Identifying changes in the active, dead, and dormant microbial community structure across a chronosequence of ancient Alaskan permafrost
Permafrost— perennially frozen soil— hosts a diversity of microorganisms. Permafrost microbial communities survive and reproduce for millennia despite extreme conditions such as water stress, subzero temperatures, high salinity, and low nutrient availability. Most studies targeting permafrost microb...
Main Author: | |
---|---|
Other Authors: | , , |
Format: | Master Thesis |
Language: | English |
Published: |
California State University, Northridge
2018
|
Subjects: | |
Online Access: | http://hdl.handle.net/10211.3/198922 |
id |
ftcalifstateuniv:oai:scholarworks:1g05ff26r |
---|---|
record_format |
openpolar |
spelling |
ftcalifstateuniv:oai:scholarworks:1g05ff26r 2024-09-30T14:36:23+00:00 Identifying changes in the active, dead, and dormant microbial community structure across a chronosequence of ancient Alaskan permafrost Burkert, Alexander Mackelprang, Rachel Cooper, Kerry K Flores, Gilberto E 1/2/2018 http://hdl.handle.net/10211.3/198922 English eng California State University, Northridge Biology http://hdl.handle.net/10211.3/198922 microbiology exobiology permafrost dormant 16S rRNA gene Dissertations Academic -- CSUN -- Biology endospore Late Pleistocene Masters Thesis 2018 ftcalifstateuniv 2024-09-10T17:06:19Z Permafrost— perennially frozen soil— hosts a diversity of microorganisms. Permafrost microbial communities survive and reproduce for millennia despite extreme conditions such as water stress, subzero temperatures, high salinity, and low nutrient availability. Most studies targeting permafrost microbial communities use DNA-based methods such as metagenomic and 16S rRNA gene sequencing. However, constant subzero temperatures may preserve DNA from dead organisms for extended periods of time making it difficult to distinguish between active, dead, and dormant cells. This is particularly concerning in increasingly ancient permafrost because dormancy may be a survival strategy and DNA from dead cells may accumulate over time. To circumvent this hurdle, we applied live/dead differential staining coupled with microscopy, endospore enrichment, and selective depletion of exogenous DNA and DNA from dead cells to permafrost microbial communities across a Pleistocene permafrost chronosequence (19 kyr, 27 kyr, and 33 kyr). Cell counts and analysis of 16S rRNA gene amplicons from live, dead, and dormant cells revealed how communities differ between these pools and how they change over geologic time. We found clear evidence that cells capable of forming endospores are not necessarily dormant and that the propensity to form spores differed between taxa. Specifically, Bacilli are more likely to form endospores in response to long-term stressors associated with life in permafrost than members of Clostridia, which are more likely to persist as vegetative cells over geologic timescales. We also found that exogenous DNA preserved within permafrost does not bias DNA sequencing results, since its removal did not significantly alter microbial community composition. Lastly, the results of our cell enumeration confirmed a previous study that permafrost age and percent ice content acted as drivers of microbial cell abundance and diversity. Total cell counts and alpha diversity decreased between our youngest and oldest samples, while the ... Master Thesis Ice permafrost Scholarworks from California State University |
institution |
Open Polar |
collection |
Scholarworks from California State University |
op_collection_id |
ftcalifstateuniv |
language |
English |
topic |
microbiology exobiology permafrost dormant 16S rRNA gene Dissertations Academic -- CSUN -- Biology endospore Late Pleistocene |
spellingShingle |
microbiology exobiology permafrost dormant 16S rRNA gene Dissertations Academic -- CSUN -- Biology endospore Late Pleistocene Burkert, Alexander Identifying changes in the active, dead, and dormant microbial community structure across a chronosequence of ancient Alaskan permafrost |
topic_facet |
microbiology exobiology permafrost dormant 16S rRNA gene Dissertations Academic -- CSUN -- Biology endospore Late Pleistocene |
description |
Permafrost— perennially frozen soil— hosts a diversity of microorganisms. Permafrost microbial communities survive and reproduce for millennia despite extreme conditions such as water stress, subzero temperatures, high salinity, and low nutrient availability. Most studies targeting permafrost microbial communities use DNA-based methods such as metagenomic and 16S rRNA gene sequencing. However, constant subzero temperatures may preserve DNA from dead organisms for extended periods of time making it difficult to distinguish between active, dead, and dormant cells. This is particularly concerning in increasingly ancient permafrost because dormancy may be a survival strategy and DNA from dead cells may accumulate over time. To circumvent this hurdle, we applied live/dead differential staining coupled with microscopy, endospore enrichment, and selective depletion of exogenous DNA and DNA from dead cells to permafrost microbial communities across a Pleistocene permafrost chronosequence (19 kyr, 27 kyr, and 33 kyr). Cell counts and analysis of 16S rRNA gene amplicons from live, dead, and dormant cells revealed how communities differ between these pools and how they change over geologic time. We found clear evidence that cells capable of forming endospores are not necessarily dormant and that the propensity to form spores differed between taxa. Specifically, Bacilli are more likely to form endospores in response to long-term stressors associated with life in permafrost than members of Clostridia, which are more likely to persist as vegetative cells over geologic timescales. We also found that exogenous DNA preserved within permafrost does not bias DNA sequencing results, since its removal did not significantly alter microbial community composition. Lastly, the results of our cell enumeration confirmed a previous study that permafrost age and percent ice content acted as drivers of microbial cell abundance and diversity. Total cell counts and alpha diversity decreased between our youngest and oldest samples, while the ... |
author2 |
Mackelprang, Rachel Cooper, Kerry K Flores, Gilberto E |
format |
Master Thesis |
author |
Burkert, Alexander |
author_facet |
Burkert, Alexander |
author_sort |
Burkert, Alexander |
title |
Identifying changes in the active, dead, and dormant microbial community structure across a chronosequence of ancient Alaskan permafrost |
title_short |
Identifying changes in the active, dead, and dormant microbial community structure across a chronosequence of ancient Alaskan permafrost |
title_full |
Identifying changes in the active, dead, and dormant microbial community structure across a chronosequence of ancient Alaskan permafrost |
title_fullStr |
Identifying changes in the active, dead, and dormant microbial community structure across a chronosequence of ancient Alaskan permafrost |
title_full_unstemmed |
Identifying changes in the active, dead, and dormant microbial community structure across a chronosequence of ancient Alaskan permafrost |
title_sort |
identifying changes in the active, dead, and dormant microbial community structure across a chronosequence of ancient alaskan permafrost |
publisher |
California State University, Northridge |
publishDate |
2018 |
url |
http://hdl.handle.net/10211.3/198922 |
genre |
Ice permafrost |
genre_facet |
Ice permafrost |
op_relation |
http://hdl.handle.net/10211.3/198922 |
_version_ |
1811639450325745664 |