Niveitalea solisilvae gen. nov., sp. nov., isolated from forest soil and emended description of the genus Flavihumibacter Zhang et al. 2010.

A Gram-stain-negative and strictly aerobic bacterial strain, designated 6-4T, was isolated from forest soil in Jeju island, South Korea. Cells showing oxidase-positive and catalase-negative reactions were thin and long non-motile rods. Growth of strain 6-4T was observed at 20-35 °C (optimum, 30 °C) and pH 6.0-9.0 (optimum, pH 7.0). Strain 6-4T contained iso-C15 : 0, anteiso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH as the major fatty acids and menaquinone-7 (MK-7) as the sole isoprenoid quinone. Phosphatidylethanolamine was the major polar lipid and five unidentified aminolipids, one unidentified aminophospholipid and one unidentified lipid were also detected as minor polar lipids. The G+C content of the genomic DNA was 45.8 mol%. Strain 6-4T was most closely related to Flavihumibacter solisilvae 3-3T with a low 16S rRNA gene sequence similarity (94.2 %) and phylogenetic analysis indicated that the strain formed a distinct phylogenetic lineage from members of the genus Flavihumibacter and other closely related genera. On the basis of phylogenetic inference and phenotypic, chemotaxonomic and molecular properties, strain 6-4T represents a novel species of a new genus of the family Chitinophagaceae, for which the name Niveitalea solisilvae gen. nov., sp. nov. is proposed. The type strain of Niveitalea solisilvae is 6-4T (=KACC 18808T=JCM 31525T). An emended description of the genus Flavihumibacter is also proposed.

The Ectocarpus genome and the independent evolution of multicellularity in brown algae.

Brown algae (Phaeophyceae) are complex photosynthetic organisms with a very different evolutionary history to green plants, to which they are only distantly related. These seaweeds are the dominant species in rocky coastal ecosystems and they exhibit many interesting adaptations to these, often harsh, environments. Brown algae are also one of only a small number of eukaryotic lineages that have evolved complex multicellularity (Fig. 1). We report the 214 million base pair (Mbp) genome sequence of the filamentous seaweed Ectocarpus siliculosus (Dillwyn) Lyngbye, a model organism for brown algae, closely related to the kelps (Fig. 1). Genome features such as the presence of an extended set of light-harvesting and pigment biosynthesis genes and new metabolic processes such as halide metabolism help explain the ability of this organism to cope with the highly variable tidal environment. The evolution of multicellularity in this lineage is correlated with the presence of a rich array of signal transduction genes. Of particular interest is the presence of a family of receptor kinases, as the independent evolution of related molecules has been linked with the emergence of multicellularity in both the animal and green plant lineages. The Ectocarpus genome sequence represents an important step towards developing this organism as a model species, providing the possibility to combine genomic and genetic approaches to explore these and other aspects of brown algal biology further.

A sequence-tagged genetic map for the brown alga Ectocarpus siliculosus provides large-scale assembly of the genome sequence.

• Ectocarpus siliculosus has been proposed as a genetic and genomic model for the brown algae and the 214 Mbp genome of this organism has been sequenced. The aim of this project was to obtain a chromosome-scale view of the genome by constructing a genetic map using microsatellite markers that were designed based on the sequence supercontigs. • To map genetic markers, a segregating F(2) population was generated from a cross between the sequenced strain (Ec 32) and a compatible strain from northern Chile. Amplified fragment length polymorphism (AFLP) analysis indicated a significant degree of polymorphism (41%) between the genomes of these two parental strains. Of 1,152 microsatellite markers that were selected for analysis based on their location on long supercontigs, their potential as markers and their predicted ability to amplify a single genomic locus, 407 were found to be polymorphic. • A genetic map was constructed using 406 markers, resulting in 34 linkage groups. The 406 markers anchor 325 of the longest supercontigs on to the map, representing 70.1% of the genome sequence. • The Ectocarpus genetic map described here not only provides a large-scale assembly of the genome sequence, but also represents an important tool for future genetic analysis using this organism.

Interactions between marine facultative epiphyte Chlamydomonas sp. (Chlamydomonadales, Chlorophyta) and ceramiaceaen algae (Rhodophyta).

Previously unrecorded marine Chlamydomonas that grew epiphytic on ceramiaceaen algae was collected from the western coast of Korea and isolated into a unialgal culture. The isolate was subjected to 18S rDNA phylogenetic analysis as well as ultrastructure and life cycle studies. It had an affinity with the marine Chlamydomonas species and was less related to freshwater/terrestrial representatives of this genus. It had flagella shorter than the cell body two-layered cell wall with striated outer surface and abundant mucilaginous material beneath the innermost layer and no contractile vacuoles. This alga grew faster in mixed cultures with ceramiaceaen algae rather than in any tested unialgal culture condition; the cells looked healthier and zoosporangia and motile flagellated vegetative cells appeared more often. These results suggested that this Chlamydomonas might be a facultative epiphyte benefiting from its hosts. Several ceramiaceaen algae were tested as host plants. Meanwhile, cell deformation or collapse of the whole thallus was caused to Aglaothamnion byssoides, and preliminary study suggested that a substance released from Chlamydomonas caused the response. This is first report on harmful epiphytic interactions between Chlamydomonas species and red ceramiaceaen algae.

Acetobacter oryzifermentans sp. nov., isolated from Korean traditional vinegar and reclassification of the type strains of Acetobacter pasteurianus subsp. ascendens (Henneberg 1898) and Acetobacter pasteurianus subsp. paradoxus (Frateur 1950) as Acetobacter ascendens sp. nov., comb. nov.

Twelve Acetobacter pasteurianus-related strains with publicly available genomes in GenBank shared high 16S rRNA gene sequence similarity (>99.59%), but average nucleotide identity (ANI) and in silico DNA-DNA hybridization (DDH) values and multilocus sequence- and genome-based relatedness analyses suggested that they were divided into four different phylogenetic lineages. Relatedness analyses based on multilocus sequences, 1,194 core genes and whole-cell MALDI-TOF profiles supported that strains LMG 1590T and LMG 1591 (previously classified as the type strains of A. pasteurianus subsp. ascendens and paradoxus, respectively) and strain SLV-7T do not belong to A. pasteurianus. Strain SLV-7T, isolated from Korean traditional vinegar, shared low ANI (<91.0%) and in silico DDH (44.2%) values with all other Acetobacter type strains analyzed in this study, indicating that strain SLV-7T represents a new Acetobacter species. The phenotypic and chemotaxonomic analyses confirmed these results and therefore a new species named Acetobacter oryzifermentans sp. nov. is proposed with SLV-7T (=KACC 19301T=JCM 31096T) as the type strain. Strains LMG 1590T and LMG 1591 shared high ANI (99.4%) and in silico DDH (96.0%) values between them, but shared low ANI (<92.3%) and in silico DDH (<49.0%) values with other type strains analyzed in this study, indicating that strains LMG 1590T and LMG 1591 should be reclassified into a new single species that should be named Acetobacter ascendens sp. nov., comb. nov., with LMD 51.1T (=LMG 1590T=NCCB 51001T) as its type strain.

Plastid and mitochondrial genomes of Coccophora langsdorfii (Fucales, Phaeophyceae) and the utility of molecular markers.

Coccophora langsdorfii (Turner) Greville (Fucales) is an intertidal brown alga that is endemic to Northeast Asia and increasingly endangered by habitat loss and climate change. We sequenced the complete circular plastid and mitochondrial genomes of C. langsdorfii. The circular plastid genome is 124,450 bp and contains 139 protein-coding, 28 tRNA and 6 rRNA genes. The circular mitochondrial genome is 35,660 bp and contains 38 protein-coding, 25 tRNA and 3 rRNA genes. The structure and gene content of the C. langsdorfii plastid genome is similar to those of other species in the Fucales. The plastid genomes of brown algae in other orders share similar gene content but exhibit large structural recombination. The large in-frame insert in the cox2 gene in the mitochondrial genome of C. langsdorfii is typical of other brown algae. We explored the effect of this insertion on the structure and function of the cox2 protein. We estimated the usefulness of 135 plastid genes and 35 mitochondrial genes for developing molecular markers. This study shows that 29 organellar genes will prove efficient for resolving brown algal phylogeny. In addition, we propose a new molecular marker suitable for the study of intraspecific genetic diversity that should be tested in a large survey of populations of C. langsdorfii.

Diversity and enzyme activity of Penicillium species associated with macroalgae in Jeju Island.

A total of 28 strains of 19 Penicillium species were isolated in a survey of extracellular enzyme-producing fungi from macroalgae along the coast of Jeju Island of Korea. Penicillium species were identified based on morphological and ß-tubulin sequence analyses. In addition, the halo-tolerance and enzyme activity of all strains were evaluated. The diversity of Penicillium strains isolated from brown algae was higher than the diversity of strains isolated from green and red algae. The commonly isolated species were Penicillium antarcticum, P. bialowiezense, P. brevicompactum, P. crustosum, P. oxalicum, P. rubens, P. sumatrense, and P. terrigenum. While many strains showed endoglucanase, ß-glucosidase, and protease activity, no alginase activity was detected. There was a positive correlation between halo-tolerance and endoglucanase activity within Penicillium species. Among 19 Penicillium species, three species-P. kongii, P. olsonii, and P. viticola-have not been previously recorded in Korea.