Data_Sheet_2_Antarctic Relic Microbial Mat Community Revealed by Metagenomics and Metatranscriptomics.PDF
Buried upslope from the modern lakes in the McMurdo Dry Valleys of Antarctica are relict lake deposits embedded in valley walls. Within these relict deposits, ancient microbial mats, or paleomats, have been preserved under extremely arid and cold conditions since the receding of larger paleolakes th...
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ftfrontimediafig:oai:figshare.com:article/7616804 2023-05-15T13:36:41+02:00 Data_Sheet_2_Antarctic Relic Microbial Mat Community Revealed by Metagenomics and Metatranscriptomics.PDF Elena Zaikova David S. Goerlitz Scott W. Tighe Nicole Y. Wagner Yu Bai Brenda L. Hall Julie G. Bevilacqua Margaret M. Weng Maya D. Samuels-Fair Sarah Stewart Johnson 2019-01-23T04:25:20Z https://doi.org/10.3389/fevo.2019.00001.s002 https://figshare.com/articles/Data_Sheet_2_Antarctic_Relic_Microbial_Mat_Community_Revealed_by_Metagenomics_and_Metatranscriptomics_PDF/7616804 unknown doi:10.3389/fevo.2019.00001.s002 https://figshare.com/articles/Data_Sheet_2_Antarctic_Relic_Microbial_Mat_Community_Revealed_by_Metagenomics_and_Metatranscriptomics_PDF/7616804 CC BY 4.0 CC-BY Evolutionary Biology Ecology Invasive Species Ecology Landscape Ecology Conservation and Biodiversity Behavioural Ecology Community Ecology (excl. Invasive Species Ecology) Ecological Physiology Freshwater Ecology Marine and Estuarine Ecology (incl. Marine Ichthyology) Population Ecology Terrestrial Ecology Antarctica cell survival DNA repair dormancy extremophiles metagenomics stress response transcriptome Dataset 2019 ftfrontimediafig https://doi.org/10.3389/fevo.2019.00001.s002 2019-01-23T23:58:05Z Buried upslope from the modern lakes in the McMurdo Dry Valleys of Antarctica are relict lake deposits embedded in valley walls. Within these relict deposits, ancient microbial mats, or paleomats, have been preserved under extremely arid and cold conditions since the receding of larger paleolakes thousands of years ago, and now serve as a sheltered niche for microbes in a highly challenging oligotrophic environment. To explore whether paleomats could be repositories for ancient lake cells or were later colonized by soil microbes, determine what types of metabolic pathways might be present, analyze potential gene expression, and explore whether the cells are in a vegetative or dormant state, we collected paleomat samples from ancient lake facies on the northern slopes of Lake Vanda in Wright Valley in December 2016. Using a gentle lysis technique optimized to preserve longer molecules, combined with a polyenzymatic treatment to maximize yields from different cell types, we isolated high-molecular weight DNA and RNA from ancient paleomat samples. Community composition analysis suggests that the paleomat community may retain a population of indigenous mat cells that may flourish once more favorable conditions are met. In addition to harboring a diverse microbial community, paleomats appear to host heterotrophs in surrounding soils utilizing the deposits as a carbon source. Whole genome long-read PacBio sequencing of native DNA and Illumina metagenomic sequencing of size-sorted DNA (>2,500 nt) indicated possible cell viability, with mat community composed of bacterial taxa. Metagenome assemblies identified genes with predicted roles in nitrogen cycling and complex carbohydrate degradation, and we identified key metabolic pathways such as stress response, DNA repair, and sporulation. Metatranscriptomic data revealed that the most abundant transcripts code for products involved in genetic information processing pathways, particularly translation, DNA replication, and DNA repair. Our results lend new insight into ... Dataset Antarc* Antarctica McMurdo Dry Valleys Frontiers: Figshare McMurdo Dry Valleys Vanda ENVELOPE(161.550,161.550,-77.533,-77.533) Wright Valley ENVELOPE(161.833,161.833,-77.517,-77.517) Lake Vanda ENVELOPE(161.600,161.600,-77.517,-77.517) Relict Lake ENVELOPE(-60.588,-60.588,-62.942,-62.942) |
institution |
Open Polar |
collection |
Frontiers: Figshare |
op_collection_id |
ftfrontimediafig |
language |
unknown |
topic |
Evolutionary Biology Ecology Invasive Species Ecology Landscape Ecology Conservation and Biodiversity Behavioural Ecology Community Ecology (excl. Invasive Species Ecology) Ecological Physiology Freshwater Ecology Marine and Estuarine Ecology (incl. Marine Ichthyology) Population Ecology Terrestrial Ecology Antarctica cell survival DNA repair dormancy extremophiles metagenomics stress response transcriptome |
spellingShingle |
Evolutionary Biology Ecology Invasive Species Ecology Landscape Ecology Conservation and Biodiversity Behavioural Ecology Community Ecology (excl. Invasive Species Ecology) Ecological Physiology Freshwater Ecology Marine and Estuarine Ecology (incl. Marine Ichthyology) Population Ecology Terrestrial Ecology Antarctica cell survival DNA repair dormancy extremophiles metagenomics stress response transcriptome Elena Zaikova David S. Goerlitz Scott W. Tighe Nicole Y. Wagner Yu Bai Brenda L. Hall Julie G. Bevilacqua Margaret M. Weng Maya D. Samuels-Fair Sarah Stewart Johnson Data_Sheet_2_Antarctic Relic Microbial Mat Community Revealed by Metagenomics and Metatranscriptomics.PDF |
topic_facet |
Evolutionary Biology Ecology Invasive Species Ecology Landscape Ecology Conservation and Biodiversity Behavioural Ecology Community Ecology (excl. Invasive Species Ecology) Ecological Physiology Freshwater Ecology Marine and Estuarine Ecology (incl. Marine Ichthyology) Population Ecology Terrestrial Ecology Antarctica cell survival DNA repair dormancy extremophiles metagenomics stress response transcriptome |
description |
Buried upslope from the modern lakes in the McMurdo Dry Valleys of Antarctica are relict lake deposits embedded in valley walls. Within these relict deposits, ancient microbial mats, or paleomats, have been preserved under extremely arid and cold conditions since the receding of larger paleolakes thousands of years ago, and now serve as a sheltered niche for microbes in a highly challenging oligotrophic environment. To explore whether paleomats could be repositories for ancient lake cells or were later colonized by soil microbes, determine what types of metabolic pathways might be present, analyze potential gene expression, and explore whether the cells are in a vegetative or dormant state, we collected paleomat samples from ancient lake facies on the northern slopes of Lake Vanda in Wright Valley in December 2016. Using a gentle lysis technique optimized to preserve longer molecules, combined with a polyenzymatic treatment to maximize yields from different cell types, we isolated high-molecular weight DNA and RNA from ancient paleomat samples. Community composition analysis suggests that the paleomat community may retain a population of indigenous mat cells that may flourish once more favorable conditions are met. In addition to harboring a diverse microbial community, paleomats appear to host heterotrophs in surrounding soils utilizing the deposits as a carbon source. Whole genome long-read PacBio sequencing of native DNA and Illumina metagenomic sequencing of size-sorted DNA (>2,500 nt) indicated possible cell viability, with mat community composed of bacterial taxa. Metagenome assemblies identified genes with predicted roles in nitrogen cycling and complex carbohydrate degradation, and we identified key metabolic pathways such as stress response, DNA repair, and sporulation. Metatranscriptomic data revealed that the most abundant transcripts code for products involved in genetic information processing pathways, particularly translation, DNA replication, and DNA repair. Our results lend new insight into ... |
format |
Dataset |
author |
Elena Zaikova David S. Goerlitz Scott W. Tighe Nicole Y. Wagner Yu Bai Brenda L. Hall Julie G. Bevilacqua Margaret M. Weng Maya D. Samuels-Fair Sarah Stewart Johnson |
author_facet |
Elena Zaikova David S. Goerlitz Scott W. Tighe Nicole Y. Wagner Yu Bai Brenda L. Hall Julie G. Bevilacqua Margaret M. Weng Maya D. Samuels-Fair Sarah Stewart Johnson |
author_sort |
Elena Zaikova |
title |
Data_Sheet_2_Antarctic Relic Microbial Mat Community Revealed by Metagenomics and Metatranscriptomics.PDF |
title_short |
Data_Sheet_2_Antarctic Relic Microbial Mat Community Revealed by Metagenomics and Metatranscriptomics.PDF |
title_full |
Data_Sheet_2_Antarctic Relic Microbial Mat Community Revealed by Metagenomics and Metatranscriptomics.PDF |
title_fullStr |
Data_Sheet_2_Antarctic Relic Microbial Mat Community Revealed by Metagenomics and Metatranscriptomics.PDF |
title_full_unstemmed |
Data_Sheet_2_Antarctic Relic Microbial Mat Community Revealed by Metagenomics and Metatranscriptomics.PDF |
title_sort |
data_sheet_2_antarctic relic microbial mat community revealed by metagenomics and metatranscriptomics.pdf |
publishDate |
2019 |
url |
https://doi.org/10.3389/fevo.2019.00001.s002 https://figshare.com/articles/Data_Sheet_2_Antarctic_Relic_Microbial_Mat_Community_Revealed_by_Metagenomics_and_Metatranscriptomics_PDF/7616804 |
long_lat |
ENVELOPE(161.550,161.550,-77.533,-77.533) ENVELOPE(161.833,161.833,-77.517,-77.517) ENVELOPE(161.600,161.600,-77.517,-77.517) ENVELOPE(-60.588,-60.588,-62.942,-62.942) |
geographic |
McMurdo Dry Valleys Vanda Wright Valley Lake Vanda Relict Lake |
geographic_facet |
McMurdo Dry Valleys Vanda Wright Valley Lake Vanda Relict Lake |
genre |
Antarc* Antarctica McMurdo Dry Valleys |
genre_facet |
Antarc* Antarctica McMurdo Dry Valleys |
op_relation |
doi:10.3389/fevo.2019.00001.s002 https://figshare.com/articles/Data_Sheet_2_Antarctic_Relic_Microbial_Mat_Community_Revealed_by_Metagenomics_and_Metatranscriptomics_PDF/7616804 |
op_rights |
CC BY 4.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.3389/fevo.2019.00001.s002 |
_version_ |
1766082578263048192 |