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.

Life experiences of elderly people with suicide ideation at the long-term care hospitals in South Korea.

OBJECTIVE: To understand the life experiences of elderly people who are living in long-term care hospitals and are afflicted with suicide ideation. METHODS: A phenomenological qualitative methodology based on Colaizzi's method was used for the study. Participants included 9 elderly people who are 65 years old or older with suicidal ideas and were admitted in any of the 3 long-term care hospitals in D City, Gyeonggi-do, South Korea. Data were collected from July to December 2014. RESULTS: Seven categories, 15 theme categories, 30 themes, and 88 significant items were identified as parts of their life experiences. The 7 categories were identified as "being a slave to one's disease", "sadness as a result of being far away from one's family", "vain care and consolation for me", "continued life in a hospital, which feels like living abroad", "plunging life", "moving toward the end of life", and "sad relief from death". CONCLUSION: The findings from this study provide a deep understanding of the lives of elderly people who were staying in long-term care hospitals, and these will help improve their quality of life. Additionally, they can be used as references in implementing high-quality nursing practices for such elderly people.

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.

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.

Comparison of attitudes towards death and perceptions of do-not-resuscitate orders between older Korean adults residing in a facility and at home.

The purpose of this study was to compare and analyse attitudes towards death and perceptions of do-not-resuscitate (DNR) orders between the elderly living in a facility and those living at home, in order to provide basic data for effective nursing interventions to help the elderly prepare for death in a positive manner. The subjects of this study were 300 persons over 65 years old who lived in a facility or home in Seoul or Gyeonggi Province, South Korea, and data were collected from 1 April to 15 August 2012. Descriptive analysis, χ(2)-test, and ANCOVA were conducted on the data using the SPSS version 20.0 program. With regard to attitudes towards death, the elderly in a facility reported that physical pain relief was most necessary for a comfortable death, and the elderly living at home reported that psychological stability was most required. With regard to perceptions of DNR orders, most of the participants agreed that DNR is sometimes necessary (institution: 86.7%, home: 78.7%). About 8% more of the elderly living in a facility considered DNR to sometimes be necessary compared with the elderly living at home. In conclusion, the elderly living in a facility were interested in physical pain relief or physical health, and the elderly living at home were focused on psychological stability or psychological health. Based on the findings, basic data for development of effective nursing interventions to help the elderly prepare for death in a positive manner can be provided.

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.

Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species.

Despite recent advances in commercially optimized identification systems, bacterial identification remains a challenging task in many routine microbiological laboratories, especially in situations where taxonomically novel isolates are involved. The 16S rRNA gene has been used extensively for this task when coupled with a well-curated database, such as EzTaxon, containing sequences of type strains of prokaryotic species with validly published names. Although the EzTaxon database has been widely used for routine identification of prokaryotic isolates, sequences from uncultured prokaryotes have not been considered. Here, the next generation database, named EzTaxon-e, is formally introduced. This new database covers not only species within the formal nomenclatural system but also phylotypes that may represent species in nature. In addition to an identification function based on Basic Local Alignment Search Tool (blast) searches and pairwise global sequence alignments, a new objective method of assessing the degree of completeness in sequencing is proposed. All sequences that are held in the EzTaxon-e database have been subjected to phylogenetic analysis and this has resulted in a complete hierarchical classification system. It is concluded that the EzTaxon-e database provides a useful taxonomic backbone for the identification of cultured and uncultured prokaryotes and offers a valuable means of communication among microbiologists who routinely encounter taxonomically novel isolates. The database and its analytical functions can be found at http://eztaxon-e.ezbiocloud.net/.

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.

Use of barcoded pyrosequencing and shared OTUs to determine sources of fecal bacteria in watersheds.

While many current microbial source tracking (MST) methods rely on the use of specific molecular marker genes to identify sources of fecal contamination, these methods often fail to determine all point and nonpoint contributors of fecal inputs into waterways. In this study, we developed a new library-dependent MST method that uses pyrosequencing-derived shared operational taxonomy units (OTUs) to define sources of fecal contamination in waterways. A total 56,841 pyrosequencing reads of 16S rDNA obtained from the feces of humans and animals were evaluated and used to compare fecal microbial diversity in three freshwater samples obtained from the Yeongsan river basin in Jeonnam Province, South Korea. Sites included an urbanized agricultural area (Y1) (Escherichia coli counts ≥ 1600 CFU/100 mL), an open area (Y2) with no major industrial activities (940 CFU/100 mL), and a typical agricultural area (Y3) (≥ 1600 CFU/100 mL). Data analyses indicated that the majority of bacteria in the feces of humans and domesticated animals were comprised of members of the phyla Bacteroidetes or Firmicutes, whereas the majority of bacteria in wild goose feces and freshwater samples were classified to the phylum Proteobacteria. Analysis of OTUs shared between the fecal and environmental samples suggested that the potential sources of the fecal contamination at the sites were of human and swine origin. Quantification of fecal contamination was also examined by comparing the density of pyrosequencing reads in each fecal sample within shared OTUs. Taken together, our results indicated that analysis of shared OTUs derived from barcoded pyrosequencing reads provide the necessary resolution and discrimination to be useful as a next generation platform for microbial source tracking studies.

Phylogenetic and functional marker genes to study ammonia-oxidizing microorganisms (AOM) in the environment.

The oxidation of ammonia plays a significant role in the transformation of fixed nitrogen in the global nitrogen cycle. Autotrophic ammonia oxidation is known in three groups of microorganisms. Aerobic ammonia-oxidizing bacteria and archaea convert ammonia into nitrite during nitrification. Anaerobic ammonia-oxidizing bacteria (anammox) oxidize ammonia using nitrite as electron acceptor and producing atmospheric dinitrogen. The isolation and cultivation of all three groups in the laboratory are quite problematic due to their slow growth rates, poor growth yields, unpredictable lag phases, and sensitivity to certain organic compounds. Culture-independent approaches have contributed importantly to our understanding of the diversity and distribution of these microorganisms in the environment. In this review, we present an overview of approaches that have been used for the molecular study of ammonia oxidizers and discuss their application in different environments.

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.

Community analysis of betaproteobacterial ammonia-oxidizing bacteria using the amoCAB operon.

The genes and intergenic regions of the amoCAB operon were analyzed to establish their potential as molecular markers for analyzing ammonia-oxidizing betaproteobacterial (beta-AOB) communities. Initially, sequence similarity for related taxa, evolutionary rates from linear regressions, and the presence of conserved and variable regions were analyzed for all available sequences of the complete amoCAB operon. The gene amoB showed the highest sequence variability of the three amo genes, suggesting that it might be a better molecular marker than the most frequently used amoA to resolve closely related AOB species. To test the suitability of using the amoCAB genes for community studies, a strategy involving nested PCR was employed. Primers to amplify the whole amoCAB operon and each individual gene were tested. The specificity of the products generated was analyzed by denaturing gradient gel electrophoresis, cloning, and sequencing. The fragments obtained showed different grades of sequence identity to amoCAB sequences in the GenBank database. The nested PCR approach provides a possibility to increase the sensitivity of detection of amo genes in samples with low abundance of AOB. It also allows the amplification of the almost complete amoA gene, with about 300 bp more sequence information than the previous approaches. The coupled study of all three amo genes and the intergenic spacer regions that are under different selection pressure might allow a more detailed analysis of the evolutionary processes, which are responsible for the differentiation of AOB communities in different habitats.

Effects of Obesity Management Program Provided by Occupational Health Nurse in Worksite.

This study was conducted on 60 male adult technicians in the worksite to examine the impact of the obesity management program on their eating habits, exercise self-efficacy, quality of life, and body components. This was a nonrandomized pretest and posttest intervention study. The obesity management program was applied for 16 weeks on diet education, exercise, and counseling provided by the occupational health nurse in the worksite. The questionnaire for measure included the general characteristics, eating habits, exercise self-efficacy, and quality of life. Body components were measured by using the InBody 720 device. The participants who received the obesity management program showed better eating habits, a higher level of exercise self-efficacy, a higher level of quality of life, lower levels of body weight and body mass index (BMI), a smaller waist and hip circumference, and a higher level of muscle mass as compared with the preapplication.

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.

Comparisons of Health Promoting Behavior, Depression, and Life Satisfaction Between Older Adults in Rural Areas in South Korea Living in Group Homes and at Home.

BACKGROUND: In South Korea, population aging is advancing at a more rapid rate in rural areas than urban areas, leading to a particularly high percentage of rural-dwelling older adults. PURPOSE: The aim of this study was to examine and compare health promoting behaviors, depression, and life satisfaction between rural-dwelling older adults who live, respectively, in group homes and at home. METHODS: A cross-sectional descriptive study design was employed. Study participants included 160 older adults aged 65 years and older who were living in group homes (n = 80) and at home (n = 80) in Gyeonggi province, South Korea. The Health Promotion Lifestyle Profile-II was used to examine health promoting behaviors, the Korean Geriatric Depression Screening Scale was used to examine depression, and the Life Satisfaction Index was used to examine life satisfaction. Data were analyzed using SPSS Version 21.0. RESULTS: The data showed significant differences between the two groups in terms of health promoting behaviors (t = -9.035, p < .001), depression (t = 20.861, p < .001), and life satisfaction (t = -12.153, p < .001). CONCLUSIONS/IMPLICATIONS FOR PRACTICE: The mean scores for health promotion behaviors and life satisfaction were higher, and the mean score for depression was lower in the group-home group than the at-home group. The findings from this study may be employed as basic data for establishing residence-appropriate nursing intervention protocols for older adults living in rural areas.

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.

Evaluation of PCR primer selectivity and phylogenetic specificity by using amplification of 16S rRNA genes from betaproteobacterial ammonia-oxidizing bacteria in environmental samples.

The effect of primer specificity for studying the diversity of ammonia-oxidizing betaproteobacteria (betaAOB) was evaluated. betaAOB represent a group of phylogenetically related organisms for which the 16S rRNA gene approach is especially suitable. We used experimental comparisons of primer performance with water samples, together with an in silico analysis of published sequences and a literature review of clone libraries made with four specific PCR primers for the betaAOB 16S rRNA gene. With four aquatic samples, the primers NitA/NitB produced the highest frequency of ammonia-oxidizing-bacterium-like sequences compared to clone libraries with products amplified with the primer combinations betaAMOf/betaAMOr, betaAMOf/Nso1255g, and NitA/Nso1225g. Both the experimental examination of ammonia-oxidizing-bacterium-specific 16S rRNA gene primers and the literature search showed that neither specificity nor sensitivity of primer combinations can be evaluated reliably only by sequence comparison. Apparently, the combination of sequence comparison and experimental data is the best approach to detect possible biases of PCR primers. Although this study focused on betaAOB, the results presented here more generally exemplify the importance of primer selection and potential primer bias when analyzing microbial communities in environmental samples.