Lutimonas zeaxanthinifaciens sp. nov., a zeaxanthin-producing marine bacterium isolated from coastal sediment

A Gram-stain-negative, yellow-pigmented, strictly aerobic, non-flagellated, motile by gliding, rod-shaped bacterium, designated strain YSD2104T, was isolated from a coastal sediment sample collected from the southeastern part of the Yellow Sea. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain YSD2104T was closely related to three type strains, Lutimonas vermicola IMCC1616T (97.4 %), Lutimonas saemankumensis SMK-142T (96.9 %), and Lutimonas halocynthiae RSS3-C1T (96.8 %). Strain YSD2104T has a single circular chromosome of 3.54 Mbp with a DNA G+C content of 38.3 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strain YSD2104T and the three type strains (L. vermicola IMCC1616 T, L. saemankumensis SMK-142T, and L. halocynthiae RSS3-C1T) were 74.0, 86.2 and 73.6 %, and 17.9, 30.3 and 17.8 %, respectively. Growth was observed at 20-30 °C (optimum, 30 °C), at pH 6.5-8.5 (optimum, pH 7.0), and with NaCl concentrations of 1.5-3.5 % (optimum, 2.5 %). The major carotenoid was zeaxanthin, and flexirubin-type pigment was not produced. The major respiratory quinone was menaquinone-6. The major fatty acids (>10 %) were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH, summed feature 3 (C16 : 1  ω6c and/or C16 : 1  ω7c), and summed feature 9 (iso-C17 : 1  ω9c and/or 10-methyl C16 : 0). The major polar lipids were phosphatidylethanolamine, one unidentified aminophospholipid, two unidentified aminolipids, and eight unidentified lipids. Conclusively, based on this polyphasic approach, we classified strain YSD2104T (=KCTC 102008T=JCM 36287T) as representing a novel species of the genus Lutimonas and proposed the name Lutimonas zeaxanthinifaciens sp. nov.

Evidence for phylogenetically and catabolically diverse active diazotrophs in deep-sea sediment

Diazotrophic microorganisms regulate marine productivity by alleviating nitrogen limitation. However, we know little about the identity and activity of diazotrophs in deep-sea sediments, a habitat covering nearly two-thirds of the planet. Here, we identify candidate diazotrophs from Pacific Ocean sediments collected at 2893 m water depth using ¹⁵N-DNA stable isotope probing and a novel pipeline for nifH sequence analysis. Together, these approaches detect an unexpectedly diverse assemblage of active diazotrophs, including members of the Acidobacteria, Firmicutes, Nitrospirae, Gammaproteobacteria, and Deltaproteobacteria. Deltaproteobacteria, predominately members of the Desulfobacterales and Desulfuromonadales, are the most abundant diazotrophs detected, and display the most microdiversity of associated nifH sequences. Some of the detected lineages, including those within the Acidobacteria, have not previously been shown to fix nitrogen. The diazotrophs appear catabolically diverse, with the potential for using oxygen, nitrogen, iron, sulfur, and carbon as terminal electron acceptors. Therefore, benthic diazotrophy may persist throughout a range of geochemical conditions and provide a stable source of fixed nitrogen over geologic timescales. Our results suggest that nitrogen-fixing communities in deep-sea sediments are phylogenetically and catabolically diverse, and open a new line of inquiry into the ecology and biogeochemical impacts of deep-sea microorganisms.

Microbial diversity of an Antarctic subglacial community and high-resolution replicate sampling inform hydrological connectivity in a polar desert

Antarctic subglacial environments host microbial ecosystems and are proving to be geochemically and biologically diverse. The Taylor Glacier, Antarctica, periodically expels iron-rich brine through a conduit sourced from a deep subglacial aquifer, creating a dramatic red surface feature known as Blood Falls. We used Illumina MiSeq sequencing to describe the core microbiome of this subglacial brine and identified previously undetected but abundant groups including the candidate bacterial phylum Atribacteria and archaeal phylum Pacearchaeota. Our work represents the first microbial characterization of samples collected from within a glacier using a melt probe, and the only Antarctic subglacial aquatic environment that, to date, has been sampled twice. A comparative analysis showed the brine community to be stable at the operational taxonomic unit level of 99% identity over a decade. Higher resolution sequencing enabled deconvolution of the microbiome of subglacial brine from mixtures of materials collected at the glacier surface. Diversity patterns between this brine and samples from the surrounding landscape provide insight into the hydrological connectivity of subglacial fluids to the surface polar desert environment. Understanding subice brines collected on the surfaces of thick ice covers has implications for analyses of expelled materials that may be sampled on icy extraterrestrial worlds.

Aestuariivivens insulae gen. nov., sp. nov., isolated from a tidal flat

A Gram-stain-negative, non-motile, aerobic, ovoid or rod-shaped bacterium, designated AH-MY3T, was isolated from a tidal flat on Aphae island of the south-western sea, South Korea, and subjected to a polyphasic taxonomic study. Strain AH-MY3T grew optimally at 35 °C, at pH 7.0–8.0 and in the presence of 2.0–3.0  % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain AH-MY3T joined the cluster comprising the type strains of Yeosuana aromativorans, Snuella lapsa and Meridianimaribacter flavus, showing sequence similarities of 93.9, 93.7 and 92.6  %, respectively. Strain AH-MY3T exhibited 16S rRNA gene sequence similarity values of 94.0–94.7  % to the type strains of ‘Aestuariibaculum scopimerae’, Winogradskyella aquimaris, Winogradskyella poriferorum and Gaetbulibacter aestuarii. Strain AH-MY3T contained MK-6 as the predominant menaquinone. The fatty acid and polar lipid profiles of strain AH-MY3T could be distinguished from those of the type strains of phylogenetically related taxa. The DNA G+C content of strain AH-MY3T was 37 mol%. The phylogenetic data and differential chemotaxonomic and other phenotypic properties revealed that strain AH-MY3T represents a novel genus and species within the family Flavobacteriaceae, for which the name Aestuariivivens insulae gen. nov., sp. nov. is proposed. The type strain of Aestuariivivens insulae is AH-MY3T ( = KCTC 42350T = NBRC 110723T).

Loktanella variabilis sp. nov., isolated from a tidal flat

Two Gram-negative, aerobic and rod-shaped or ovoid bacterial strains with different colony colours (greyish yellow and moderate orange), designated J-MR2-YT and J-MR2-O, were isolated from a tidal flat in the South Sea of South Korea. The two novel strains grew optimally at 35–37 °C. Strains J-MR2-YT and J-MR2-O showed no difference in their 16S rRNA gene sequences, and the mean DNA–DNA relatedness between them was 94 %. Phylogenetic trees based on 16S rRNA gene sequences revealed that strains J-MR2-YT and J-MR2-O clustered consistently with the type strains of Loktanella soesokkakensis , L. hongkongensis and L. cinnabarina , with which it exhibited 97.83–99.06 % sequence similarity. Sequence similarities to the type strains of the other recognized species of the genus Loktanella were 94.01–96.26 %. Both strains contained Q-10 as the predominant ubiquinone, C18 : 1ω7c as the major fatty acid and phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified glycolipid and one unidentified aminolipid as the major polar lipids. The DNA G+C contents of strains J-MR2-YT and J-MR2-O were 68.1 and 68.4 mol%, respectively, and DNA–DNA relatedness values with the type strains of L. soesokkakensis , L. hongkongensis and L. cinnabarina were 19–37 %. Differential phenotypic properties, together with their phylogenetic and genetic distinctiveness, revealed that the two novel strains are separated from other species of the genus Loktanella . On the basis of the data presented, strains J-MR2-YT and J-MR2-O are proposed to represent a novel species of the genus Loktanella , for which the name Loktanella variabilis sp. nov. is proposed. The type strain is J-MR2-YT ( = KCTC 42074T = CECT 8572T).

Description of Lutimonas halocynthiae sp. nov., isolated from a golden sea squirt (Halocynthia aurantium), reclassification of Aestuariicola saemankumensis as Lutimonas saemankumensis comb. nov. and emended description of the genus Lutimonas

A Gram-stain-negative, non-motile, coccoid, ovoid or rod-shaped bacterial strain, designated RSS3-C1T, was isolated from a golden sea squirt (Halocynthia aurantium) collected from the East Sea, South Korea. Strain RSS3-C1T was found to grow optimally at 20–25 °C, at pH 7.0–8.0 and in the presence of 2.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain RSS3-C1T clustered with the type strains of Lutimonas vermicola and Aestuariicola saemankumensis . Strain RSS3-C1T exhibited 98.8 % 16S rRNA gene sequence similarity to each type strain. Strain RSS3-C1T contained MK-6 as the predominant menaquinone and iso-C15 : 0, iso-C17 : 0 3-OH and anteiso-C15 : 0 as the major fatty acids. The major polar lipids of strain RSS3-C1T were phosphatidylethanolamine and two unidentified lipids. The DNA G+C content of strain RSS3-C1T was 39.2 mol%, and DNA–DNA relatedness to the type strains of and was 21±5.3 and 26±7.5 %, respectively. The differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain RSS3-C1T is separated from and . On the basis of the data presented, strain RSS3-C1T is considered to represent a novel species of the genus Lutimonas , for which the name Lutimonas halocynthiae sp. nov. is proposed. The type strain is RSS3-C1T ( = KCTC 32537T = CECT 8444T). In this study, it is also proposed that Aestuariicola saemankumensis should be reclassified as a member of the genus Lutimonas , as Lutimonas saemankumensis comb. nov. (type strain SMK-142T = KCTC 22171T = CCUG 55329T), and the description of the genus Lutimonas is emended.

Seonamhaeicola aphaedonensis gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from a tidal flat sediment

A Gram-stain-negative, non-motile, rod-shaped bacterial strain, AH-M5T, which was isolated from a tidal flat sediment at Aphae Island in South Korea, was characterized taxonomically. Strain AH-M5T grew optimally at 25 °C, at pH 7.0–8.0 and in presence of 2.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain AH-M5T clustered coherently with the type strains of Mangrovimonas yunxiaonensis and Meridianimaribacter flavus , showing 93.4–94.3 % sequence similarity. The novel strain exhibited 16S rRNA gene sequence similarity values of less than 93.4 % to the type strains of other recognized species. Strain AH-M5T contained MK-6 as the predominant menaquinone and iso-C15 : 1 G, iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) as the major fatty acids. The polar lipid profile of strain AH-M5T containing phosphatidylethanolamine and one unidentified lipid as major components was differentiated from those of the type strains of Mangrovimonas yunxiaonensis and Meridianimaribacter flavus . The DNA G+C content of strain AH-M5T was 34.8 mol%. Differential phenotypic properties, together with the phylogenetic and chemotaxonomic data, demonstrated that strain AH-M5T is distinguished from Mangrovimonas yunxiaonensis and Meridianimaribacter flavus . On the basis of the data presented, strain AH-M5T is considered to represent a novel genus and species within the family Flavobacteriaceae , for which the name Seonamhaeicola aphaedonensis gen. nov., sp. nov. is proposed. The type strain of the type species is AH-M5T ( = KCTC 32578T = CECT 8487T).

Sabulilitoribacter multivorans gen. nov., sp. nov., a polysaccharide-degrading bacterium of the family Flavobacteriaceae isolated from seashore sand

A Gram-negative, aerobic, non-flagellated, non-gliding and rod-shaped bacterial strain, designated M-M16(T), was isolated from seashore sand around a seaweed farm on the South Sea, South Korea, and its taxonomic position was investigated by using a polyphasic study. Strain M-M16(T) grew optimally at 30 °C, at pH 7.0-8.0 and in the presence of 2 % (w/v) NaCl. Strain M-M16(T) exhibited the highest 16S rRNA gene sequence similarity values to the type strains of Gaetbulibacter lutimaris (96.5 %) and Flaviramulus basaltis (95.8 %). Neighbour-joining and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences revealed that strain M-M16(T) clustered with the type strains of Gaetbulibacter species and F. basaltis. Strain M-M16(T) contained MK-6 as the predominant menaquinone and iso-C15:1 G, iso-C15:0 and iso-C17:0 3-OH as the major fatty acids. The major polar lipids detected in strain M-M16(T) were phosphatidylethanolamine and one unidentified lipid. The DNA G+C content of strain M-M16(T) was 37.4 mol%. The phylogenetic and chemotaxonomic data and other phenotypic properties revealed that strain M-M16(T) represents a novel genus and species within the family Flavobacteriaceae, for which the name Sabulilitoribacter multivorans gen. nov., sp. nov. is proposed. The type strain of S. multivorans is M-M16(T) (= KCTC 32326(T) = CCUG 63831(T)).

Sungkyunkwania multivorans gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from seawater from a seaweed farm

A Gram-staining-negative, non-flagellated, non-gliding and rod-shaped bacterial strain, designated PDB-16T, was isolated from seawater from a seaweed farm on the South Sea in Korea, and its taxonomic position was investigated using a polyphasic approach. Strain PDB-16T grew optimally at 30 °C, at pH 7.0–7.5 and in the presence of 2 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain PDB-16T formed an independent lineage within the evolutionary radiation encompassed by the family Flavobacteriaceae . Strain PDB-16T contained MK-6 as the predominant menaquinone and iso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH as the major fatty acids. The major polar lipids detected in strain PDB-16T were phosphatidylethanolamine and two unidentified lipids. The DNA G+C content of strain PDB-16T was 42.1 mol%. Strain PDB-16T exhibited very low 16S rRNA gene sequence similarities of less than 89.7 % to the type strains of any bacterial species with validly published names and less than 90.1 % to uncultured bacteria clones. The 16S rRNA gene sequence similarity values and the differences in phenotypic properties between strain PDB-16T and some phylogenetically related genera were sufficient to support the proposal that strain PDB-16T should be distinguished from previously known genera of the family Flavobacteriaceae . On the basis of the data presented, strain PDB-16T is considered to represent a new genus and novel species, for which the name Sungkyunkwania multivorans gen. nov., sp. nov. is proposed. The type strain of Sungkyunkwania multivorans is PDB-16T ( = KCTC 32138T = CCUG 62952T).

Aureivirga marina gen. nov., sp. nov., a marine bacterium isolated from the Mediterranean sponge Axinella verrucosa

Two bacterial strains, VI.14 and VIII.04T, were isolated from the Mediterranean sponge Axinella verrucosa collected off the Israeli coast near Sdot Yam. The non-motile, aerobic, Gram-negative isolates were oxidase-negative and catalase-positive, and formed golden-brown colonies on marine agar 2216. The pigment was neither diffusible nor flexirubin-like. Strain VIII.04T grew at 15–37 °C, at pH 6.0–9.0, in the presence of 20–50 g NaCl l−1 and 20–80 g sea salts l−1, The spectrum was narrower for strain VI.14, with growth at pH 7.0–8.0. and in the presence of 30–50 g NaCl l−1 and 30–70 g sea salts l−1. The predominant fatty acid (>50 %) in both strains was iso-C15 : 0, and the major respiratory quinone was MK-6. The DNA G+C content was 30.7 and 31.1 mol% for VIII.04T and VI.14, respectively. Results from 16S rRNA sequence similarity and phylogenetic analyses indicated that both strains are closely related to members of the family Flavobacteriaceae within the phylum Bacteroidetes , with as much as 91.7 % 16S rRNA sequence similarity. On the basis of data from the polyphasic analysis, we suggest that the strains represent a novel species in a new genus within the family Flavobacteriaceae , for which the name Aureivirga marina gen. nov., sp. nov. is proposed. Strain VIII.04T ( = ATCC BAA-2394T = LMG 26721T) is the type strain of Aureivirga marina.

Namhaeicola litoreus gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from seawater

A Gram-staining-negative, non-flagellated, non-gliding and pleomorphic bacterial strain, designated DPG-25T, was isolated from seawater in a seaweed farm in the South Sea in Korea and its taxonomic position was investigated by using a polyphasic approach. Strain DPG-25T grew optimally at 25 °C, at pH 7.0–7.5 and in the presence of 2 % (w/v) NaCl. Flexirubin-type pigments were not produced. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DPG-25T formed a cluster with the type strains of Actibacter sediminis , Aestuariicola saemankumensis and Lutimonas vermicola . Strain DPG-25T exhibited 16S rRNA gene sequence similarity values of 95.3, 93.1 and 93.6 % to the type strains of Actibacter sediminis , Aestuariicola saemankumensis and L. vermicola , respectively. Strain DPG-25T contained MK-6 as the predominant menaquinone and iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids. The major polar lipids detected in strain DPG-25T were phosphatidylethanolamine and one unidentified lipid. The DNA G+C content was 39.9 mol%. Differential phenotypic properties and the phylogenetic distinctiveness of strain DPG-25T demonstrated that this strain is distinguishable from Actibacter sediminis , Aestuariicola saemankumensis and L. vermicola . On the basis of the data presented here, strain DPG-25T represents a novel species in a novel genus of the family Flavobacteriaceae , for which the name Namhaeicola litoreus gen. nov., sp. nov. is proposed. The type strain of Namhaeicola litoreus is DPG-25T ( = KCTC 23702T  = CCUG 61485T).

Marinobacterium lutimaris sp. nov., isolated from a tidal flat

A Gram-staining-negative, moderately halophilic bacterium, designated strain AN9T, was isolated from a tidal flat of the Taean coast in South Korea. Cells were catalase- and oxidase-positive short rods that were motile by means of a single polar flagellum. Growth of strain AN9T was observed at 15–40 °C (optimum, 25–30 °C) and at pH 6.0–8.0 (optimum, pH 6.5–7.5). Strain AN9T contained ubiquinone Q-8 as the predominant isoprenoid quinone and C10 : 0 3-OH (31.7 %), C18 : 1 ω7c (24.8 %), C16 : 0 (14.7 %) and summed feature 3 (comprising C16 : 1 ω7c and/or iso-C15 : 0 2-OH, 10.72 %) as the major fatty acids. The G+C content of the genomic DNA of strain AN9T was 58 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain AN9T was related to members of the genus Marinobacterium and was related most closely to Marinobacterium litorale IMCC1877T (96.8 % similarity). On the basis of chemotaxonomic and molecular data, strain AN9T is considered to represent a novel species of the genus Marinobacterium, for which the name Marinobacterium lutimaris sp. nov. is proposed. The type strain is AN9T (=KACC 13703T =DSM 22012T).