Microbial assemblages and associated biogeochemical processes in Lake Bonney, a permanently ice-covered lake in the McMurdo Dry Valleys, Antarctica.

BACKGROUND: Lake Bonney, which is divided into a west lobe (WLB) and an east lobe (ELB), is a perennially ice-covered lake located in the McMurdo Dry Valleys of Antarctica. Despite previous reports on the microbial community dynamics of ice-covered lakes in this region, there is a paucity of information on the relationship between microbial genomic diversity and associated nutrient cycling. Here, we applied gene- and genome-centric approaches to investigate the microbial ecology and reconstruct microbial metabolic potential along the depth gradient in Lake Bonney. RESULTS: Lake Bonney is strongly chemically stratified with three distinct redox zones, yielding different microbial niches. Our genome enabled approach revealed that in the sunlit and relatively freshwater epilimnion, oxygenic photosynthetic production by the cyanobacterium Pseudanabaena and a diversity of protists and microalgae may provide new organic carbon to the environment. CO-oxidizing bacteria, such as Acidimicrobiales, Nanopelagicales, and Burkholderiaceae were also prominent in the epilimnion and their ability to oxidize carbon monoxide to carbon dioxide may serve as a supplementary energy conservation strategy. In the more saline metalimnion of ELB, an accumulation of inorganic nitrogen and phosphorus supports photosynthesis despite relatively low light levels. Conversely, in WLB the release of organic rich subglacial discharge from Taylor Glacier into WLB would be implicated in the possible high abundance of heterotrophs supported by increased potential for glycolysis, beta-oxidation, and glycoside hydrolase and may contribute to the growth of iron reducers in the dark and extremely saline hypolimnion of WLB. The suboxic and subzero temperature zones beneath the metalimnia in both lobes supported microorganisms capable of utilizing reduced nitrogens and sulfurs as electron donors. Heterotrophs, including nitrate reducing sulfur oxidizing bacteria, such as Acidimicrobiales (MAG72) and Salinisphaeraceae (MAG109), and denitrifying bacteria, such as Gracilimonas (MAG7), Acidimicrobiales (MAG72) and Salinisphaeraceae (MAG109), dominated the hypolimnion of WLB, whereas the environmental harshness of the hypolimnion of ELB was supported by the relatively low in metabolic potential, as well as the abundance of halophile Halomonas and endospore-forming Virgibacillus. CONCLUSIONS: The vertical distribution of microbially driven C, N and S cycling genes/pathways in Lake Bonney reveals the importance of geochemical gradients to microbial diversity and biogeochemical cycles with the vertical water column.

CO2 Hydrogenation on Carbides Formed in situ on Carbon-Supported Iron-Based Catalysts in High-Density Supercritical Medium.

CO2 conversion via hydrogenation on iron-based catalysts on non-carbon supports produces mainly CO or methane by the Sabatier reaction, while the formation of C2+ hydrocarbons is of greatest interest. CxHy production from CO2 may be considered as a two-step process with the initial formation of carbon monoxide by the reverse water gas shift reaction followed by the Fischer-Tropsch synthesis (FTS). In the present work CO2 hydrogenation over iron-based catalysts (Fe, FeCr, FeK) deposited on a carbon carrier has been studied. The catalyst structure has been investigated by XRD, TEM, XPS, Mössbauer spectroscopy and in situ magnetometry. Spinel-type oxide phases (magnetite Fe3O4; maggemite γ-Fe2O3, and, in the case of FeCr/C catalyst, iron chromite Fe1+xCr2-xO4) are formed on the catalysts, and they contribute exclusively to the CO production. Iron carbides, active in FTS, are formed on Fe- and FeK-catalysts during pre-activation in reducing environment and then during the reaction. The reaction over the 20Fe1K/C catalyst in supercritical high-density CO2/H2 substrate (400°C, 8.5 MPa) leads to 72% selectivity for C1-C12+ hydrocarbons (alkanes and alkenes). Under the same conditions, iron carbides do not form on the FeCr/C catalysts, and CO2 hydrogenation results in the CO formation with the selectivity of 90-100%.

Environmental Adaptation of Psychrophilic Bacteria Subtercola spp. Isolated from Various Cryospheric Habitats.

Subtercola boreus K300T is a novel psychrophilic strain that was isolated from permanently cold groundwater in Finland and has also been found in several places in Antarctica including lake, soil, and rocks. We performed genomic and transcriptomic analyses of 5 strains from Antarctica and a type strain to understand their adaptation to different environments. Interestingly, the isolates from rocks showed a low growth rate and smaller genome size than strains from the other isolation sources (lake, soil, and groundwater). Based on these habitat-dependent characteristics, the strains could be classified into two ecotypes, which showed differences in energy production, signal transduction, and transcription in the clusters of orthologous groups of proteins (COGs) functional category. In addition, expression pattern changes revealed differences in metabolic processes, including uric acid metabolism, DNA repair, major facilitator superfamily (MFS) transporters, and xylose degradation, depending on the nutritional status of their habitats. These findings provide crucial insights into the environmental adaptation of bacteria, highlighting genetic diversity and regulatory mechanisms that enable them to thrive in the cryosphere.

Glaciers as microbial habitats: current knowledge and implication.

Glaciers, formed from the gradual accumulation of snow, can be continuous records representing past environments and recognized as a time capsule of our planetary evolution. Due to extremely harsh conditions, glacial ice has long been considered an uninhabitable ecosystem for microorganisms to sustain their life. However, recent developments in microbiological analysis techniques revealed the presence of unexpectedly diverse microbial strains. Glacial microorganisms could also provide valuable information, including not only biological diversity and structure but also molecular systematics, metabolic profiles, and evolutionary changes from the past climate and ecosystem. However, there are several obstacles in investigating the glacier environment, such as low regional accessibility, technical difficulties of ice coring, potential contamination during the sampling process, and low microbial biomass. This review aims to summarize recent knowledge on decontamination methods, biomass, diversity based on culture-dependent and -independent methods, application of biological proxies, greenhouse gas production and adaptive strategies in glaciers from various regions and to imply further directions for a comprehensive understanding of habitatility in an icy world including outer of our planet.

Draft Genome Sequence of the Chitin-Degrading Psychrotolerant Bacterium Pedobacter jejuensis TN23, Isolated from Antarctic Soil.

Pedobacter jejuensis TN23 was isolated from soil from Terra Nova Bay, Victoria Land, Antarctica. The assembled draft genome size is 4,795,808 bp, and it contains a total of 4,095 genes with 3,970 coding sequences, including genes putatively involved in the degradation of chitin.

Draft Genome Sequence of the Psychrotolerant Bacterium Methylobacterium sp. Strain BTF04, Isolated from Freshwater in Antarctica.

Methylobacterium sp. strain BTF04, a pink-pigmented psychrotolerant bacterium, was isolated from freshwater on Barton Peninsula, King George Island, Antarctica. Here, we report the assembled draft genome sequence of Methylobacterium sp. strain BTF04.

Draft Genome Sequence of Arthrobacter oryzae TNBS02, a Bacterium Containing Heavy Metal Resistance Genes, Isolated from Soil of Antarctica.

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.

The latitudinal gradient in rock-inhabiting bacterial community compositions in Victoria Land, Antarctica.

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. Because this region is inhospitable to higher-level organisms and receives least external influences, it can be an ideal environment to investigate the relationship between rock-inhabiting bacterial communities and environmental factors. In such conditions, inorganics dissolved from minerals can be considered as key factors influencing rock-inhabiting bacterial communities. Thus, the present study attempted to explore rock-inhabiting bacterial communities throughout Victoria Land, to identify environmental parameters that are more influential on bacterial community compositions, and to investigate latitudinal gradients in environmental parameters and rock-inhabiting bacterial communities. The results suggested that (i) rock-inhabiting bacterial communities in Victoria Land predominately consisted of either Actinobacteria or Proteobacteria; (ii) latitudinal gradients in rock-inhabiting bacterial community compositions and some environmental parameters were observed; (iii) latitude, pH, nitrate, and sulfate significantly correlated with the dominant phyla; and (iv) the Classification and Regression Tree (CART) analysis demonstrated that latitude, pH, and sulfate concentrations could explain the dominant phylum with 89% accuracy. These findings can provide important insight into the link between environmental factors and rock-inhabiting bacterial community compositions in conditions with extremely cold temperatures and high levels of radiation, which could also be of interest in astrobiology.

Erratum: Socio-demographic factors and diet-related characteristics of community-dwelling elderly individuals with dysphagia risk in South Korea.

[This corrects the article on p. 406 in vol. 12, PMID: 30323908.].

Socio-demographic factors and diet-related characteristics of community-dwelling elderly individuals with dysphagia risk in South Korea.

BACKGROUND/OBJECTIVES: The objective of this study was to determine dysphagia risk among community-dwelling elderly people living at home. We also examined the impact of socio-demographic variables on dysphagia risk as well as the relationship between dysphagia risk and dietary characteristics. SUBJECTS/METHODS: The study sample included 568 community-dwelling individuals, aged 65 years and above, who were living independently in their own home in Seoul, Gyeonggi, or Gwangju in South Korea. We used a dysphagia risk assessment scale to screen for dysphagia risk and the Mini nutritional assessment to evaluate the nutritional status. Associations between dysphagia risk and other variables were assessed using logistic regression analysis. RESULTS: Of the 568 subjects, 350 (61.6%) were classified into the dysphagia risk group (DR) and 218 (38.4%) were classified into the normal group (non-DR). Being female (odds ratio (OR) = 1.82, 95% confidence interval (CI) = 1.28-2.59), being 75 years and older (OR = 2.40, 95% CI = 1.69-3.42), having a lower education level (OR = 2.29, 95% CI = 1.33-3.97), and having a lower perceived economic status (OR = 2.18, 95% CI = 1.32-3.60) were more frequently observed with dysphagia risk compared to those who did not have such characteristics. Lowered mastication ability (OR = 14.40, 95% CI = 4.43-46.95), being at risk of malnutrition or malnourished (OR = 2.72, 95% CI = 1.75-4.23), lowered appetite (OR = 3.27, 95% CI = 2.16-4.93), and decreased food intake (OR = 2.95, 95% CI = 1.83-4.78) were observed more frequently in the DR group than in the non-DR group when adjusting for potential confounding factors. CONCLUSIONS: It is necessary to develop and apply integrated programs to improve the dietary habits and nutritional status of elderly individuals at risk for dysphagia, especially for women aged 75 years or older with lower educational and economic levels.

Effects of students' satisfaction with school meal programs on school happiness in South Korea.

BACKGROUND/OBJECTIVES: School meals are not just meals consumed at school, they are part of the culture, education, and life experience at school. Nevertheless, few studies have revealed the influence of school meals on students' school lives. The purpose of this study was to investigate the effect of satisfaction with the school meal program on students' school happiness. SUBJECTS/METHODS: A survey conducted in December 2015 asked 2,336 students (1,062 elementary school students, 880 middle school students, and 394 high school students) about their satisfaction with the school meal program and their school happiness. Multiple regression analyses were used to examine the relation between the students' school meal satisfaction and their happiness level. RESULTS: The average level of satisfaction with school meals of elementary school students was 4.1 out of 5 points, comparatively higher than that of middle and high school students, with a significant difference between school levels (P < 0.001). In addition, school happiness, as well as overall happiness, of elementary school students was higher than that of middle and high school students (P < 0.001). The school meal operation factor (0.232, P < 0.001) had the most influence on students' school happiness, followed by the school meal environment factor (0.219, P < 0.001) and school meal quality factor (0.136, P < 0.001). Overall satisfaction (0.097, P = 0.001) and school meal hygiene factor (0.095, P = 0.001) also had significant influences on students' school happiness. CONCLUSIONS: Students' satisfaction with the school meal program was related to their school happiness. Therefore, plans to enhance students' satisfaction with a school meal program needs to be implemented, with emphasis on placing a priority on school meal operation and school environment factors, in order to improve students' level of happiness.

[18F]FET PET is a useful tool for treatment evaluation and prognosis prediction of anti-angiogenic drug in an orthotopic glioblastoma mouse model.

O-2-18F-fluoroethyl-l-tyrosine ([18F]FET) has been widely used for glioblastomas (GBM) in clinical practice, although evaluation of its applicability in non-clinical research is still lacking. The objective of this study was to examine the value of [18F]FET for treatment evaluation and prognosis prediction of anti-angiogenic drug in an orthotopic mouse model of GBM. Human U87MG cells were implanted into nude mice and then bevacizumab, a representative anti-angiogenic drug, was administered. We monitored the effect of anti-angiogenic agents using multiple imaging modalities, including bioluminescence imaging (BLI), magnetic resonance imaging (MRI), and positron emission tomography-computed tomography (PET/CT). Among these imaging methods analyzed, only [18F]FET uptake showed a statistically significant decrease in the treatment group compared to the control group (P=0.02 and P=0.03 at 5 and 20 mg/kg, respectively). This indicates that [18F]FET PET is a sensitive method to monitor the response of GBM bearing mice to anti-angiogenic drug. Moreover, [18F]FET uptake was confirmed to be a significant parameter for predicting the prognosis of anti-angiogenic drug (P=0.041 and P=0.007, on Days 7 and 12, respectively, on Pearson's correlation; P=0.048 and P=0.030, on Days 7 and 12, respectively, on Cox regression analysis). However, results of BLI or MRI were not significantly associated with survival time. In conclusion, this study suggests that [18F]FET PET imaging is a pertinent imaging modality for sensitive monitoring and accurate prediction of treatment response to anti-angiogenic agents in an orthotopic model of GBM.

Complete Genome Sequence of a Psychrotolerant Denitrifying Bacterium, Janthinobacterium svalbardensis PAMC 27463.

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.

Complete genome sequence of Pseudomonas antarctica PAMC 27494, a bacteriocin-producing psychrophile isolated from Antarctica.

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 27494. The strain contains a gene cluster encoding microcin B which inhibits DNA regulations by targeting the DNA gyrase. PAMC 27494 may produce R-type pyocins and also contains a complete set of proteins for the biosynthesis of adenosylcobalamin and possibly induces plant growth by supplying pyrroloquinoline quionone molecules.

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

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.

Influence of Soil Characteristics and Proximity to Antarctic Research Stations on Abundance of Antibiotic Resistance Genes in Soils.

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 alters those is a first step in understanding our environmental resistome. Toward this goal, 62 samples were collected over 3 years from soils near the 30-year old Gondwana Research Station and for 4 years before and during development of the new Jang Bogo Research Station, both at Terra Nova Bay in Antarctica. These sites reflect limited and more extensive human impact, respectively. A qPCR array with 384 primer sets targeting antibiotic resistance genes and mobile genetic elements (MGEs) was used to detect and quantify these genes. A total of 73 ARGs and MGEs encompassing eight major antibiotic resistance gene categories were detected, but most at very low levels. Antarctic soil appeared to be a common reservoir for seven ARGs since they were present in most samples (42%-88%). If the seven widespread genes were removed, there was a correlation between the relative abundance of MGEs and ARGs, more typical of contaminated sites. There was a relationship between ARG content and distance from both research stations, with a significant effect at the Jang Bogo Station especially when excluding the seven widespread genes; however, the relative abundance of ARGs did not increase over the 4 year period. Silt, clay, total organic carbon, and SiO2 were the top edaphic factors that correlated with ARG abundance. Overall, this study identifies that human activity and certain soil characteristics correlate with antibiotic resistance genes in these oligotrophic Antarctic soils and provides a baseline of ARGs and MGEs for future comparisons.

Complete Genome Sequence of Cryobacterium arcticum Strain PAMC 27867, Isolated from a Sedimentary Rock Sample in Northern Victoria Land, Antarctica.

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.

Complete Genome Sequence of Psychrobacter alimentarius PAMC 27889, a Psychrophile Isolated from an Antarctic Rock Sample.

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.

Tumorigenicity Evaluation of Umbilical Cord Blood-derived Mesenchymal Stem Cells.

Mesenchymal stem cells (MSCs) have been identified in multiple types of tissue and exhibit characteristic self-renewal and multi-lineage differentiation abilities. However, the possibility of oncogenic transformation after transplantation is concerning. In this study, we investigated the tumorigenic potential of umbilical cord blood-derived MSCs (hUCB-MSCs) relative to MRC-5 and HeLa cells (negative and positive controls, respectively) both in vitro and in vivo. To evaluate tumorigenicity in vitro, anchorage-independent growth was assessed using the soft agar colony formation assay. hUCB-MSCs and MRC-5 cells formed few colonies, while HeLa cells formed a greater number of larger colonies, indicating that hUCB-MSCs and MRC-5 cells do not have anchorage-independent proliferation potential. To detect tumorigenicity in vivo, hUCB-MSCs were implanted as a single subcutaneous injection into BALB/c-nu mice. No tumor formation was observed in mice transplanted with hUCB-MSCs or MRC-5 cells based on macroand microscopic examinations; however, all mice transplanted with HeLa cells developed tumors that stained positive for a human gene according to immunohistochemical analysis. In conclusion, hUCB-MSCs do not exhibit tumorigenic potential based on in vitro and in vivo assays under our experimental conditions, providing further evidence of their safety for clinical applications.

Complete genome sequence of Pedobacter cryoconitis PAMC 27485, a CRISPR-Cas system-containing psychrophile isolated from Antarctica.

Pedobacter cryoconitis PAMC 27485, an aerobic, Gram-negative, facultatively psychrophilic bacterium, was isolated from Antarctic soil. Here we report the complete genome of P. cryoconitis PAMC 27485, which contains a type II CRISPR-Cas system and genes encoding useful enzymes (e.g. proteases). The genome sequence of P. cryoconitis PAMC 27485 could provide insights into its adaptive immune system against foreign genetic elements and biotechnological potential.