Genome-based analysis of the family Paracoccaceae and description of Ostreiculturibacter nitratireducens gen. nov., sp. nov., isolated from an oyster farm on a tidal flat.

Two bacterial strains, designated FR2A1T and MT2-5-38, were isolated from the surface sediments of an oyster farm on a tidal flat in Quanzhou Bay, China. Both strains were Gram-stain-negative, rod-shaped, aerobic, catalase-positive, and oxidase-positive. The 16S rRNA gene sequences of the two strains were 100% identical and had the highest similarity (97.1%) with Phaeovulum vinaykumarii JA123T. The average nucleotide identity (ANI) value and digital DNA-DNA hybridization (DDH) value indicated that the two strains belonged to a single species. Gene annotation revealed that the two strains contained a gene cluster for nitrate reduction and a gene cluster for sulfur oxidation, indicating a possible role in N and S cycling in the tidal flat sediment. The phylogeny inferred from the 16S rRNA gene and 120 conserved proteins indicated that the two strains formed a distinct monophyletic clade within the family Paracoccaceae. The respiratory quinone was Q-10. The major fatty acids consisted of summed feature 8 (C18:1ω7c and/or C18:1ω6c) and C18:0. The polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, and several unidentified phospholipids. Based on the above characteristics, strains FR2A1T and MT2-5-38 represent a novel genus and a novel species, for which we propose the name Ostreiculturibacter nitratireducens gen. nov., sp. nov. The type strain is FR2A1T (=MCCC 1K08809T = KCTC 8317T). Phylogenomic analysis of 1,606 high-quality genomes of the family Paracoccaceae, including type strains, non-type strains, and uncultivated bacteria, was performed using the Genome Taxonomic Database Toolkit (GTDB-Tk), and the average amino acid identity (AAI) value of the phylogenetic clade was estimated. We found that 35 species of the family Paracoccaceae needed re-classification, and an AAI value of 70% was chosen as the genus boundary within the family Paracoccaceae.

Rhodobacteraceae are key players in microbiome assembly of the diatom Asterionellopsis glacialis.

The complex interactions between bacterioplankton and phytoplankton have prompted numerous studies that investigate phytoplankton microbiomes with the aim of characterizing beneficial or opportunistic taxa and elucidating core bacterial members. Oftentimes, this knowledge is garnered through 16S rRNA gene profiling of microbiomes from phytoplankton isolated across spatial and temporal scales, yet these studies do not offer insight into microbiome assembly and structuring. In this study, we aimed to identify taxa central to structuring and establishing the microbiome of the ubiquitous diatom Asterionellopsis glacialis. We introduced a diverse environmental bacterial community to A. glacialis in nutrient-rich or nutrient-poor media in a continuous dilution culture setup and profiled the bacterial community over 7 days. 16S rRNA amplicon sequencing showed that cyanobacteria (Coleofasciculaceae) and Rhodobacteraceae dominate the microbiome early on and maintain a persistent association throughout the experiment. Differential abundance, co-abundance networks, and differential association analyses revealed that specific members of the family Rhodobacteraceae, particularly Sulfitobacter amplicon sequence variants, become integral members in microbiome assembly. In the presence of the diatom, Sulfitobacter species and other Rhodobacteraceae developed positive associations with taxa that are typically in high abundance in marine ecosystems (Pelagibacter and Synechococcus), leading to restructuring of the microbiome compared to diatom-free controls. These positive associations developed predominantly under oligotrophic conditions, highlighting the importance of investigating phytoplankton microbiomes in as close to natural conditions as possible to avoid biases that develop under routine laboratory conditions. These findings offer further insight into phytoplankton-bacteria interactions and illustrate the importance of Rhodobacteraceae, not merely as phytoplankton symbionts but as key taxa involved in microbiome assembly. IMPORTANCE: Most, if not all, microeukaryotic organisms harbor an associated microbial community, termed the microbiome. The microscale interactions that occur between these partners have global-scale consequences, influencing marine primary productivity, carbon cycling, and harmful algal blooms to name but a few. Over the last decade, there has been a growing interest in the study of phytoplankton microbiomes, particularly within the context of bloom dynamics. However, long-standing questions remain regarding the process of phytoplankton microbiome assembly. The significance of our research is to tease apart the mechanism of microbiome assembly with a particular focus on identifying bacterial taxa, which may not merely be symbionts but architects of the phytoplankton microbiome. Our results strengthen the understanding of the ecological mechanisms that underpin phytoplankton-bacteria interactions in order to accurately predict marine ecosystem responses to environmental perturbations.

Rhodobacteraceae methanethiol oxidases catalyze methanethiol degradation to produce sulfane sulfur other than hydrogen sulfide.

Methanethiol (MT) is a sulfur-containing compound produced during dimethylsulfoniopropionate (DMSP) degradation by marine bacteria. The C-S bond of MT can be cleaved by methanethiol oxidases (MTOs) to release a sulfur atom. However, the cleaving process remains unclear, and the species of sulfur product is uncertain. It has long been assumed that MTOs produce hydrogen sulfide (H2S) from MT. Herein, we studied the MTOs in the Rhodobacteraceae family-whose members are important DMSP degraders ubiquitous in marine environments. We identified 57 MTOs from 1,904 Rhodobacteraceae genomes. These MTOs were grouped into two major clusters. Cluster 1 members share three conserved cysteine residues, while cluster 2 members contain one conserved cysteine residue. We examined the products of three representative MTOs both in vitro and in vivo. All of them produced sulfane sulfur other than H2S from MT. Their conserved cysteines are substrate-binding sites in which the MTO-S-S-CH3 complex is formed. This finding clarified the sulfur product of MTOs and enlightened the MTO-catalyzing process. Moreover, this study connected DMSP degradation with sulfane sulfur metabolism, filling a critical gap in the DMSP degradation pathway and representing new knowledge in the marine sulfur cycle field. IMPORTANCE: This study overthrows a long-time assumption that methanethiol oxidases (MTOs) cleave the C-S bond of methanethiol to produce both H2S and H2O2-the former is a strong reductant and the latter is a strong oxidant. From a chemistry viewpoint, this reaction is difficult to happen. Investigations on three representative MTOs indicated that sulfane sulfur (S0) was the direct product, and no H2O2 was produced. Finally, the products of MTOs were corrected to be S0 and H2O. This finding connected dimethylsulfoniopropionate (DMSP) degradation with sulfane sulfur metabolism, filling a critical gap in the DMSP degradation pathway and representing new knowledge in the marine sulfur cycle field.

Fontisubflavum oceani gen. nov., sp. nov., isolated from the deep-sea cold seep water of South China Sea.

In this study, we report a Gram-stain-negative, rod-shaped, atrichous and aerobic bacterial strain named CSW1921T, which was isolated from the deep-sea water of a cold seep in South China Sea. Growth of strain CSW1921T occurred at 10.0-35.0 °C (optimum, 30 °C), pH 5.0-10.0 (optimum, pH 8.0-9.0) and with 0-9.0 % (w/v) NaCl (optimum, 1.0-2.0 %). Phylogenetic tree analysis based on 16S rRNA gene sequence or the genomic sequence indicated that strain CSW1921T belonged to the family Rhodobacteraceae and was closely related to Rhodophyticola porphyridii MA-7-27T (97.5 % sequence similarity). Genomic analysis indicated that strain CSW1921T contains a circular chromosome of 3 592 879 bp with G+C content of 60.5 mol%. The predominant respiratory quinone of CSW1921T was ubiquinone-10. The polar lipids of CSW1921T contained phosphatidylglycerol, three unidentified aminolipids, two unidentified phospholipids and two unidentified lipids. The major fatty acids of strain CSW1921T contained C16 : 0, C18 : 1 ω7c 11-methyl and summed feature 8 (C18 : 1 ω7c). The average nucleotide identity, DNA-DNA hybridization and average amino acid identity values between strain CSW1921T and members of its related species were 68.02-69.08 %, 12.7-12.9 % and 46.87-48.08 %, respectively, which were lower than the recommended threshold values for bacterial species or genus delineation. Phylogenetic, physiological, biochemical and morphological analyses suggested that strain CSW1921T represents a novel genus and a novel species of the family Rhodobacteraceae, and the name Fontisubflavum oceani gen. nov., sp. nov. is proposed with the type strain CSW1921T (=MCCC 1K08371T=KCTC 92834T).

Metagenome-assembled genomes reveal greatly expanded taxonomic and functional diversification of the abundant marine Roseobacter RCA cluster.

BACKGROUND: The RCA (Roseobacter clade affiliated) cluster belongs to the family Roseobacteracea and represents a major Roseobacter lineage in temperate to polar oceans. Despite its prevalence and abundance, only a few genomes and one described species, Planktomarina temperata, exist. To gain more insights into our limited understanding of this cluster and its taxonomic and functional diversity and biogeography, we screened metagenomic datasets from the global oceans and reconstructed metagenome-assembled genomes (MAG) affiliated to this cluster. RESULTS: The total of 82 MAGs, plus five genomes of isolates, reveal an unexpected diversity and novel insights into the genomic features, the functional diversity, and greatly refined biogeographic patterns of the RCA cluster. This cluster is subdivided into three genera: Planktomarina, Pseudoplanktomarina, and the most deeply branching Candidatus Paraplanktomarina. Six of the eight Planktomarina species have larger genome sizes (2.44-3.12 Mbp) and higher G + C contents (46.36-53.70%) than the four Pseudoplanktomarina species (2.26-2.72 Mbp, 42.22-43.72 G + C%). Cand. Paraplanktomarina is represented only by one species with a genome size of 2.40 Mbp and a G + C content of 45.85%. Three novel species of the genera Planktomarina and Pseudoplanktomarina are validly described according to the SeqCode nomenclature for prokaryotic genomes. Aerobic anoxygenic photosynthesis (AAP) is encoded in three Planktomarina species. Unexpectedly, proteorhodopsin (PR) is encoded in the other Planktomarina and all Pseudoplanktomarina species, suggesting that this light-driven proton pump is the most important mode of acquiring complementary energy of the RCA cluster. The Pseudoplanktomarina species exhibit differences in functional traits compared to Planktomarina species and adaptations to more resource-limited conditions. An assessment of the global biogeography of the different species greatly expands the range of occurrence and shows that the different species exhibit distinct biogeographic patterns. They partially reflect the genomic features of the species. CONCLUSIONS: Our detailed MAG-based analyses shed new light on the diversification, environmental adaptation, and global biogeography of a major lineage of pelagic bacteria. The taxonomic delineation and validation by the SeqCode nomenclature of prominent genera and species of the RCA cluster may be a promising way for a refined taxonomic identification of major prokaryotic lineages and sublineages in marine and other prokaryotic communities assessed by metagenomics approaches. Video Abstract.

Falsirhodobacter algicola sp. nov., a member of the Rhodobacteraceae isolated from the marine red algae Grateloupia sp.

A Gram-negative, pale yellow-pigmented, non-flagellated, motile, rod-shaped and aerobic bacterium, designated strain PG104T, was isolated from red algae Grateloupia sp. collected from the coastal area of Pohang, Republic of Korea. Growth of strain PG104T was observed at 15-35 °C (optimum, 30 °C), pH 6.0-10.0 (optimum, pH 7.5-8.0) and in the presence of 0-8.0 % (w/v) NaCl (optimum, 5.0 %). The predominant fatty acids included C17 : 0, C18 : 0, 11-methyl C18 : 1 ω7c and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and the major respiratory quinone was Q-10. Polar lipids included phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified lipid and one unidentified aminolipid. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain PG104T formed a phylogenetic lineage with members of the genus Falsirhodobacter and exhibited 16S rRNA gene sequence similarities of 97.1 and 96.6 % to Falsirhodobacter deserti W402T and Falsirhodobacter halotolerans JA744T, respectively. The complete genome of strain PG104T consisted of a single circular chromosome of approximately 2.8 Mbp with five plasmids. Based on polyphasic taxonomic data, strain PG104T represents a novel species in the genus Falsirhodobacter, for which the name Falsirhodobacter algicola sp. nov. is proposed. The type strain of Falsirhodobacter algicola is PG104T (=KCTC 82230T=JCM 34380T).

Defluviimonas sediminis sp. nov., isolated from mangrove sediment.

A Gram-stain-negative, facultatively aerobic, motile and ovoid- to rod-shaped bacterium, designated as FT324T, was isolated from a surface mangrove sediment sample from Shenzhen, PR China. The taxonomic position of strain FT324T was determined by a combination of phylogenetic, physiological, biochemical and chemotaxonomic analyses. Strain FT324T grew at 20-40 °C (optimum, 30-37 °C), pH 5.0-9.0 (optimum, pH 8.0) and in the presence of 0-3 % (w/v) NaCl (optimum, 1 %). Its full-length 16S rRNA gene sequence was the most similar to Frigidibacter oleivorans XJ4T (97.4 %), followed by Defluviimonas denitrificans DSM 18921T (96.62 %), Pseudothioclava arenosa CAU 1312T (96.54 %) and Defluviimonas nitratireducens DL5-4T (96.47 %). The major fatty acids (>10 %) of FT324T were C19 : 0 cyclo ω8c (51.9 %) and summed feature 8(29.6 %). The predominant respiratory quinone was Q-10. Its polar lipid profile contained phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified aminolipid, one unidentified lipid and two unidentified phospholipids. Its estimated genome size was 4 294 115 bp and the genomic DNA G+C content was 69.6 mol%. Based on its distinct phenotypic, chemotaxonomic and phylogenetic characteristics, strain FT324T should represent a novel species of the genus Defluviimonas, for which the name Defluviimonas sediminis sp. nov. is proposed (=MCCC 1K07685T=KCTC 92477T).

Adverse effects of polystyrene nanoplastics on sea cucumber Apostichopus japonicus and their association with gut microbiota dysbiosis.

The mariculture environment is a sink of microplastics (MPs) due to its enclosed nature and mass use of plastics. Nanoplastics (NPs) are MPs with a diameter <1 µm that have a more toxic effect on aquatic organisms than other MPs. However, little is known about the underlying mechanisms of NP toxicity on mariculture species. Here, we performed a multi-omics investigation to explore gut microbiota dysbiosis and associated health problems induced by NPs in juvenile sea cucumber Apostichopus japonicus, a commercially and ecologically important marine invertebrate. We observed significant differences in gut microbiota composition after 21 days of NP exposure. Ingestion of NPs significantly increased core gut microbes, especially Rhodobacteraceae and Flavobacteriaceae families. Additionally, gut gene expression profiles were altered by NPs, especially those related to neurological diseases and movement disorders. Correlation and network analyses indicated close relationships between transcriptome changes and gut microbiota variation. Furthermore, NPs induced oxidative stress in sea cucumber intestines, which may be associated with intraspecies variation in Rhodobacteraceae in the gut microbiota. The results suggested that NPs were harmful to the health of sea cucumbers, and they highlighted the importance of the gut microbiota in the responses to NP toxicity in marine invertebrates.

Description of Defluviimonas salinarum sp. nov. with the potential of benzene-degradation isolated from saltern in the Yellow Seacoast.

Strain CAU 1641T was isolated from saltern collected in Ganghwa Island, Republic of Korea. The bacterium was an aerobic, Gram-negative, catalase-positive, oxidase-positive, motile, and rod-shaped bacterium. Cell of strain CAU 1641T could grow at 20-40°C and pH 6.0-9.0 with 1.0-3.0% (w/v) NaCl. Stain CAU 1641T shared high 16S rRNA gene sequence similarities with Defluviimonas aquaemixtae KCTC 42108T (98.0%), Defluviimonas denitrificans DSM 18921T (97.6%), and Defluviimonas aestuarii KACC 16442T (97.5%). Phylogenetic trees based on the 16S rRNA gene and the core-genome sequences indicated that strain CAU 1641T belonged to genus Defluviimonas. Strain CAU 1641T contained ubiquinone-10 (Q-10) as the sole respiratory quinone and and summed feature 8 (C18:1ω6c and/or C18:1ω7c) as the predominant fatty acid (86.1%). The pan-genome analysis indicated that the genomes of the strain CAU 1641T and 15 reference strains contain a small core genome. The Average Nucleotide Identity and digital DNA-DNA hybridization values among strain CAU 1641T and reference strains of the genus Defluviimonas were in the range of 77.6%-78.8% and 21.1-22.1%, respectively. The genome of strain CAU 1641T has several genes of benzene degradation. The genomic G + C content was 66.6%. Based on polyphasic and genomic analyses, strain CAU 1641T represents a novel species of the genus Defluviimonas, for which the name Defluviimonas salinarum sp. nov., is proposed. The type strain is CAU 1641T ( = KCTC 92081T = MCCC 1K07180T).

Shell Disease Syndrome Is Associated with Reduced and Shifted Epibacterial Diversity on the Carapace of the Crustacean Cancer pagurus.

Cancer pagurus is highly susceptible to shell disease syndrome. However, little is known about concomitant changes in the epibacterial community. We compared the bacterial communities of black spot affected and nonaffected areas of the carapace by amplicon sequencing of 16S rRNA genes and 16S rRNA. Within each spot, bacterial communities of affected areas were less diverse compared to communities from nonaffected areas. Communities of different affected spots were, however, more divergent from each other, compared to those of different nonaffected areas. This indicates a reduced and shifted microbial community composition caused by the black spot disease. Different communities found in black spots likely indicate different stages of the disease. In affected areas, Flavobacteriaceae rose to one of the most abundant and active families due to the increase of Aquimarina spp., suggesting a significant role in shell disease syndrome. We isolated 75 bacterial strains from diseased and healthy areas, which are primarily affiliated with Proteobacteria and Bacteroidetes, reflecting the dominant phyla detected by amplicon sequencing. The ability to degrade chitin was mainly found for Gammaproteobacteria and Aquimarina spp. within the Flavobacteriia, while the ability to use N-acetylglucosamine, the monomer of the polysaccharide chitin, was observed for most isolates, including many Alphaproteobacteria. One-third of the isolates, including most Aquimarina spp., showed antagonistic properties, indicating a high potential for interactions between the bacterial populations. The combination of bacterial community analysis and the physiological properties of the isolates provided insights into a functional complex epibacterial community on the carapace of C. pagurus. IMPORTANCE In recent years, shell disease syndrome has been detected for several ecologically and economically important crustacean species. Large proportions of populations are affected, e.g., >60% of the widely distributed species Cancer pagurus in different North Sea areas. Bacteria play a significant role in the development of different forms of shell disease, all characterized by microbial chitinolytic degradation of the outer shell. By comparing the bacterial communities of healthy and diseased areas of the shell of C. pagurus, we demonstrated that the disease causes a reduced bacterial diversity within affected areas, a phenomenon co-occurring also with many other diseases. Furthermore, the community composition dramatically changed with some taxa rising to high relative abundances and showing increased activity, indicating strong participation in shell disease. Characterization of bacterial isolates obtained from affected and nonaffected spots provided deeper insights into their physiological properties and thus the possible role within the microbiome.

Limibaculum sediminis sp. nov., isolated from mangrove sediment.

A Gram-stain-negative, cream-coloured, aerobic, motile and ovoid- to rod-shaped bacterium, designated as FT325T, was isolated from mangrove sediment collected in Shenzhen, PR China. The taxonomic position of strain FT325T was established by phylogenetic, physiological, biochemical and chemotaxonomic analyses. Strain FT325T grew optimally at 37-40 °C and pH 6.0 in the presence of 0 % (w/v) NaCl. Results of 16S rRNA gene sequence analysis showed that strain FT325T was most similarly related to Limibaculum halophilum CAU 1123T (96.2 %), Phaeovulum vinaykumarii DSM 18714T (93.9%) and Amaricoccus solimangrovi HB 172011T (93.7 %). The major fatty acids (>10 %) were C18 : 1 ω7c (60.0 %) and 11-methyl C18 : 1 ω7c (16.7 %). The sole respiratory quinone was Q-10. The polar lipids were phosphatidylglycerol, one unidentified glycolipid, three unidentified aminolipids and three unidentified phospholipids. Its estimated genome size was 4 318 768 bp and the genomic DNA G+C content was 69.6 mol%. Based on its distinct phenotypic, chemotaxonomic and phylogenetic characteristics, strain FT325T represents a novel species of the genus Limibaculum, for which the name Limibaculum sediminis sp. nov. is proposed (=MCCC 1K07397T=KCTC 92313T).

Algicella marina gen. nov., sp. nov., a novel marine bacterium isolated from a Pacific red alga.

A novel Gram-staining negative, strictly aerobic, rod-shaped, and non-motile bacterium, designated strain 9Alg 56T, was isolated from the red alga Tichocarpus crinitus. The phylogenetic analysis based on 16S rRNA gene sequences placed the novel strain within the family Rhodobacteraceae, the order Rhodobacterales, the class Alphaproteobacteria, the phylum Pseudomonadota. The nearest neighbors of the new strain were Pontivivens insulae KCTC 42458T, Oceanibium sediminis KCTC 62076T, Halovulum dunhuangense YYQ-30T and Monaibacterium marinum C7T with 16S rRNA gene sequence similarity of 94.7, 94.4%, 93.1 and 92.7%, respectively. The AAI/ANI/dDDH values between 9Alg 56T and the five species of the closest genera (Pontivivens, Oceanibium, Halovulum, Monaibacterium, and 'Oceanomicrobium') were 58.63-63.91%/ 75.91-77.37%/ 19.3-20.4%. The prevalent fatty acids of strain 9Alg 56T were C18:1 ω7c, C18:0 and C14:0 3-OH. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, phosphatidic acid, phosphatidylcholine, and two unidentified lipids. The DNA G+C content of strain 9Alg 56T was 61.5 mol%. A combination of the genotypic and phenotypic data showed that the algal isolate represents a novel genus and species, for which the name Algicella marina gen. nov., sp. nov. is proposed. The type strain is 9Alg 56T (= KCTC 72005T = KMM 6775T).

Sedimentimonas flavescens gen. nov., sp. nov., isolated from sediment of Clam Island, Liaoning Province.

A novel Gram-stain negative, aerobic and ovoid to short rod shaped bacterium with a single polar flagellum, named strain B57T, was isolated from sediment of Clam Island, Liaoning Province, China. The optimal growth of this strain was found to occur at 37 °C, pH 6-6.5, and in the presence of 2% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain B57T forms a distinct lineage within the family Rhodobacteraceae, sharing high 16S rRNA gene sequence similarity with Sinirhodobacter populi sk2b1T (97.4%). The average amino acid identity of B57T and the closely related species were lower than the threshold level for genus delineation. The dominant respiratory quinone of strain B57T was identified as Q-10. The major fatty acids were found to be Summed Feature 8 (C18:1ω7c and/or C18:1ω6c), Summed Feature 3 (C16:1ω7c and/or C16:1ω6c) and C16: 0. The polar lipids were identified as phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, diphosphatidylglycerol, two unidentified phospholipids, one unidentified glycolipid, and one unidentified lipid. The DNA G + C content of strain B57T was determined to be 64.1 mol%. Based on the biochemical, phylogenetic and chemotaxonomic analysis, strain B57T is concluded to represent a novel species of a novel genus, for which the name Sedimentimonas flavescens gen. nov., sp. nov.is proposed. The type strain is B57T (= CGMCC1.19488T = KCTC 92053T).

Thalassococcus arenae sp. nov. isolated from sea sand.

A Gram-negative, aerobic, rod-shaped bacterium, designated strain CAU 1522T, was isolated from a sea sand sample collected from the Republic of Korea. Optimal growth of strain CAU 1522T ensued at 30 °C, pH 7.5, and 1.0% (w/v) NaCl. Strain CAU 1522T was affiliated to the genus Thalassococcus with high similarity to T. lentus KCTC 32084T (97.5%), T. profundi MCCC 1K03253T (96.5%), and T. halodurans JCM 13833T (96.1%) according to phylogenetic analysis based on 16S rRNA gene sequences. The whole genome of strain CAU 1522T was 3.7 Mb in length and included 7 contigs and 3599 protein-coding genes, with a G + C content of 65.4 mol%. The predominant cellular fatty acids were C18:1 ω6c and/or C18:1 ω7c (summed feature 8), with Q-10 being the sole isoprenoid quinone. The polar lipids included phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, phosphoglycolipid, and an unidentified lipid. These phenotypic, chemotaxonomic, and phylogenetic data support that strain CAU 1522T is a novel Thalassococcus species, for which the name T. arenae sp. nov. is proposed. The type strain is CAU 1522T (= KCTC 72545T = MCCC 1K04064T).

Bacterial Community Assembly, Succession, and Metabolic Function during Outdoor Cultivation of Microchloropsis salina.

Outdoor cultivation of microalgae has promising potential for renewable bioenergy, but there is a knowledge gap on the structure and function of the algal microbiome that coinhabits these ecosystems. Here, we describe the assembly mechanisms, taxonomic structure, and metabolic potential of bacteria associated with Microchloropsis salina cultivated outdoors. Open mesocosms were inoculated with algal cultures that were either free of bacteria or coincubated with one of two different strains of alga-associated bacteria and were sampled across five time points taken over multiple harvesting rounds of a 40-day experiment. Using quantitative analyses of metagenome-assembled genomes (MAGs), we tracked bacterial community compositional abundance and taxon-specific functional capacity involved in algal-bacterial interactions. One of the inoculated bacteria (Alteromonas sp.) persisted and dispersed across mesocosms, whereas the other inoculated strain (Phaeobacter gallaeciensis) disappeared by day 17 while a taxonomically similar but functionally distinct Phaeobacter strain became established. The inoculated strains were less abundant than 6 numerically dominant newly recruited taxa with functional capacities for mutualistic or saprophytic lifestyles, suggesting a generalist approach to persistence. This includes a highly abundant unclassified Rhodobacteraceae species that fluctuated between 25% and 77% of the total community. Overall, we did not find evidence for priority effects exerted by the distinct inoculum conditions; all mesocosms converged with similar microbial community compositions by the end of the experiment. Instead, we infer that the 15 total populations were retained due to host selection, as they showed high metabolic potential for algal-bacterial interactions such as recycling alga-produced carbon and nitrogen and production of vitamins and secondary metabolites associated with algal growth and senescence, including B vitamins, tropodithietic acid, and roseobacticides. IMPORTANCE Bacteria proliferate in nutrient-rich aquatic environments, including engineered algal biofuel systems, where they remineralize photosynthates, exchange secondary metabolites with algae, and can influence system output of biomass or oil. Despite this, knowledge on the microbial ecology of algal cultivation systems is lacking, and the subject is worthy of investigation. Here, we used metagenomics to characterize the metabolic capacities of the predominant bacteria associated with the biofuel-relevant microalga Microchloropsis salina and to predict testable metabolic interactions between algae and manipulated communities of bacteria. We identified a previously undescribed and uncultivated organism that dominated the community. Collectively, the microbial community may interact with the alga in cultivation via exchange of secondary metabolites which could affect algal success, which we demonstrate as a possible outcome from controlled experiments with metabolically analogous isolates. These findings address the scalability of lab-based algal-bacterial interactions through to cultivation systems and more broadly provide a framework for empirical testing of genome-based metabolic predictions.

Pontibrevibacter nitratireducens gen. nov., sp. nov., a member of the family Rhodobacteraceae isolated from seawater of the Indian Ocean and intertidal zone.

Two Gram-stain-negative, facultatively anaerobic, non-motile, rod-shaped bacteria, strains h42T and ALG8, were isolated individually from the Indian Ocean and intertidal zone of Zhoushan, China. The results of 16S rRNA gene sequence analysis showed that the sequence similarity between strains h42T and ALG8 was 99.7 %, and the closest related strains were Monaibacterium marinum C7T (97.77 and 97.62 %) and Pontivivens insulae GYSW-23T (95.31 and 95.45 %). Phylogenetic analysis based on 16S rRNA gene sequences shows that these two novel strains belong to a distinct new lineage of the family Rhodobacteraceae in the order Rhodobacterales. The average nucleotide identity and in silico DNA-DNA hybridization values between the two novel strains and M. marinum C7T and P. insulae GYSW-23T were 72.73-78.15 % and 19.70-20.80 %, respectively. The DNA G+C content of strains h42T and ALG8 was 62.36 % and 62.17 mol %. The major fatty acids (>10 %) in strain h42T were C18 : 0, C19 : 0 cyclo ω8c and summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c), and in strain ALG8 were C19 : 0 cyclo ω8c and summed feature 8 (C18 : 1ω6c and/or C18 : 1 ω7c). The predominant isoprenoid ubiquinone of the two novel strains was Q-10; their major polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, two unidentified glycolipids, an unidentified aminoglycolipid, an unidentified phospholipid and an unidentified lipid. Based on the results of the morphological, physiological, chemotaxonomic and phylogenetic analysis of these two strains, a novel species of a new genus in the family Rhodobacteraceae is proposed, named as Pontibrevibacter nitratireducens gen. nov., sp. nov. The type strain and non-type strain of P. nitratireducens are h42T (=KCTC 72875T=CGMCC 1.17849T=MCCC 1K04735T) and ALG8 (=KCTC 82194=MCCC 1K04733).

Pseudophaeobacter flagellatus sp. nov., isolated from coastal water.

A Gram-stain-negative, aerobic, motile, rod-shaped novel bacterial strain, designated as MA21411-1T, was isolated from the Korean coast. The colonies were white-yellow-coloured, smooth, convex and entire, spherical and 1.0-1.8 mm in diameter. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain MA21411-1T is closely related to species of the genus Pseudophaeobacter. The 16S rRNA gene sequence similarities between strain MA21411-1T and Pseudophaeobacter arcticus DSM 23566T, Phaeobacter porticola DSM 103148T and Pseudophaeobacter leonis DSM 25627T were 98.31, 97.80 and 97.28 %, respectively. Strain MA21411-1T has a draft genome size of 4 294 042 bp, annotated with 4125 protein-coding genes, and 53 tRNA, three rRNA and one tmRNA genes. The genomic DNA G+C content was 59.2 mol%. Comparative genome analysis revealed that the average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity values among strain MA21411-1T and other related species were below the cut-off levels of 95, 70 and 95.5 %, respectively. The growth temperature range for growth was 15-28 °C (optimum, 25 °C), pH range was 6.0-9.0 (optimum, pH 6.0), and salt tolerance range was 0.5-4 % (optimum 0.5 %). Ubiquinone-10 was the sole quinone present in MA21411-1T and all three closely related strains. The major cellular fatty acid (>10 %) of the strain was summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The polar lipid profile contained phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and four unidentified polar lipids. Based on the phylogenetic tree, as well as phenotypic, chemotaxonomic and genomic features, strain MA21411-1T represents a novel species of the genus Pseudophaeobacter, for which the name Pseudophaeobacter flagellatus sp. nov. is proposed. The type strain is MA21411-1T (=KCTC 92095T=GDMCC 1.2988T).

Neotabrizicola shimadae gen. nov., sp. nov., an aerobic anoxygenic phototrophic bacterium harbouring photosynthetic genes in the family Rhodobacteraceae, isolated from a terrestrial hot spring.

A bacteriochlorophyll-containing bacterium, designated as strain N10T, was isolated from a terrestrial hot spring in Nagano Prefecture, Japan. Gram-stain-negative, oxidase- and catalase-positive and ovoid to rod-shaped cells showed the features of aerobic anoxygenic phototrophic bacteria, i.e., strain N10T synthesised bacteriochlorophylls under aerobic conditions and could not grow anaerobically even under illumination. Genome analysis found genes for bacteriochlorophyll and carotenoid biosynthesis, light-harvesting complexes and type-2 photosynthetic reaction centre in the chromosome. Phylogenetic analyses based on the 16S rRNA gene sequence and 92 core proteins revealed that strain N10T was located in a distinct lineage near the type species of the genera Tabrizicola and Xinfangfangia and some species in the genus Rhodobacter (e.g., Rhodobacter blasticus). Strain N10T shared < 97.1% 16S rRNA gene sequence identity with those species in the family Rhodobacteraceae. The digital DNA-DNA hybridisation, average nucleotide identity and average amino acid identity values with the relatives, Tabrizicola aquatica RCRI19T (an aerobic anoxygenic phototrophic bacterium), Xinfangfangia soli ZQBWT and R. blasticus ATCC 33485T were 19.9-20.7%, 78.2-79.1% and 69.1-70.1%, respectively. Based on the phenotypic features, major fatty acid and polar lipid compositions, genome sequence and phylogenetic position, a novel genus and species are proposed for strain N10T, to be named Neotabrizicola shimadae (= JCM 34381T = DSM 112087T). Strain N10T which is phylogenetically located among aerobic anoxygenic phototrophic bacteria (Tabrizicola), bacteriochlorophyll-deficient bacteria (Xinfangfangia) and anaerobic anoxygenic phototrophic bacteria (Rhodobacter) has great potential to promote studies on the evolution of photosynthesis in Rhodobacteraceae.

Sagittula salina sp. nov., isolated from marine waste.

A novel Gram-stain-negative, non-motile, halophilic bacterium designated strain M10.9XT was isolated from the inner sediment of an aluminium can collected from the Mediterranean Sea (València, Spain). Cells of strain M10.9XT were rod-shaped and occasionally formed aggregates. The strain was oxidase-negative and catalase-positive, and showed a slightly psychrophilic, neutrophilic and slightly halophilic metabolism. The phylogenetic analyses revealed that strain M10.9XT was closely related to Sagittula stellata E-37T and Sagittula marina F028-2T. The genomic G+C content of strain M10.9XT was 65.2 mol%. The average nucleotide identity and digital DNA-DNA hybridization values were 76.6 and 20.9 %, respectively, confirming its adscription to a new species within the genus Sagittula. The major cellular fatty acids were C18 : 1 ω7c/C18 : 1 ω6c and C16 : 0. The polar lipids consisted of phosphatidylglycerol, phosphatidylethanolamine, an unidentified aminolipid, an unidentified glycolipid, an unidentified phospholipid and an unidentified lipid. According to the resuts of a polyphasic study, strain M10.9XT represents a novel species of the genus Sagittula for which the name Sagittula salina sp. nov. (type strain M10.9XT=DSM 112301T=CECT 30307T) is proposed.