Soon Gyu Hong

Korea Polar Research Institute | KOPRI · Division of Life Sciences

Gram-staining-negative, aerobic, white-cream-pearly colony, coccobacilli, and non-motile bacterial strain, PAMC 29798T was isolated from an Antarctic lichen. The strain was acidotolerant and psychrotolerant growing at pH 4.0–7.5 (optimally at pH 4.0–6.5) and 0–25 °C (optimally at 10–20 °C). The major fatty acids are Summed Feature 8, C18:1 2OH, and...

Mosses are vital components of ecosystems, exhibiting remarkable adaptability across diverse habitats from deserts to polar ice caps. Sanionia uncinata (Hedw.) Loeske, a dominant Antarctic moss survives extreme environmental condition through perennial lifecycles involving growth and dormancy alternation. This study explores genetic controls and mo...

Since the floristic study of lichens at the Barton and Weaver Peninsulas of King George Island in 2006, there have been intense investigations of the lichen flora of the two peninsulas as well as that of Fildes Peninsula and Ardley Island in Maxwell Bay, King George Island, South Shetland Islands, maritime Antarctic. In this study, a total of 104 s...

Gram-stain-negative, strictly aerobic, red-pink-coloured, rod-shaped and non-motile bacterial strains PAMC 29290, PAMC 29294 T and PAMC 29296 were isolated from marine surface sediment sampled in the East Siberian Sea and strains PAMC 26553 and PAMC 26554 T were obtained from an Antarctic lichen. Strains PAMC 29290, PAMC 29294 T and PAMC 29296 were...

Snow cover plays an important role in water supply through melting of snow/ice in polar ecosystem and environments, in particular, Antarctica. Although a site access to Antarctica is high-priced, measurements of ground surface temperature (GST) using small self-recording temperature sensors (iButtons) can provide a powerful and relatively inexpensi...

Heteropolymer humic substances (HS) are the largest constituents of soil organic matter and are key components that affect plant and microbial growth in maritime Antarctic tundra. We investigated HS decomposition in Antarctic tundra soils from distinct sites by incubating samples at 5°C or 8°C (within a natural soil thawing temperature range of −3....

Spectral information is a proxy for understanding the characteristics of ground targets without a potentially disruptive contact. A spectral library is a collection of this information and serves as reference data in remote sensing analyses. Although widely used, data of this type for most ground objects in polar regions are notably absent. Remote...

The diversity of lichen-associated bacteria from lichen taxa Cetraria, Cladonia, Megaspora, Pseudephebe, Psoroma, and Sphaerophorus was investigated by sequencing of 16S rRNA gene amplicons. Physiological characteristics of the cultured bacterial isolates were investigated to understand possible roles in the lichen ecosystem. Proteobacteria (with a...

Based on phylogenetic analyses of the ITS, nuclear large subunit rRNA, mitochondrial small subunit rRNA, and MCM7 genes, species previously treated as Pannaria hispidula and P. isabellina are shown to represent two new Pannariaceae genera, Hispidopannaria and Phormospsora. Each genus forms monophyletic clades, both in multilocus phylogeny and in si...

The new species Psoroma capense and P. esterhuyseniae are described from four alpine localities in the Western Cape Province of South Africa and are the only known Psoroma species from Africa. The specimens were all collected from moist sites near watercourses, on cool and mostly south-facing cliffs. Psoroma capense resembles P. tenue in gross morp...

Although groundwater is an important component of the water cycle in the polar regions, groundwater in Antarctica has rarely been studied. This study evaluated the physical and chemical characteristics of groundwater, surface water, and snow in two lakes on the Barton Peninsula, King George Island, Antarctica, with a particular focus on groundwater...

Two Gram-stain-negative, facultative anaerobic, chemoheterotrophic, pink-coloured, rod-shaped and non-motile bacterial strains, PAMC 26568 and PAMC 26569 T , were isolated from an Antarctic lichen. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains PAMC 26568 and PAMC 26569 T belong to the family Acetobacteraceae and the m...

Lichens are miniature ecosystems that contain fungi, microalgae, and bacteria. It is generally accepted that symbiosis between mycobiont and photobiont and microbial contribution to the ecosystem support the wide distribution of lichens in terrestrial ecosystems, including polar areas. The composition of symbiotic components can be affected by subt...

Floristic check-lists were compiled for the first time for Duvefjorden Bay on Nordaustlandet, Svalbard, based on field work in July 2012 and on data from literature and herbaria. The check-lists include 172 species of lichens and 51 species of vascular plants. Several species rare in Svalbard and in the Arctic were discovered: Candelariella boreali...

Proteorhodopsin (PR) is discovered from marine bacteria and it has proton pumping activity from inside to outside of the cell using light energy. In general, PR classified into two groups by the maximum absorption spectra. In this study, we isolated the two of a full sequence of opsin homologues by PCR from the seawater sample near King George Isla...

Two Gram-stain-negative, facultative anaerobic chemoheterotrophic, pink-coloured, rod-shaped and non-motile bacterial strains, PAMC 29128 and PAMC 29148T, were isolated from lichen. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strains PAMC 29128 and PAMC 29148T belong to lichen-associated Rhizobiales-1 (LAR1), an uncultu...

Barton Peninsula is an ice-free area located in the southwest corner of King George Island (South Shetland Islands, Antarctica). Following the Last Glacial Maximum, several geomorphological features developed in newly exposed ice-free terrain and their distribution provide insights about past environmental evolution of the area. Three moraine syste...

Arthrobacter oryzae TNBS02 was isolated from soil at Terra Nova Bay of Victoria Land, Antarctica. The genome consists of a chromosome with 4,248,670 bp which contains a total of 3,994 genes. It was identified that this strain has many heavy metal resistance genes similar to other Arthrobacter strains isolated from contaminated environments.

Fungal endophytes comprise one of the most ubiquitous groups of plant symbionts. They live asymptomatically within vascular plants, bryophytes and also in close association with algal photobionts inside lichen thalli. While endophytic diversity in land plants has been well studied, their diversity in lichens and bryophytes are poorly understood. He...

The harsh conditions in Victoria Land, Antarctica have formed a simple ecosystem dominated by microbes that use rocks as shelters to avoid environmental stressors. The area is composed of basement rocks that illustrate the history of complex deformation, thus it is highly valuable not only in perspectives of geology but also in biological aspects....

Candidate phylum Atribacteria JS1 lineage is one of the predominant bacterial groups in anoxic subseafloor sediments, especially in organic-rich or gas hydrate-containing sediments. However, due to the lack of axenic culture representatives, metabolic potential and biogeochemical roles of this phylum have remained elusive. Here, we examined the mic...

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 p...

Agarose gel electrophoresis showing total RNA extracted from S. uncinata under various conditions. (A) cold stress, (B) drought stress, (C) water gradients in the field. (PDF)

Verification of primer specificity for reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) amplification. (A) Agarose gel (2.0%) showing the amplified products of the 17 candidate reference genes at the expected sizes. (B) Melting curves of the 17 candidate reference genes. (PDF)

Amplification efficiencies of primers used in this study. (PDF)

The contig sequences for candidate genes. The regions for RT-qPCR amplification were highlighted in red color. (DOCX)

Expression values of the 17 candidate genes of S. uncinata from the transcriptome under cold stress. (XLSX)

Expression values of LEA and Hsp70 in S. uncinata from the transcriptome under cold stress. (XLSX)

Icefree, terrestrial, Antarctic ecosystems have a polar desert-like appearance with a scarce vegetation cover, completely dominated by bryophytes and lichens. Knowledge of the rich Antarctic lichen biodiversity, including c. 400 species, is therefore necessary, also for studies of other ecosystem components. The genus Psoroma is partly dominant the...

Although the maritime Antarctic has undergone rapid warming, the effects on indigenous soil‐inhabiting microorganisms are not well known. Passive warming experiments using open‐top chamber (OTC) have been performed on the Fildes Peninsula in the maritime Antarctic since 2008. When the soil temperature was measured at a depth of 2–5 cm during the 20...

We report here the complete genome sequence of Janthinobacterium svalbardensis PAMC 27463 isolated from a freshwater lake on Barton Peninsula on King George Island, Antarctica. The genome consists of a chromosome with 6,274,078 bp which contains 5,585 genes, including 121 RNA genes.

This study examined the genetic diversity of small-spored Alternaria species in the southwest desert of the USA by sampling 552 isolates from different habitats (soil and plant debris) in different locations (urban and an undisturbed desert). To estimate the genetic diversity, Amplified Fragment Length Polymorphism (AFLP) fingerprinting analysis wa...

Aim: To investigate the impact of glacier retreat on perennial ice-embedded microbial communities, we examined the microbial diversity from glacier ice and subglacial streams of various locations of King George Island, NW Antarctica, in two consecutive years.

Antimicrobial-producing, cold-adapted microorganisms have great potential for biotechnological applications in food, pharmaceutical, and cosmetic industries. Pseudomonas antarctica PAMC 27494, a psychrophile exhibiting antimicrobial activity, was isolated from an Antarctic freshwater sample. Here we report the complete genome of P. antarctica PAMC...

The impact of environmental geochemistry on the bacterial and fungal communities from glacier ice and subglacial streams was investigated on various locations of King George Island, NW Antarctica. Subglacial stream samples (42) and ice samples (63) from glacier transects of Barton Peninsula, Weaver Peninsula and Potter Cove areas were collected dur...

Caballeronia sordidicola strain PAMC 26577 was isolated from Cladonia sp., a lichen collected from Svalbard Archipelago in the Arctic Ocean. Draft genomic sequences of PAMC 26577 were determined using Illumina and 182 contigs were submitted to GenBank and N50 value was 159,226. The genome of PAMC 26577 was comprised of 8,334,211 base pairs and %G+C...

Caballeronia sordidicola strain PAMC 26510 was isolated from Psoroma sp., a lichen material, collected from Barton Peninsula of King George Island in Antarctica. The draft genome sequence of PAMC 26510 consisted of 224 contigs and they was 7,872,143 base pairs with 59.7% G+C content. The genome included 7,580 protein coding sequences and 6 ribosoma...

Background Chemolithoautotrophic primary production sustains dense invertebrate communities at deep-sea hydrothermal vents and hydrocarbon seeps. Symbiotic bacteria that oxidize dissolved sulfur, methane, and hydrogen gases nourish bathymodiolin mussels that thrive in these environments worldwide. The mussel symbionts are newly acquired in each gen...

Caballeronia sordidicola strain PAMC 26592 was isolated from Umbilicaria sp., a lichen material collected from Svalbard Archipelago in the Arctic Ocean. We report the draft genome sequence of the strain PAMC 26592, a metabolic generalist. As we have observed in previous genomic studies in the genus Caballeronia draft genomic sequences of PAMC 26592...

Deinococcus marmoris strain PAMC 26562 was isolated from Usnea sp., a lichen collected from King George Island, Antarctica. We report here the draft genome sequence of strain PAMC 26562, which has xanthorhodopsin and carbon monoxide dehydrogenase genes in addition to major metabolic pathways presented in deinococcal genomes.

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 i...

The new species Asterochloris sejongensis sp. nov. has been collected from four localities of King George Island, Antarctica, and is described as a phycobiont of the lichen species Cladonia pyxidata and Sphaerophorus globosus. This discovery is based on morphological and molecular data obtained using light microscopy, confocal laser microscopy, tra...

Here we report the draft genome sequence of the Caballeronia sordidicola strain PAMC 26633, isolated from Psoroma species, a lichen material from Barton Peninsula, King George Island in Antarctica. As we have observed in previous genomic studies in the genus Caballeronia from polar lichen, draft genomic sequences of PAMC 26633 had an assortment of...

Soil is an important environmental reservoir of antibiotic resistance genes (ARGs), which are increasingly recognized as environmental contaminants. Methods to assess the risks associated with the acquisition or transfer of resistance mechanisms are still underdeveloped. Quantification of background levels of antibiotic resistance genes and what al...

Cryobacterium arcticum PAMC 27867, a psychrotolerant, Gram-positive bacterium, was isolated from a sedimentary rock sample collected at Eureka Spurs in northern Victoria Land, Antarctica. Here, we report the genome sequence of C. arcticum PAMC 27867.

To date, many studies surveying the bacterial communities in lichen thalli from diverse geographical areas have shown that Alphaproteobacteria is the predominant bacterial class in most lichens. In this study, bacterial communities in several Antarctic lichens with different growth form and substrates were analysed. The bacterial community composit...

Psychrobacter alimentarius PAMC 27889, a Gram-negative, psychrophilic bacterium, was isolated from an Antarctic rock sample. Here, we report the complete genome of P. alimentarius PAMC 27889, which has the nonmevalonate methylerythritol phosphate pathway of terpenoid biosynthesis and a complete gene cluster for benzoate degradation.

Background: In this article, it was analyzed how snow melting affects the assembly of lichen and moss communities in a small area of the coastal region of Barton Peninsula, which is in maritime Antarctic. In the small area, even though there is a huge gap of difference of the environment between the snow-filled area and snow-melt one, the latter di...

Gibbosporina, a new genus for foliose and tripartite, Palaeotropic Pannariaceae species previously assigned to Psoroma – ERRATUM - Volume 48 Issue 3 - Arve ELVEBAKK, Soon Gyu HONG, Chae Haeng PARK, Eli Helene ROBERTSEN, Per Magnus JØRGENSEN

Compared to planktonic bacterial populations, biofilms have distinct bacterial community structures and play important ecological roles in various aquatic environments. Despite their ecological importance in nature, bacterial community structure and its succession during biofilm development in the Antarctic marine environment have not been elucidat...

High-throughput sequencing can produce hundreds of thousands of 16S rRNA sequence reads corresponding to different organisms present in the environmental samples. Typically, analysis of microbial diversity in bioinformatics starts from pre-processing followed by clustering 16S rRNA reads into relatively fewer operational taxonomic units (OTUs). The...

Determination of optimal granularity. Running time analysis for distributing different number of sequence pairs to 5 and 10 cluster nodes. (TIF)

XML configuration file example and description. The properties of CLUSTOM-CLOUD application are defined into “clustom.xml” file. (PDF)

The CLUSTOM-CLOUD manual. The introduction, system requirements, configuration and usage are described. (PDF)

Classification of human microbiome datasets according to microbial complexity. 16S rRNA sequence data from 18 human body sites was analyzed for richness and evenness. Sampling sites were pooled into high (rectangle), intermediate (circle), and low (triangle) complexity datasets. (TIF)

The role of aerial dispersal in shaping patterns of biodiversity remains poorly understood, mainly due to a lack of coordinated efforts in gathering data at appropriate temporal and spatial scales. It has been long known that the rate of dispersal to an ecosystem can significantly influence ecosystem dynamics, and that aerial transport has been ide...