Soon Gyu Hong

Genome Sequence of Janthinobacterium sp. Strain PAMC 25724, Isolated from Alpine Glacier Cryoconite

The draft genome of Janthinobacterium sp. strain PAMC 25724, which is a violacein-producing psychrotolerant bacterium, was determined. The strain was isolated from glacier cryoconite of the Alps mountain permafrost region. The sequence will allow identification and characterization of the genetic determination of its cold-adaptive properties.

Algal and Fungal Diversity in Antarctic Lichens

The composition of lichen ecosystems except mycobiont and photobiont has not been evaluated intensively. In addition, recent studies to identify algal genotypes have raised questions about the specific relationship between mycobiont and photobiont. In the current study, we analyzed algal and fungal community structures in lichen species from King George Island, Antarctica, by pyrosequencing of eukaryotic large subunit (LSU) and algal internal transcribed spacer (ITS) domains of the nuclear rRNA gene. The sequencing results of LSU and ITS regions indicated that each lichen thallus contained diverse algal species. The major algal operational taxonomic unit (OTU) defined at a 99% similarity cutoff of LSU sequences accounted for 78.7–100% of the total algal community in each sample. In several cases, the major OTUs defined by LSU sequences were represented by two closely related OTUs defined by 98% sequence similarity of ITS domain. The results of LSU sequences indicated that lichen‐associated fungi belonged to the Arthoniomycetes, Eurotiomycetes, Lecanoromycetes, Leotiomycetes, and Sordariomycetes of the Ascomycota, and Tremellomycetes and Cystobasidiomycetes of the Basidiomycota. The composition of major photobiont species and lichen‐associated fungal community were mostly related to the mycobiont species. The contribution of growth forms or substrates on composition of photobiont and lichen‐associated fungi was not evident.

Genome Sequence of a Novel Member of the Genus Psychrobacter Isolated from Antarctic Soil

Psychrobacter spp. have shown characteristics indicating remarkable capabilities at subzero temperatures that identify them as potential model organisms for the study of low-temperature adaptations. Here we present the draft genome sequence of Psychrobacter sp. PAMC 21119, which was isolated from permafrost soil of Antarctica; this information could provide insight into adaptation and evolution strategies under extreme environmental conditions.

Psorophorus and Xanthopsoroma , two new genera for yellow-green, corticolous and squamulose lichen species, previously in Psoroma

Psoroma microlepideum is reduced to a synonym of P. fuegiense . The species differs in several characters from P. pholidotum , and it overlaps geographically with the latter, which is neotypified here. These two species are now placed in the new southern South American genus Psorophorus , differing from Psoroma s. str. in being corticolous, having adpressed squamules on a distinct, dark prothallus, lacking melanins, having a thin cortical layer and a simpler IKI+ apical ascus structure. Two other widespread, panaustral species are the only ones in Pannariacae containing usnic acid. The primarily fertile species has been known as Psoroma pholidotoides , but the type contains pannarin rather than usnic acid, and the correct name for the primarily fertile taxon with usnic acid is Psoroma contextum Stirt. This is together with P. soccatum R. Br. ex Crombie is now placed in the new genus Xanthopsoroma . In addition to usnic acid, both species have a series of distinct terpenoids, some in major quantities. Like Psorophorus , they are corticolous, but have long, more or less nodulose, apical perispore extensions, and an IKI+ apical ascus tube structure which is longer and thinner, including a diffuse tholus reaction, and often an external apical sheet. Phylogenetically, these two genera are shown to be monophyletic and different from Psoroma s. str. based on an analysis of ITS and nrLSU rDNA. This analysis also shows that among the ten species focused on in this study, nine species (two in Xanthopsoroma , two in Psorophorus and five in Psoroma s. str.) are monophyletic, based on two to six sequences of each species. Psoroma hypnorum remains polyphyletic. All names now belonging in Psorophorus and Xanthopsoroma are typified.

Differential degradation of bicyclics with aromatic and alicyclic rings by Rhodococcus sp. strain DK17

ABSTRACT The metabolically versatile Rhodococcus sp. strain DK17 is able to grow on tetralin and indan but cannot use their respective desaturated counterparts, 1,2-dihydronaphthalene and indene, as sole carbon and energy sources. Metabolite analyses by gas chromatography-mass spectrometry and nuclear magnetic resonance spectrometry clearly show that (i) the meta-cleavage dioxygenase mutant strain DK180 accumulates 5,6,7,8-tetrahydro-1,2-naphthalene diol, 1,2-indene diol, and 3,4-dihydro-naphthalene-1,2-diol from tetralin, indene, and 1,2-dihydronaphthalene, respectively, and (ii) when expressed in Escherichia coli, the DK17 o-xylene dioxygenase transforms tetralin, indene, and 1,2-dihydronaphthalene into tetralin cis-dihydrodiol, indan-1,2-diol, and cis-1,2-dihydroxy-1,2,3,4-tetrahydronaphthalene, respectively. Tetralin, which is activated by aromatic hydroxylation, is degraded successfully via the ring cleavage pathway to support growth of DK17. Indene and 1,2-dihydronaphthalene do not serve as growth substrates because DK17 hydroxylates them on the alicyclic ring and further metabolism results in a dead-end metabolite. This study reveals that aromatic hydroxylation is a prerequisite for proper degradation of bicyclics with aromatic and alicyclic rings by DK17 and confirms the unique ability of the DK17 o-xylene dioxygenase to perform distinct regioselective hydroxylations.

Gibbosporina, a new genus for foliose and tripartite, Palaeotropic Pannariaceae species previously assigned to Psoroma

Reports of ‘ Psoroma sphinctrinum ’ from Palaeotropical areas are shown to represent instead species of the genus Gibbosporina, which is described here as new to science. This genus is superficially similar to tripartite, austral Pannaria species, such as the species now referred to as Pannaria sphinctrina (Mont.) Tuck. ex Hue. A phylogram based on an analysis of the nuclear large subunit rDNA (LSU) locus shows that Gibbosporina is instead a clade in a Pannariaceae branch referred to as the ‘ Physma group’, a most unexpected addition to Pannariaceae dealt with by several previous studies. Genera assigned to this group have very contrasting general appearances. However, this diverse group shares distinctly ring-like thalline excipular margins; strongly amyloid internal ascus structures; well-developed perispores which have irregular gibbae and/or nodulose or acuminate apical extensions, but not verrucae; lacks TLC-detectable secondary compounds and have tropical distributions. Gibbosporina is the only tripartite genus in the group, with distinct, nodulose, placodioid, mini-fruticose to mini-foliose cephalodia with a high diversity of Nostoc cyanobionts. The cyanomorphs can apparently exist independently in some cases, although the apothecia on such cephalodia on a specimen from Reunion were unexpectedly found to belong to the chloromorph. The genus and related genera forming the ‘ Physma group’ are probably evolutionarily old, and their weak affinity to the remaining part of Pannariaceae , concentrated in the Southern Hemisphere, is discussed. The genus includes 13 known species, and the generitype is Gibbosporina boninensis from the Japanese Ogasawara Islands, originally described as Psoroma boninense and recombined here. The following 12 species are described here as new to science, seven of them with molecular support in an LSU and ITS-based phylogram: Gibbosporina acuminata (Australia, the Philippines), G. amphorella (New Caledonia), G. bifrons (Malaysia, New Caledonia, the Philippines, Solomon Islands), G. didyma (Mauritius, Reunion), G. elixii (Australia), G. leptospora (Australia, Papua New Guinea), G. nitida (Australia, Papua New Guinea, the Philippines), G. mascarena (Mauritius, Reunion, Sri Lanka), G. papillospora (the Philippines), G. phyllidiata (Solomon Islands), G. sphaerospora (Australia, Indonesia, Malaysia, the Philippines, Samoa, and with Psoroma sphinctrinum var. endoxanthellum as a new synonym), and G. thamnophora (Australia and the Philippines). Except for the phyllidiate G. phyllidiata and for G. thamnophora which has cephalodia adapted for vegetative propagation, the species are all primarily fertile. A key for determining the species is provided.

Anthranilate degradation by a cold-adapted Pseudomonas sp.

An alpine soil bacterium Pseudomonas sp. strain PAMC 25931 was characterized as eurypsychrophilic (both psychrophilic and mesotolerant) with a broad temperature range of 5–30 °C both for anthranilate (2‐aminobenzoate) degradation and concomitant cell growth. Two degradative gene clusters (antABC and catBCA) were detected from a fosmid clone in the PAMC 25931 genomic library; each cluster was confirmed to be specifically induced by anthranilate. When expressed in Escherichia coli, the recombinant AntABC (anthranilate 1,2‐dioxygenase, AntDO) converted anthranilate into catechol, exhibiting strict specificity toward anthranilate. Recombinant CatA (catechol 1,2‐dioxygenase, C12O) from the organism was active over a broad temperature range (5–37 °C). However, CatA rapidly lost the enzyme activity when incubated at above 25 °C. For example, 1 h‐preincubation at 37 °C resulted in 100% loss of enzyme activity, while a counterpart from mesophilic Pseudomonas putida mt‐2 did not show any negative effect on the initial enzyme activity. These results suggest that CatA is a new cold‐adapted thermolabile enzyme, which might be a product through the adaptation process of PAMC 25931 to naturally cold environments and contribute to its ability to grow on anthranilate there.

Niche specialization of bacteria in permanently ice-covered lakes of the McMurdo Dry Valleys, Antarctica

Summary Perennially ice‐covered lakes in the McMurdo Dry Valleys, Antarctica, are chemically stratified with depth and have distinct biological gradients. Despite long‐term research on these unique environments, data on the structure of the microbial communities in the water columns of these lakes are scarce. Here, we examined bacterial diversity in five ice‐covered Antarctic lakes by 16S rRNA gene‐based pyrosequencing. Distinct communities were present in each lake, reflecting the unique biogeochemical characteristics of these environments. Further, certain bacterial lineages were confined exclusively to specific depths within each lake. For example, candidate division WM88 occurred solely at a depth of 15 m in Lake Fryxell, whereas unknown lineages of Chlorobi were found only at a depth of 18 m in Lake Miers, and two distinct classes of Firmicutes inhabited East and West Lobe Bonney at depths of 30 m. Redundancy analysis revealed that community variation of bacterioplankton could be explained by the distinct conditions of each lake and depth; in particular, assemblages from layers beneath the chemocline had biogeochemical associations that differed from those in the upper layers. These patterns of community composition may represent bacterial adaptations to the extreme and unique biogeochemical gradients of ice‐covered lakes in the McMurdo Dry Valleys.

Identification of reference genes for RT-qPCR in the Antarctic moss Sanionia uncinata under abiotic stress conditions

Sanionia uncinata is a dominant moss species in the maritime Antarctic. Due to its high adaptability to harsh environments, this extremophile plant has been considered a good target for studying the molecular adaptation mechanisms of plants to a variety of environmental stresses. Despite the importance of S. uncinata as a representative Antarctic plant species for the identification and characterization of genes associated with abiotic stress tolerance, suitable reference genes, which are critical for RT-qPCR analyses, have not yet been identified. In this report, 11 traditionally used and 6 novel candidate reference genes were selected from transcriptome data of S. uncinata and the expression stability of these genes was evaluated under various abiotic stress conditions using three statistical algorithms; geNorm, NormFinder, and BestKeeper. The stability ranking analysis selected the best reference genes depending on the stress conditions. Among the 17 candidates, the most stable references were POB1 and UFD2 for cold stress, POB1 and AKB for drought treatment, and UFD2 and AKB for the field samples from a different water contents in Antarctica. Overall, novel genes POB1 and AKB were the most reliable references across all samples, irrespective of experimental conditions. In addition, 6 novel candidate genes including AKB, POB1 and UFD2, were more stable than the housekeeping genes traditionally used for internal controls, indicating that transcriptome data can be useful for identifying novel robust normalizers. The reference genes validated in this study will be useful for improving the accuracy of RT-qPCR analysis for gene expression studies of S. uncinata in Antarctica and for further functional genomic analysis of bryophytes.