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Bacterial Biogeography Influenced by Shelf-Basin Exchange in the Arctic Surface Sediment at the Chukchi Borderland.

https://arctichealth.org/en/permalink/ahliterature266585
Source
Environ Microbiol. 2015 Sep 28;
Publication Type
Article
Date
Sep-28-2015
Author
Dukki Han
Seung-Il Nam
Ho Kyung Ha
Hyoungjun Kim
Michael J Sadowsky
Yoo Kyung Lee
Hor-Gil Hur
Source
Environ Microbiol. 2015 Sep 28;
Date
Sep-28-2015
Language
English
Publication Type
Article
Abstract
It has been known that continental shelves around the Arctic Ocean play a major role in the ventilation of the deep basins as a consequence of shelf-basin exchange. In the present study, we found that bacterial assemblage of the surface sediment was different from that of seawater while seawater harbored local bacterial assemblages in response to the Arctic hydrography. This finding suggests that the Arctic seafloor sediments may have distinctive bacterial biogeography. Moreover, the distribution of bacterial assemblages and physicochemical properties in surface sediments changed gradually from the Arctic continental shelf to deep-sea basin. Based on the results, bacterial biogeography in the Arctic seafloor sediments may be influenced by winnowing and redeposition of surface sediments through the sediment gravity flow. The present study offers a deeper understanding of shelf convection and its role for the construction of bacterial assemblages in the Arctic Ocean.
PubMed ID
26411339 View in PubMed
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Bacterial communities of surface mixed layer in the Pacific sector of the western Arctic Ocean during sea-ice melting.

https://arctichealth.org/en/permalink/ahliterature257813
Source
PLoS One. 2014;9(1):e86887
Publication Type
Article
Date
2014
Author
Dukki Han
Ilnam Kang
Ho Kyung Ha
Hyun Cheol Kim
Ok-Sun Kim
Bang Yong Lee
Jang-Cheon Cho
Hor-Gil Hur
Yoo Kyung Lee
Author Affiliation
Korea Polar Research Institute, KIOST, Incheon, Republic of Korea ; School of Environmental Science and Engineering, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea.
Source
PLoS One. 2014;9(1):e86887
Date
2014
Language
English
Publication Type
Article
Keywords
Alphaproteobacteria - classification - genetics - growth & development
Ammonium Compounds - analysis
Arctic Regions
Bacteria - classification - genetics - growth & development
Ecosystem
Flavobacteriaceae - classification - growth & development
Fresh Water - chemistry - microbiology
Gammaproteobacteria - classification - genetics - growth & development
Geography
Ice Cover - chemistry - microbiology
Linear Models
Nitrates - analysis
Nitrogen Dioxide - analysis
Oceans and Seas
Phosphates - analysis
Phylogeny
RNA, Ribosomal, 16S - genetics
Salinity
Seasons
Seawater - chemistry - microbiology
Sequence Analysis, DNA
Silicon Dioxide - analysis
Temperature
Abstract
From July to August 2010, the IBRV ARAON journeyed to the Pacific sector of the Arctic Ocean to monitor bacterial variation in Arctic summer surface-waters, and temperature, salinity, fluorescence, and nutrient concentrations were determined during the ice-melting season. Among the measured physicochemical parameters, we observed a strong negative correlation between temperature and salinity, and consequently hypothesized that the melting ice decreased water salinity. The bacterial community compositions of 15 samples, includicng seawater, sea-ice, and melting pond water, were determined using a pyrosequencing approach and were categorized into three habitats: (1) surface seawater, (2) ice core, and (3) melting pond. Analysis of these samples indicated the presence of local bacterial communities; a deduction that was further corroborated by the discovery of seawater- and ice-specific bacterial phylotypes. In all samples, the Alphaproteobacteria, Flavobacteria, and Gammaproteobacteria taxa composed the majority of the bacterial communities. Among these, Alphaproteobacteria was the most abundant and present in all samples, and its variation differed among the habitats studied. Linear regression analysis suggested that changes in salinity could affect the relative proportion of Alphaproteobacteria in the surface water. In addition, the species-sorting model was applied to evaluate the population dynamics and environmental heterogeneity in the bacterial communities of surface mixed layer in the Arctic Ocean during sea-ice melting.
Notes
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PubMed ID
24497990 View in PubMed
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Bacterial community structure and soil properties of a subarctic tundra soil in Council, Alaska.

https://arctichealth.org/en/permalink/ahliterature257928
Source
FEMS Microbiol Ecol. 2014 Aug;89(2):465-75
Publication Type
Article
Date
Aug-2014
Author
Hye Min Kim
Ji Young Jung
Etienne Yergeau
Chung Yeon Hwang
Larry Hinzman
Sungjin Nam
Soon Gyu Hong
Ok-Sun Kim
Jongsik Chun
Yoo Kyung Lee
Author Affiliation
Korea Polar Research Institute, KIOST, Incheon, Korea; School of Biological Sciences, Seoul National University, Seoul, Korea.
Source
FEMS Microbiol Ecol. 2014 Aug;89(2):465-75
Date
Aug-2014
Language
English
Publication Type
Article
Keywords
Actinobacteria - genetics
Alaska
Biomass
Carbon - chemistry
Hydrogen-Ion Concentration
Molecular Sequence Data
Molecular Typing
Nitrogen - chemistry
Phylogeny
Proteobacteria - genetics
RNA, Bacterial - genetics
RNA, Ribosomal, 16S - genetics
Sequence Analysis, DNA
Soil - chemistry
Soil Microbiology
Abstract
The subarctic region is highly responsive and vulnerable to climate change. Understanding the structure of subarctic soil microbial communities is essential for predicting the response of the subarctic soil environment to climate change. To determine the composition of the bacterial community and its relationship with soil properties, we investigated the bacterial community structure and properties of surface soil from the moist acidic tussock tundra in Council, Alaska. We collected 70 soil samples with 25-m intervals between sampling points from 0-10 cm to 10-20 cm depths. The bacterial community was analyzed by pyrosequencing of 16S rRNA genes, and the following soil properties were analyzed: soil moisture content (MC), pH, total carbon (TC), total nitrogen (TN), and inorganic nitrogen (NH4+ and NO3-). The community compositions of the two different depths showed that Alphaproteobacteria decreased with soil depth. Among the soil properties measured, soil pH was the most significant factor correlating with bacterial community in both upper and lower-layer soils. Bacterial community similarity based on jackknifed unweighted unifrac distance showed greater similarity across horizontal layers than through the vertical depth. This study showed that soil depth and pH were the most important soil properties determining bacterial community structure of the subarctic tundra soil in Council, Alaska.
Notes
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PubMed ID
24893754 View in PubMed
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Chemical Structure of the Lipid A component of Pseudomonas sp. strain PAMC 28618 from Thawing Permafrost in Relation to Pathogenicity.

https://arctichealth.org/en/permalink/ahliterature296930
Source
Sci Rep. 2017 05 19; 7(1):2168
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Date
05-19-2017
Author
Han-Gyu Park
Ganesan Sathiyanarayanan
Cheol-Hwan Hwang
Da-Hee Ann
Jung-Ho Kim
Geul Bang
Kyoung-Soon Jang
Hee Wook Ryu
Yoo Kyung Lee
Yung-Hun Yang
Yun-Gon Kim
Author Affiliation
Department of Chemical Engineering, Soongsil University, Seoul, 06978, Korea.
Source
Sci Rep. 2017 05 19; 7(1):2168
Date
05-19-2017
Language
English
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Keywords
Lipid A - chemistry
Molecular Structure
Permafrost - microbiology
Phenotype
Phylogeny
Plant Diseases
Pseudomonas - classification - pathogenicity - physiology
Soil Microbiology
Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
Structure-Activity Relationship
Abstract
Climate change causes permafrost thawing, and we are confronted with the unpredictable risk of newly discovered permafrost microbes that have disease-causing capabilities. Here, we first characterized the detailed chemical structure of the lipid A moiety from a Pseudomonas species that was isolated from thawing arctic permafrost using MALDI-based mass spectrometric approaches (i.e., MALDI-TOF MS and MALDI-QIT-TOF MSn). The MALDI multi-stage mass spectrometry (MS) analysis of lipid A extracted from the Pseudomonas sp. strain PAMC 28618 demonstrated that the hexaacyl lipid A ([M-H]- at m/z 1616.5) contains a glucosamine (GlcN) disaccharide backbone, two phosphates, four main acyl chains and two branched acyl chains. Moreover, the lipid A molecule-based structural activity relationship with other terrestrial Gram-negative bacteria indicated that strain PAMC 28618 has an identical lipid A structure with the mesophilic Pseudomonas cichorii which can cause rot disease in endive (Cichorium endivia) and that their bacterial toxicities were equivalent. Therefore, the overall lipid A validation process provides a general strategy for characterizing bacteria that have been isolated from arctic permafrost and analyzing their respective pathogenicities.
PubMed ID
28526845 View in PubMed
Less detail

Chemical Structure of the Lipid A component of Pseudomonas sp. strain PAMC 28618 from Thawing Permafrost in Relation to Pathogenicity.

https://arctichealth.org/en/permalink/ahliterature282745
Source
Sci Rep. 2017 May 19;7(1):2168
Publication Type
Article
Date
May-19-2017
Author
Han-Gyu Park
Ganesan Sathiyanarayanan
Cheol-Hwan Hwang
Da-Hee Ann
Jung-Ho Kim
Geul Bang
Kyoung-Soon Jang
Hee Wook Ryu
Yoo Kyung Lee
Yung-Hun Yang
Yun-Gon Kim
Source
Sci Rep. 2017 May 19;7(1):2168
Date
May-19-2017
Language
English
Publication Type
Article
Abstract
Climate change causes permafrost thawing, and we are confronted with the unpredictable risk of newly discovered permafrost microbes that have disease-causing capabilities. Here, we first characterized the detailed chemical structure of the lipid A moiety from a Pseudomonas species that was isolated from thawing arctic permafrost using MALDI-based mass spectrometric approaches (i.e., MALDI-TOF MS and MALDI-QIT-TOF MS(n)). The MALDI multi-stage mass spectrometry (MS) analysis of lipid A extracted from the Pseudomonas sp. strain PAMC 28618 demonstrated that the hexaacyl lipid A ([M-H](-) at m/z 1616.5) contains a glucosamine (GlcN) disaccharide backbone, two phosphates, four main acyl chains and two branched acyl chains. Moreover, the lipid A molecule-based structural activity relationship with other terrestrial Gram-negative bacteria indicated that strain PAMC 28618 has an identical lipid A structure with the mesophilic Pseudomonas cichorii which can cause rot disease in endive (Cichorium endivia) and that their bacterial toxicities were equivalent. Therefore, the overall lipid A validation process provides a general strategy for characterizing bacteria that have been isolated from arctic permafrost and analyzing their respective pathogenicities.
Notes
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PubMed ID
28526845 View in PubMed
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Comparing rock-inhabiting microbial communities in different rock types from a high arctic polar desert.

https://arctichealth.org/en/permalink/ahliterature299360
Source
FEMS Microbiol Ecol. 2018 06 01; 94(6):
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Date
06-01-2018
Author
Yong-Hoe Choe
Mincheol Kim
Jusun Woo
Mi Jung Lee
Jong Ik Lee
Eun Ju Lee
Yoo Kyung Lee
Author Affiliation
Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea.
Source
FEMS Microbiol Ecol. 2018 06 01; 94(6):
Date
06-01-2018
Language
English
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Keywords
Antarctic Regions
Arctic Regions
Bacteria - classification - genetics - isolation & purification
Fungi - classification - genetics - isolation & purification
Geologic Sediments - microbiology
Microbiota
Norway
RNA, Ribosomal, 16S - genetics
RNA, Ribosomal, 28S - genetics
Soil Microbiology
Svalbard
Abstract
Although rocks are habitable places for microbes in extreme environments, microbial diversity in these lithic environments is still poorly understood. The diversity and abundance of rock-inhabiting microbial communities in different types of rock in Svalbard, Norwegian High Arctic were examined using NGS sequencing of bacterial 16S rRNA genes and fungal 28S rRNA genes. Compositions of both bacterial and fungal communities varied across different rock types: sandstone, limestone, basalt, granite and travertine. Bacterial communities were dominated by Actinobacteria, Proteobacteria, Chloroflexi, Bacteroidetes and Acidobacteria. Fungal communities consisted of Eurotiomycetes, Lecanoromycetes, Dothideomycetes and Leotiomycetes. Both bacterial and fungal community compositions were significantly correlated with the geochemical characteristics of rocks. Bacterial communities were considerably correlated with the rock elements such as Mg and Ca. Fungal communities were considerably correlated with Fe. Interestingly, many dominant bacterial and fungal operational taxonomic units in the investigated rocks from the study area were closely affiliated to those found in other cold regions such as Alpine area, Arctic and Antarctica, suggesting that environmental constraints such as cold temperature may lead to convergence in microbial community composition. These results confirm that rocks in cold environments act as reservoirs of diverse bacteria and fungi, which may improve our understanding of lithic microbial ecology in the cold desert.
PubMed ID
29688499 View in PubMed
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Comparing rock-inhabiting microbial communities in different rock types from a high arctic polar desert.

https://arctichealth.org/en/permalink/ahliterature291405
Source
FEMS Microbiol Ecol. 2018 Jun 01; 94(6):
Publication Type
Journal Article
Date
Jun-01-2018
Author
Yong-Hoe Choe
Mincheol Kim
Jusun Woo
Mi Jung Lee
Jong Ik Lee
Eun Ju Lee
Yoo Kyung Lee
Author Affiliation
Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea.
Source
FEMS Microbiol Ecol. 2018 Jun 01; 94(6):
Date
Jun-01-2018
Language
English
Publication Type
Journal Article
Abstract
Although rocks are habitable places for microbes in extreme environments, microbial diversity in these lithic environments is still poorly understood. The diversity and abundance of rock-inhabiting microbial communities in different types of rock in Svalbard, Norwegian High Arctic were examined using NGS sequencing of bacterial 16S rRNA genes and fungal 28S rRNA genes. Compositions of both bacterial and fungal communities varied across different rock types: sandstone, limestone, basalt, granite and travertine. Bacterial communities were dominated by Actinobacteria, Proteobacteria, Chloroflexi, Bacteroidetes and Acidobacteria. Fungal communities consisted of Eurotiomycetes, Lecanoromycetes, Dothideomycetes and Leotiomycetes. Both bacterial and fungal community compositions were significantly correlated with the geochemical characteristics of rocks. Bacterial communities were considerably correlated with the rock elements such as Mg and Ca. Fungal communities were considerably correlated with Fe. Interestingly, many dominant bacterial and fungal operational taxonomic units in the investigated rocks from the study area were closely affiliated to those found in other cold regions such as Alpine area, Arctic and Antarctica, suggesting that environmental constraints such as cold temperature may lead to convergence in microbial community composition. These results confirm that rocks in cold environments act as reservoirs of diverse bacteria and fungi, which may improve our understanding of lithic microbial ecology in the cold desert.
PubMed ID
29688499 View in PubMed
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CspB of an arctic bacterium, Polaribacter irgensii KOPRI 22228, confers extraordinary freeze-tolerance.

https://arctichealth.org/en/permalink/ahliterature285029
Source
Braz J Microbiol. 2017 Jul 31;
Publication Type
Article
Date
Jul-31-2017
Author
Youn Hong Jung
Yoo Kyung Lee
Hong Kum Lee
Kyunghee Lee
Hana Im
Source
Braz J Microbiol. 2017 Jul 31;
Date
Jul-31-2017
Language
English
Publication Type
Article
Abstract
Freezing temperatures are a major challenge for life at the poles. Decreased membrane fluidity, uninvited secondary structure formation in nucleic acids, and protein cold-denaturation all occur at cold temperatures. Organisms adapted to polar regions possess distinct mechanisms that enable them to survive in extremely cold environments. Among the cold-induced proteins, cold shock protein (Csp) family proteins are the most prominent. A gene coding for a Csp-family protein, cspB, was cloned from an arctic bacterium, Polaribacter irgensii KOPRI 22228, and overexpression of cspB greatly increased the freeze-survival rates of Escherichia coli hosts, to a greater level than any previously reported Csp. It also suppressed the cold-sensitivity of an E. coli csp-quadruple deletion strain, BX04. Sequence analysis showed that this protein consists of a unique domain at its N-terminal end and a well conserved cold shock domain at its C-terminal end. The most common mechanism of Csp function in cold adaption is melting of the secondary structures in RNA and DNA molecules, thus facilitating transcription and translation at low temperatures. P. irgensii CspB bound to oligo(dT)-cellulose resins, suggesting single-stranded nucleic acid-binding activity. The unprecedented level of freeze-tolerance conferred by P. irgensii CspB suggests a crucial role for this protein in survival in polar environments.
PubMed ID
28807609 View in PubMed
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Distinct Microbial Communities in Adjacent Rock and Soil Substrates on a High Arctic Polar Desert.

https://arctichealth.org/en/permalink/ahliterature303685
Source
Front Microbiol. 2020; 11:607396
Publication Type
Journal Article
Date
2020
Author
Yong-Hoe Choe
Mincheol Kim
Yoo Kyung Lee
Author Affiliation
Korea Polar Research Institute, Incheon, South Korea.
Source
Front Microbiol. 2020; 11:607396
Date
2020
Language
English
Publication Type
Journal Article
Abstract
Understanding microbial niche variability in polar regions can provide insights into the adaptive diversification of microbial lineages in extreme environments. Compositions of microbial communities in Arctic soils are well documented but a comprehensive multidomain diversity assessment of rocks remains insufficiently studied. In this study, we obtained two types of rocks (sandstone and limestone) and soils around the rocks in a high Arctic polar desert (Svalbard), and examined the compositions of archaeal, bacterial, fungal, and protistan communities in the rocks and soils. The microbial community structure differed significantly between rocks and soils across all microbial groups at higher taxonomic levels, indicating that Acidobacteria, Gemmatimonadetes, Latescibacteria, Rokubacteria, Leotiomycetes, Pezizomycetes, Mortierellomycetes, Sarcomonadea, and Spirotrichea were more abundant in soils, whereas Cyanobacteria, Deinococcus-Thermus, FBP, Lecanoromycetes, Eurotiomycetes, Trebouxiophyceae, and Ulvophyceae were more abundant in rocks. Interestingly, fungal communities differed markedly between two different rock types, which is likely to be ascribed to the predominance of distinct lichen-forming fungal taxa (Verrucariales in limestone, and Lecanorales in sandstone). This suggests that the physical or chemical properties of rocks could be a major determinant in the successful establishment of lichens in lithic environments. Furthermore, the biotic interactions among microorganisms based on co-occurrence network analysis revealed that Polyblastia and Verrucaria in limestone, and Atla, Porpidia, and Candelariella in sandstone play an important role as keystone taxa in the lithic communities. Our study shows that even in niches with the same climate regime and proximity to each other, heterogeneity of edaphic and lithic niches can affect microbial community assembly, which could be helpful in comprehensively understanding the effects of niche on microbial assembly in Arctic terrestrial ecosystems.
PubMed ID
33488547 View in PubMed
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Distinct Taxonomic and Functional Profiles of the Microbiome Associated With Different Soil Horizons of a Moist Tussock Tundra in Alaska.

https://arctichealth.org/en/permalink/ahliterature301894
Source
Front Microbiol. 2019; 10:1442
Publication Type
Journal Article
Date
2019
Author
Binu M Tripathi
Hye Min Kim
Ji Young Jung
Sungjin Nam
Hyeon Tae Ju
Mincheol Kim
Yoo Kyung Lee
Author Affiliation
Korea Polar Research Institute, Incheon, South Korea.
Source
Front Microbiol. 2019; 10:1442
Date
2019
Language
English
Publication Type
Journal Article
Abstract
Permafrost-underlain tundra soils in Northern Hemisphere are one of the largest reservoirs of terrestrial carbon, which are highly sensitive to microbial decomposition due to climate warming. However, knowledge about the taxonomy and functions of microbiome residing in different horizons of permafrost-underlain tundra soils is still limited. Here we compared the taxonomic and functional composition of microbiome between different horizons of soil cores from a moist tussock tundra ecosystem in Council, Alaska, using 16S rRNA gene and shotgun metagenomic sequencing. The composition, diversity, and functions of microbiome varied significantly between soil horizons, with top soil horizon harboring more diverse communities than sub-soil horizons. The vertical gradient in soil physico-chemical parameters were strongly associated with composition of microbial communities across permafrost soil horizons; however, a large fraction of the variation in microbial communities remained unexplained. The genes associated with carbon mineralization were more abundant in top soil horizon, while genes involved in acetogenesis, fermentation, methane metabolism (methanogenesis and methanotrophy), and N cycling were dominant in sub-soil horizons. The results of phylogenetic null modeling analysis showed that stochastic processes strongly influenced the composition of the microbiome in different soil horizons, except the bacterial community composition in top soil horizon, which was largely governed by homogeneous selection. Our study expands the knowledge on the structure and functional potential of microbiome associated with different horizons of permafrost soil, which could be useful in understanding the effects of environmental change on microbial responses in tundra ecosystems.
PubMed ID
31316487 View in PubMed
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