Spatial variability in polar soil ecosystems: An integrated study of genes, microbial biodiversity and landform evolution as a baseline for monitoring climate change
Entry ID:
ASAC_2952
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Summary
Abstract:
Metadata record for data from ASAC Project 2952. See the link below for public details on this project. By studying microbial within species adaptation, species distribution, ecosystem composition, structure and biogeochemical rates and functions, and relating these parameters to specific landforms at a range of spatial scales we aim to determine whether: Aspects of the Antarctic environment ... influence the scales and rates of biogeochemical processes and soil microbial population dynamics. and if so: Whether polar soil ecosystems are more sensitive to anthropogenic climate change than temperate regions.
Project objectives:
Do aspects of the Antarctic environment influence the scales and rates of biogeochemical processes and soil microbial population dynamics?
If so,
Are polar soil ecosystems more sensitive to anthropogenic climate change than temperate regions?
We aim to answer these two questions by studying within species adaptation, species distribution, ecosystem composition, structure and biogeochemical rates and functions. To do this, we will collect samples that relate to specific landforms at a range of spatial scales. We will then test the hypothesis that there are differences between sites (landforms), along gradients, between locations and between regions. This Antarctic data can then be compared to data from a much larger International Polar Year (IPY) latitudinal gradients project involving data from the Arctic (Canada and Norway) and temperate and tropical regions (Australia, Europe and low latitude Canada).
Taken from the 2008-2009 Progress Report:
Progress against objectives:
Soil samples have been collected from several sites in Antarctica and the Arctic in the past several years. These have been catalogued in a Sample Tracking Database developed by the EPiC group at the AAD. We have been concentrating on developing our methodology and devising a soil analysis system describing how each sample is subsampled and designating each subsample for particular chemical or genetic analysis. The method concentrates on making the most of the scarce amount of soil available due to the lack of soil development in most Antarctic coastal regions. We have reviewed the soil subsampling protocols and have sub-sampled the soils from the Robinsons Ridge and Main Powerhouse sites. Soil moisture content has been determined for these two sets of soil samples.
Herring Island, Mitchell Peninsula and Casey MPH (Bailey Peninsula) transects have already been subsampled and 10g samples processed at Macquarie University for the integron project. Duplicate DNA samples have been extracted from the Robinsons and Main Powerhouse soils. One set of DNA extractions is stored at Macquarie University, while the duplicate set is stored at the AAD. DNA extractions have been confirmed as PCR competent, further PCR analysis has confirmed the presence of integrons and gene cassettes in these samples. We have begun to use amplification of a hypervariable region of the 16S rDNA gene followed by high resolution electrophoretic analysis to generate an overview of bacterial diversity along all soil transects. All subsamples have been entered into the Sample Tracking Database.
Taken from the 2009-2010 Progress Report:
Soil samples have been collected that relate to specific landforms at a range of spatial scales from several sites in Antarctica and the Arctic.
Analysis of biogeochemical processes within these soils samples is being conducted. All 450 samples from the Antarctic transects have been analysed using the Mid-range infra red spectrometer, we also have total carbon and water content data for all these samples. The data for water content has been collected for the Norway transects (186 samples). The soil sub samples designated for different physical, chemical or genetic analysis have been distributed.
Duplicate DNA has been extracted for all Antarctic transects (Herring Island, Mitchell Peninsula, Browning Peninsula, Robinsons Ridge and Main Power House - Casey) and two Norwegian transects; Vestpynton Longyearbyen (Norway SV) and Spitsbergan Norway (Norway SS). This represents 2320 extractions in total, and the first steps towards investigating soil microbial population d ynamics. All DNA extractions have been confirmed as PCR competent.
Further work towards understanding if aspects of the Antarctic environment influence the scales and rates of biogeochemical processes and soil microbial population dynamics has been conducted through examining the presence of integrons and gene cassettes in the samples Integrons and gene cassettes have been confirmed by sequencing and interrogation of BLAST databases. The focus of these investigations has been the Main Power House (MPH) transect. We have cloned sequences that show homology with gene cassettes from Cape Denison, Antarctica (ornothogenic soil) and with Halifax Bay marine sediment that are hydrocarbon contaminated. We are concentrating on intense cloning and sequencing of samples from MPH. This information will be use to develop quick method to identify Integrons and gene cassettes in the rest of samples. We are also trying to identify the integron found in Antarctic soil samples and driving the capture and expression of adaptive genes. Our laboratory is designing primers to target and amplify the integron and the first gene cassette.
We have begun to use amplification of part of the hypervariable region of the 16S rDNA gene followed by high resolution electophretic analysis to generate an overview of bacterial diversity along all soil transects.
A sub sample of every soil sample collected has been logged in the -80oC soil library at AAD and these samples have been catalogued in the Sample Tracking Database managed by the EPiC group. 
Related URL
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Description:
Project home page
Description:
Citation reference for this metadata record and dataset.
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Geographic Coverage
(Click for Interactive Map)
Spatial coordinates
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N: -66.28
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S: -68.58
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E: 110.53
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W: 77.96
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Temporal Coverage
Start Date:
2007-09-30
Stop Date:
2012-03-31
Quality
Values provided in temporal and spatial coverage are approximate only.
Taken from the 2008-2009 Progress Report:
Field work:
Location and collection date of samples that have been collected are as follows:
Robinsons Ridge - 12/12/2005
Browning Peninsula - 15/12/2005
... Bailey Peninsula - 08/03/2006
Longyearbyen, Vestpynton (Norway) - 29/05/2006
Longyearbyen, Town (Norway) - 31/05/2006
Simpson Lake - DEW line site (Canada) - 18/07/2006
Ross Point - DEW line site (Canada) - 19/07/2006
TrueLove Station (Canada) - 29/07/2006
Herring Island - 27-28/11/2006
Mitchell Peninsula - 8/12/2006
We are planning to sample transects from Macquarie Island (2008/2009 season), to complete our sampling from the Casey Station region in the 2009/2010 season and to commence sampling in the region surrounding Davis Station (2010/2011). Sampling of the the tip site near Wilkes Station was not able to be completed in 2006/07 because the melt was insufficient to allow easy and safe access to the site. It is planned that this site should be sampled because it provides a second contaminated site for study in comparison to the Main Powerhouse Spill site (Bailey Peninsula). We will also attempt to complete the Casey Station (main powerhouse site) transects.
Laboratory activity/analysis:
Previous work has been dedicated to developing a soil analysis system and testing various soil analysis protocols. DNA has been extracted from the samples from Herring Island, Mitchell Peninsula, Robinsons Ridge and the Main Powerhouse site. PCR analysis has commenced on these samples and we have initial data confirming the presence of integrons in the samples. This level of analysis is expected at this early stage of the project. The work plan timeline for analysis is as follows:
2008-2009 - continued
Soils textural and chemical analysis of Casey unsorted soils
q-PCR and integron analysis of Casey unsorted soils (as part of AAS2746)
TRFLP analysis of Casey unsorted soils (as part of AAS2746)
q-PCR and integron analysis of Casey sorted soils
Establish respirometry and compare biogeochemical rates with relevant genes
2009-2010
Casey temporal field monitoring of biogeochemical processes and function genes
Soils textural and chemical analysis of Davis unsorted soils
q-PCR and integron analysis of Davis unsorted soils
TRFLP analysis of Davis unsorted soils
q-PCR and integron analysis of Davis unsorted soils
Establish respirometry and compare biogeochemical rates with relevant genes
2010-2011
Soils textural and chemical analysis of Davis sorted soils
q-PCR and integron analysis of Davis sorted soils
TRFLP analysis of Davis sorted soils
q-PCR and integron analysis of Davis sorted soils
Establish respirometry and compare biogeochemical rates with relevant genes
2011-2012
Finish any remaining sample analyses
Statistical analysis and publication of result
Taken from the 2009-2010 Progress Report:
Field work:
Location and collection date of samples that have been collected are as follows:
Robinsons Ridge - 12/12/2005
Browning Peninsula - 15/12/2005
Bailey Peninsula - 08/03/2006
Longyearbyen, Vestpynton (Norway) - 29/05/2006
Longyearbyen, Town (Norway) - 31/05/2006
Simpson Lake - DEW line site (Canada) - 18/07/2006
Ross Point - DEW line site (Canada) - 19/07/2006
TrueLove Station (Canada) - 29/07/2006
Herring Island - 27-28/11/2006
Mitchell Peninsula - 8/12/2006
We are planning to commence sampling in the region surrounding Davis Station (2010/2011). Sampling of the the tip site near Wilkes Station was not able to be completed in 2006/07 because the melt was insufficient to allow easy and safe access to the site. It is planned that this site should be sampled because it provides a second contaminated site for study in comparison to the Main Powerhouse Spill site (Bailey Peninsula). We will also attempt to complete the Casey Station (main powerhouse site) transects.
Laboratory activity/analysis:
Previous work has been dedicated to developing a soil analysis system and testing various soil analysis protocols.
DNA has been extracted from every soil sample (2320 extractions).
Gene cassette presence has been confirmed by sequencing and interrogation of BLAST databases.
We have cloned sequences that show homology with gene cassettes from Cape Denison, Antarctica (ornothogenic soil) and with Halifax Bay marine sediment that are hydrocarbon contaminated. We have been concentrating on intense cloning and sequencing of samples from MPH - which will be used to develop quick methods to ID the rest of the samples.
We have begun PCR amplification of a hypervariable region of the 16S rDNA gene followed by high resolution electophretic analysis to generate an overview of bacterial diversity along all soil transects.
We are investigating 454 sequencing (next generation sequencing) for the 16S hypervariable region.
Our laboratory is designing primers to target and amplify the integron and the first gene cassette. This will assist with identifying the integron itself.
All 450 samples from the Antarctic transects have been analysed on the Mid-range infra red spectrometer, we also have total carbon and water content data for all these samples.
The work plan timeline for analysis is as follows:
2010-2011
Conduct grainsize analysis
Compete mid-range infra red spectrometer analysis and total carbon and water content data for Norwegian samples
q-PCR and integron analysis of Casey unsorted soils (as part of AAS2746)
TRFLP analysis of Casey unsorted soils (as part of AAS2746)
q-PCR and integron analysis of Casey sorted soils
Establish respirometry and compare biogeochemical rates with relevant genes
Casey temporal field monitoring of biogeochemical processes and function genes
Soils textural and chemical analysis of Davis unsorted soils
q-PCR and integron analysis of Davis unsorted soils
TRFLP analysis of Davis unsorted soils
q-PCR and integron analysis of Davis unsorted soils
Establish respirometry and compare biogeochemical rates with relevant genes
2011-2012
Finish any remaining sample analyses
Statistical analysis and publication of result
Access Constraints
These data are not yet publicly available for download.
Use Constraints
This data set conforms to the PICCCBY Attribution License
(http://creativecommons.org/licenses/by/3.0/).
Please follow instructions listed in the citation reference at the provided URL when using these data.
This
"Spatial variability in polar soil ecosystems: An integrated study of genes, microbial biodiversity and landform evolution as a baseline for monitoring climate change" is licensed under a Creative Commons Attribution 3.0 Unported License.
Data Set Progress
IN WORK
Personnel
Role:
INVESTIGATOR
Phone:
+61 2 9850 8199
Fax:
+61 3 6226 2973
Email:
michael.gillings at mq.edu.au
Contact Address:
Macquarie University
Biological Sciences
City:
Macquarie University
Province or State:
NSW
Postal Code:
2109
Country:
Australia
Role:
TECHNICAL CONTACT
Phone:
+61 3 6232 3538
Fax:
+61 3 6232 3351
Email:
susan.ferguson at aad.gov.au
Contact Address:
Australian Antarctic Division
203 Channel Highway
City:
Kingston
Province or State:
Tasmania
Postal Code:
7050
Country:
Australia
Role:
DIF AUTHOR
Phone:
+61 3 6221 5038 (international)
Phone:
(03) 6221 5038 (within Australia)
Fax:
+61 3 6221 5050 (international)
Fax:
(03) 6221 5050 (within Australia)
Email:
Alicja.Mosbauer at oceans.gov.au
Contact Address:
National Oceans Office
GPO Box 2139
City:
Hobart
Province or State:
Tasmania
Postal Code:
7000
Country:
AUSTRALIA
Publications/References
Gillings, M.R., Holley, M.P. and Stokes, H.W. (2009), Evidence for dynamic exchange of qac gene cassettes between class 1 integrons and other integrons in freshwater biofilms., FEMS Microbiology Letters, 296, 282-288, doi:10.1111/j.1574-6968.2009.01646.x
Gillings, M.R., Xuejun, D., Hardwick, S.A., Holley, M.P. and Stokes, H.W. (2009), Gene cassettes encoding resistance to quaternary ammonium compounds in environmental samples: A potential role in the origin of clinical class 1 integrons., ISME Journal, 3, 209-215, doi:10.1038/ismej.2008.98
Creation and Review Dates
DIF Creation Date:
2008-02-19
Last DIF Revision Date:
2011-07-29
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