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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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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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Dynamics of microbial communities and CO2 and CH4 fluxes in the tundra ecosystems of the changing Arctic.

https://arctichealth.org/en/permalink/ahliterature297552
Source
J Microbiol. 2019 Jan 16; :
Publication Type
Journal Article
Review
Date
Jan-16-2019
Author
Min Jung Kwon
Ji Young Jung
Binu M Tripathi
Mathias Göckede
Yoo Kyung Lee
Mincheol Kim
Author Affiliation
Korea Polar Research Institute, Incheon, 21990, Republic of Korea.
Source
J Microbiol. 2019 Jan 16; :
Date
Jan-16-2019
Language
English
Publication Type
Journal Article
Review
Abstract
Arctic tundra ecosystems are rapidly changing due to the amplified effects of global warming within the northern high latitudes. Warming has the potential to increase the thawing of the permafrost and to change the landscape and its geochemical characteristics, as well as terrestrial biota. It is important to investigate microbial processes and community structures, since soil microorganisms play a significant role in decomposing soil organic carbon in the Arctic tundra. In addition, the feedback from tundra ecosystems to climate change, including the emission of greenhouse gases into the atmosphere, is substantially dependent on the compositional and functional changes in the soil microbiome. This article reviews the current state of knowledge of the soil microbiome and the two most abundant greenhouse gas (CO2 and CH4) emissions, and summarizes permafrost thaw-induced changes in the Arctic tundra. Furthermore, we discuss future directions in microbial ecological research coupled with its link to CO2 and CH4 emissions.
PubMed ID
30656588 View in PubMed
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Dynamics of microbial communities and CO2 and CH4 fluxes in the tundra ecosystems of the changing Arctic.

https://arctichealth.org/en/permalink/ahliterature300914
Source
J Microbiol. 2019 May; 57(5):325-336
Publication Type
Journal Article
Review
Date
May-2019
Author
Min Jung Kwon
Ji Young Jung
Binu M Tripathi
Mathias Göckede
Yoo Kyung Lee
Mincheol Kim
Author Affiliation
Korea Polar Research Institute, Incheon, 21990, Republic of Korea.
Source
J Microbiol. 2019 May; 57(5):325-336
Date
May-2019
Language
English
Publication Type
Journal Article
Review
Keywords
Arctic Regions
Carbon Dioxide - metabolism
Global warming
Greenhouse Gases - metabolism
Methane - metabolism
Microbiota - physiology
Permafrost - microbiology
Russia
Soil - chemistry
Soil Microbiology
Abstract
Arctic tundra ecosystems are rapidly changing due to the amplified effects of global warming within the northern high latitudes. Warming has the potential to increase the thawing of the permafrost and to change the landscape and its geochemical characteristics, as well as terrestrial biota. It is important to investigate microbial processes and community structures, since soil microorganisms play a significant role in decomposing soil organic carbon in the Arctic tundra. In addition, the feedback from tundra ecosystems to climate change, including the emission of greenhouse gases into the atmosphere, is substantially dependent on the compositional and functional changes in the soil microbiome. This article reviews the current state of knowledge of the soil microbiome and the two most abundant greenhouse gas (CO2 and CH4) emissions, and summarizes permafrost thaw-induced changes in the Arctic tundra. Furthermore, we discuss future directions in microbial ecological research coupled with its link to CO2 and CH4 emissions.
PubMed ID
30656588 View in PubMed
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The relationships of present vegetation, bacteria, and soil properties with soil organic matter characteristics in moist acidic tundra in Alaska.

https://arctichealth.org/en/permalink/ahliterature311249
Source
Sci Total Environ. 2021 Jun 10; 772:145386
Publication Type
Journal Article
Date
Jun-10-2021
Author
Sungjin Nam
Josu G Alday
Mincheol Kim
Hyemin Kim
Yongkang Kim
Taesung Park
Hyoun Soo Lim
Bang Yong Lee
Yoo Kyung Lee
Ji Young Jung
Author Affiliation
Korea Polar Research Institute, Incheon 21990, Republic of Korea.
Source
Sci Total Environ. 2021 Jun 10; 772:145386
Date
Jun-10-2021
Language
English
Publication Type
Journal Article
Keywords
Alaska
Bacteria - genetics
Ecosystem
RNA, Ribosomal, 16S - genetics
Soil
Soil Microbiology
Tundra
Abstract
Soil organic matter (SOM) is related to vegetation, soil bacteria, and soil properties; however, not many studies link all these parameters simultaneously, particularly in tundra ecosystems vulnerable to climate change. Our aim was to describe the relationships between vegetation, bacteria, soil properties, and SOM composition in moist acidic tundra by integrating physical, chemical, and molecular methods. A total of 70 soil samples were collected at two different depths from 36 spots systematically arranged over an area of about 300 m × 50 m. Pyrolysis-gas chromatography/mass spectrometry and pyrosequencing of the 16S rRNA gene were used to identify the molecular compositions of the SOM and bacterial community, respectively. Vegetation and soil physicochemical properties were also measured. The sampling sites were grouped into three, based on their SOM compositions: Sphagnum moss-derived SOM, lipid-rich materials, and aromatic-rich materials. Our results show that SOM composition is spatially structured and linked to microtopography; however, the vegetation, soil properties, and bacterial community composition did not show overall spatial structuring. Simultaneously, soil properties and bacterial community composition were the main factors explaining SOM compositional variation, while vegetation had a residual effect. Verrucomicrobia and Acidobacteria were related to polysaccharides, and Chloroflexi was linked to aromatic compounds. These relationships were consistent across different hierarchical levels. Our results suggest that SOM composition at a local scale is closely linked with soil factors and the bacterial community. Comprehensive observation of ecosystem components is recommended to understand the in-situ function of bacteria and the fate of SOM in the moist acidic tundra.
PubMed ID
33770858 View in PubMed
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Sensitive change of iso-branched fatty acid (iso-15:0) in Bacillus pumilus PAMC 23174 in response to environmental changes.

https://arctichealth.org/en/permalink/ahliterature267881
Source
Bioprocess Biosyst Eng. 2015 Nov 13;
Publication Type
Article
Date
Nov-13-2015
Author
Da-Hye Yi
Ganesan Sathiyanarayanan
Hyung Min Seo
Jung-Ho Kim
Shashi Kant Bhatia
Yun-Gon Kim
Sung-Hee Park
Ji-Young Jung
Yoo Kyung Lee
Yung-Hun Yang
Source
Bioprocess Biosyst Eng. 2015 Nov 13;
Date
Nov-13-2015
Language
English
Publication Type
Article
Abstract
In this study, the environmental adaptive metabolic processes were investigated using a psychrotrophic polar bacterium Bacillus pumilus PAMC 23174 in response to various temperatures and nutrients, especially in regard to the synthesis of fatty acids. Fatty acid methyl ester analysis was performed using gas chromatography-mass spectrometry and we found that a sensitive changes in iso-branched fatty acid (iso-15:0) synthesis occurred when adjusting the nutritional ratio of branched chain fatty acids (anteiso/iso) with different temperatures, resulting in a change in the balance of anteiso- and iso-form fatty acids. We also observed that this Arctic bacterium preferred amino acid leucine for the synthesis of fatty acids. The increased and decreased synthesis of iso-form fatty acids in response to different temperatures and leucine preference, changes the fatty acid ratio in bacteria, which further affects the membrane fluidity and it is also directly correlated with survival of bacteria in an extreme environment. Hence, this study suggests that B. pumilus PAMC 23174 is a potential model organism for the analysis of the unique ecological adaptations of polar bacteria in changing and the extreme environments.
PubMed ID
26566954 View in PubMed
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Shifts in bacterial community structure during succession in a glacier foreland of the High Arctic.

https://arctichealth.org/en/permalink/ahliterature277132
Source
FEMS Microbiol Ecol. 2016 Oct 17;
Publication Type
Article
Date
Oct-17-2016
Author
Mincheol Kim
Ji Young Jung
Dominique Laffly
Hye Young Kwon
Yoo Kyung Lee
Source
FEMS Microbiol Ecol. 2016 Oct 17;
Date
Oct-17-2016
Language
English
Publication Type
Article
Abstract
Primary succession after glacier retreat has been widely studied in plant communities, but bacterial succession is still poorly understood. In particular, few studies of microbial succession have been performed in the Arctic. We investigated the shifts in bacterial community structure and soil physicochemical properties along a successional gradient in a 100-year glacier foreland of the High Arctic. Multivariate analyses revealed that time after glacier retreat played a key role in associated bacterial community structure during succession. However, environmental filtering (i.e., pH and soil temperature) also accounted for a different, but substantial, proportion of the bacterial community structure. Using the functional trait-based approach, we found that average rRNA operon (rrn) copy number of bacterial communities are high in earlier successional stages and decreased over time. This suggests that soil bacterial taxa with higher rrn copy number have a selective advantage in early successional stages due to their ability of rapidly responding to nutrient inputs in newly exposed soils after glacier retreat. Taken together, our results demonstrate that both deglaciation time and environmental filters play key roles in structuring bacterial communities and soil bacterial groups with different ecological strategies occur in different stages of succession in this glacier foreland.
PubMed ID
27756770 View in PubMed
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Vertical distribution of bacterial community is associated with the degree of soil organic matter decomposition in the active layer of moist acidic tundra.

https://arctichealth.org/en/permalink/ahliterature277378
Source
J Microbiol. 2016 Nov;54(11):713-723
Publication Type
Article
Date
Nov-2016
Author
Hye Min Kim
Min Jin Lee
Ji Young Jung
Chung Yeon Hwang
Mincheol Kim
Hee-Myong Ro
Jongsik Chun
Yoo Kyung Lee
Source
J Microbiol. 2016 Nov;54(11):713-723
Date
Nov-2016
Language
English
Publication Type
Article
Abstract
The increasing temperature in Arctic tundra deepens the active layer, which is the upper layer of permafrost soil that experiences repeated thawing and freezing. The increasing of soil temperature and the deepening of active layer seem to affect soil microbial communities. Therefore, information on soil microbial communities at various soil depths is essential to understand their potential responses to climate change in the active layer soil. We investigated the community structure of soil bacteria in the active layer from moist acidic tundra in Council, Alaska. We also interpreted their relationship with some relevant soil physicochemical characteristics along soil depth with a fine scale (5 cm depth interval). The bacterial community structure was found to change along soil depth. The relative abundances of Acidobacteria, Gammaproteobacteria, Planctomycetes, and candidate phylum WPS-2 rapidly decreased with soil depth, while those of Bacteroidetes, Chloroflexi, Gemmatimonadetes, and candidate AD3 rapidly increased. A structural shift was also found in the soil bacterial communities around 20 cm depth, where two organic (upper Oi and lower Oa) horizons are subdivided. The quality and the decomposition degree of organic matter might have influenced the bacterial community structure. Besides the organic matter quality, the vertical distribution of bacterial communities was also found to be related to soil pH and total phosphorus content. This study showed the vertical change of bacterial community in the active layer with a fine scale resolution and the possible influence of the quality of soil organic matter on shaping bacterial community structure.
PubMed ID
27796925 View in PubMed
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8 records – page 1 of 1.