sediment

A novel Gram-stain-negative, rod-to-spiral-shaped, oxidase- and catalase- positive and facultatively aerobic bacterium, designated HS6(T), was isolated from marine sediment of Yellow Sea, China. It can reduce nitrate to nitrite and grow well in marine broth 2216 (MB, Hope Biol-Technology Co., Ltd) with an optimal temperature for growth of 30-33 °C (range 12-45 °C) and in the presence of 2-3% (w/v) NaCl (range 0.5-7%, w/v). The pH range for growth was pH 6.2-9.0, with an optimum at 6.5-7.0. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that the novel isolate was 93.3% similar to the type strain of Neptunomonas antarctica, 93.2% to Neptunomonas japonicum and 93.1% to Marinobacterium rhizophilum, the closest cultivated relatives. The polar lipid profile of the novel strain consisted of phosphatidylethanolamine, phosphatidylglycerol and some other unknown lipids. Major cellular fatty acids were summed feature 3 (C(16:1) ω7c/iso-C15:0 2-OH), C(18:1) ω7c and C(16:0) and the main respiratory quinone was Q-8. The DNA G+C content of strain HS6(T) was 61.2 mol%. Based on the phylogenetic, physiological and biochemical characteristics, strain HS6(T) represents a novel genus and species and the name Motiliproteus sediminis gen. nov., sp. nov., is proposed. The type strain is HS6(T) (=ATCC BAA-2613(T)=CICC 10858(T)).

Sinobacterium caligoides gen. nov., sp. nov., a new member of the family Oceanospirillaceae isolated from the South China Sea, and emended description of Amphritea japonica

A taxonomic study was carried out on strain SCSWE24T, isolated from a seawater sample collected from the South China Sea. Cells of strain SCSWE24T were Gram-negative, rod-shaped, non-motile, moderately halophilic and capable of reducing nitrate to nitrite. Growth was observed at salinities from 1.5 to 4.5 % and at 4–37 °C; it was unable to degrade gelatin. The dominant fatty acids (>15 %) were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c; 50.4 %) and C16 : 0 (21.1 %). The G+C content of the chromosomal DNA was 58.8 mol%. 16S rRNA gene sequence comparisons showed that strain SCSWE24T was most closely related to an uncultured bacterium clone Tun3b.F5 (98 %; GenBank accession no. FJ169216), and showed 92 % similarity to an endosymbiont bacterium from the bone-eating worm Osedax mucofloris (clone Omu 9 c4791; FN773233). Levels of similarity between strain SCSWE24T and type strains of recognized species in the family Oceanospirillaceae were less than 93 %; the highest similarity was 92 %, to both Amphritea japonica JAMM 1866T and ‘Oceanicoccus sagamiensis’ PZ-5. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain SCSWE24T formed a distinct evolutionary lineage within the family Oceanospirillaceae . Strain SCSWE24T was distinguishable from members of phylogenetically related genera by differences in several phenotypic properties. On the basis of the phenotypic and phylogenetic data, strain SCSWE24T represents a novel species of a new genus, for which the name Sinobacterium caligoides gen. nov., sp. nov. is proposed. The type strain of Sinobacterium caligoides is SCSWE24T ( = CCTCC AB 209289T  = LMG 25705T  = MCCC 1F01088T). An emended description of Amphritea japonica is also provided.