Proteorhodopsins in Southern Ocean Bacteria

Federal Geographic Data Committee (FGDC) Metadata:


Identification_Information:
Citation:
Citation_Information:
Originator: Bowman, J.
Publication_Date: 20141009
Title: Proteorhodopsins in Southern Ocean Bacteria
Edition:
Geospatial_Data_Presentation_Form:
Series_Information:
Series_Name: CAASM Metadata
Issue_Identification:
Publication_Information:
Publication_Place:
Publisher: Australian Antarctic Data Centre
Other_Citation_Details:
Online_Linkage: https://data.aad.gov.au/aadc/metadata/metadata_redirect.cfm?md=/AMD/AU/AAS_3127
Description:
Abstract:
Metadata record for data from AAS Project 3127 See the link below for public details on this project. Bacteria in marine environments have been found to be able to partially support growth by using light to generate energy in a non-photosynthetic process. This is possible due to a special protein called proteorhodopsin. It is hypothesised that formation of proteorhodopsin has evolved to cope with extreme lack of nutrients. The goal is to determine the significance of proteorhodopsins in the productivity of Southern Ocean microbial communities. This includes determination of proteorhodopsin distribution, presence in seawater and sea-ice samples using molecular techniques, and determination of how important environmental factors (light, nutrient availability, temperature) may drive its synthesis and activity. Taken from the 2009-2010 Progress Report Project objectives: 1. Determine incidence of proteorhodopsins in Southern Ocean water and sea-ice derived bacteria (Year 1) and other Antarctic aquatic environments (Year 2 and 3). 2. Determine whether proteorhodopsins contribute to food web energy budgets. 3. Determine how proteorhodopsin contributions are influenced by physicochemical features of the environment including light availability, temperature and nutrients. Progress against objectives: Proteorhodopsin is a light harvesting membrane protein that has been found recently to occur in 30-70% of marine bacterial cells. The role of this protein is uncertain but believed to be highly important in energy and nutrient budgets in food webs as it is capable of generating a proton gradient. Amongst a cultured set of Antarctic bacteria we have discovered many PR-producing species. These include many Antarctic lake species. Research is ongoing to determine affect of light on the physiology of these bacteria in particular the genome sequenced species Psychroflexus torquis, an extremely cold-adapted resident of Antarctic sea-ice. 1. Completed screen of Antarctic bacterial collection for proteorhodopsin (PR) genes using PCR-based approaches 2. Proteomic-based analysis of PR-bearing sea-ice species Psychroflexus torquis is currently ongoing 3. Light/dark defined growth-based experiments determining conditions leading to biomass enhancement are ongoing
Purpose:
Not Available
Supplemental_Information:
REFERENCE: Bianca Porteus, Chawalit Kocharunchitt, Rolf E. Nilsson,Tom Ross and John P. Bowman 2011 Utility of gel-free, label-free shotgun proteomics approaches to investigate microorganisms Appl Microbiol Biotechnol 90 407-416 DOI 10.1007/s00253-011-3172-z
Time_Period_of_Content:
Time_Period_Information:
Range_of_Dates/Times:
Beginning_Date: 20090930
Ending_Date: 20120331
Currentness_Reference:Unknown
Status:
Progress: Complete
Maintenance_and_Update_Frequency: As needed
Spatial_Domain:
Description_of_Geographic_Extent:
Bounding_Coordinates:
West_Bounding_Coordinate: 60.0
East_Bounding_Coordinate: 160.0
North_Bounding_Coordinate: -54.0
South_Bounding_Coordinate: -67.0
Keywords:
Theme:
Theme_Keyword_Thesaurus: GCMD SCIENCE PARAMETERS
Theme_Keyword_Thesaurus: GCMD PLATFORM
Theme_Keyword_Thesaurus: ANCILLARY KEYWORDS
Theme_Keyword_Thesaurus: ISO TOPIC CATEGORY
Theme_Keyword_Thesaurus: DATA SET LANGUAGE
Theme_Keyword: EARTH SCIENCE > OCEANS > OCEAN CHEMISTRY > NUTRIENTS
Theme_Keyword: EARTH SCIENCE > BIOLOGICAL CLASSIFICATION > BACTERIA/ARCHAEA
Theme_Keyword: SHIPS
Theme_Keyword: LABORATORY
Theme_Keyword: Bacteria
Theme_Keyword: Proteorhodopsin
Theme_Keyword: Pcr
Theme_Keyword: BIOTA
Theme_Keyword: OCEANS
Theme_Keyword: ENGLISH
Place:
Place_Keyword_Thesaurus: GCMD
Place_Keyword: OCEAN > SOUTHERN OCEAN
Place_Keyword: GEOGRAPHIC REGION > POLAR
Access_Constraints: These data are publicly available for download from the provided URL.
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 provided at http://data.aad.gov.au/aadc/metadata/citation.cfm?entry_id=AAS_3127 when using these data.
Point_of_Contact:
Contact_Information:
Contact_Person_Primary:
Contact_Person: JOHN BOWMAN
Contact_Position: INVESTIGATOR
Contact_Position: TECHNICAL CONTACT
Contact_Address:
Address_Type: Mailing and Physical Address
Address: School of Agricultural Science
Address: University of Tasmania
Address: Private Bag 54
City: Hobart
State_or_Province: Tasmania
Postal_Code: 7001
Country: Australia
Contact_Voice_Telephone: +61 3 6226 6380
Contact_Facsimile_Telephone: +61 3 6226 2642
Contact_Electronic_Mail_Address: john.bowman@utas.edu.au
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Data_Quality_Information:
Attribute_Accuracy:
Attribute_Accuracy_Report:
Values provided in temporal and spatial coverage are approximate only. Taken from the 2009-2010 Progress Report: Variations to work plan or objectives: No field work to collect samples was able to be performed, all activities to date have been laboratory based. 1. PCR analysis of PR in 65 Antarctic bacterial strains (obtained from previous AAD-supported activity) by marine science student Jaume Bibloni. Results to date indicate extensive presence of PR genes in Antarctic lake bacteria including undescribed species. PR presence in sea-ice bacteria was more restricted. Obvious strain-dependency occurs in PR distribution. Sequence data obtained for most PR positive strains. Limitations in the analysis include the need to use highly degenerate primer oligonucleotides (due to high level of variability PR sequences at the nucleotide level). Work is ongoing to retest several strains giving equivocal results in the PCR asays. 2. Proteomics analysis has been initiated (Clare Rutherford Honours student) for analysis of response of Psychroflexus torquis to light and dark conditions grown at 2 C (grown in a modified marine medium). The proteomics involves shotgun analysis using a 2-dimensional HPLC separation of trypsinised protein extracts (recovered using the QProteome proteoin extraction kit and extraction with membrane protein surfactant C7BzO, Sigma-Aldrich) coupled to nano-flow LTQ-Orbitrap mass spectrometry. This work is done in collaboration with Dr Edwin Lowe, Central Sciences Laboratory. The goal of this experiment is to determine whether the presence of light induces PR translation (abundance) and it cognate carotenoid hydroxylase as well as other changes to the proteome. Based on recent experiments on other bacteria (E. coli and L. monocytogenes) as much as 50% of the proteome can be recovered using this approach (termed "MudPit" - multidimensional protein information technology). This will be first time such ana analysis has been performed on a marine bacterial species. 3. Growth experiments have been initiated by Clare Rutherford and Jaume Bibloni to determine conditions inducing growth rates and yields in the presence of light for the PR-bearing species P. torquis. The conditions being focused on are nutritional. The experiments involve utilisation of 96-well trays and spectrophotometry using a plate reader. Initial results suggest that light induces growth when certain critical nutrients are low, potentially either iron and/or certain vitamins (cobalamin), suggesting that PR may aid in generating a proton gradient helping drive enhanced nutrient uptake.
Logical_Consistency_Report:
Not Available
Completeness_Report:
Not Available
Lineage:
Process_Step:
Process_Description:
Not Available
Process_Date: Unknown
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Spatial_Reference_Information:
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Distribution_Information:
Distributor:
Contact_Information:
Contact_Organization_Primary:
Contact_Organization: AU/AADC > Australian Antarctic Data Centre, Australia
Contact_Person: DATA OFFICER AADC
Contact_Position: DATA CENTER CONTACT
Contact_Address:
Address_Type: Mailing and Physical Address
Address: Australian Antarctic Division
Address: 203 Channel Highway
City: Kingston
State_or_Province: Tasmania
Postal_Code: 7050
Country: Australia
Contact_Voice_Telephone: +61 3 6232 3244
Contact_Facsimile_Telephone: +61 3 6232 3351
Contact_Electronic_Mail_Address: metadata@aad.gov.au
Resource_Description: AAS_3127
Distribution_Liability:
Not Available
Standard_Order_Process:
Digital_Form:
Digital_Transfer_Information:
Format_Name: Excel, PDF
Transfer_Size: 2.8 MB
Digital_Transfer_Option:
Online_Option:
Computer_Contact_Information:
Network_Address:
Network_Resource_Name:
http://data.aad.gov.au
Access_Instructions:
DATA CENTER URL
Digital_Transfer_Option:
Online_Option:
Computer_Contact_Information:
Network_Address:
Network_Resource_Name:
http://data.aad.gov.au/aadc/portal/download_file.c...
Access_Instructions:
Download point for the data
Digital_Transfer_Option:
Online_Option:
Computer_Contact_Information:
Network_Address:
Network_Resource_Name:
https://secure3.aad.gov.au/proms/public/projects/r...
Access_Instructions:
Public information for AAS project 3127
Digital_Transfer_Option:
Online_Option:
Computer_Contact_Information:
Network_Address:
Network_Resource_Name:
http://data.aad.gov.au/aadc/metadata/citation.cfm?...
Access_Instructions:
Citation reference for this metadata record and dataset
Fees: Free
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Metadata_Reference_Information:
Metadata_Date: 20100415
Metadata_Review_Date: 20141009
Metadata_Contact:
Contact_Information:
Contact_Person_Primary:
Contact_Person: DAVE J. CONNELL
Contact_Position: DIF AUTHOR
Contact_Address:
Address_Type: Mailing and Physical Address
Address: Australian Antarctic Division
Address: 203 Channel Highway
City: Kingston
State_or_Province: Tasmania
Postal_Code: 7050
Country: Australia
Contact_Voice_Telephone: +61 3 6232 3244
Contact_Facsimile_Telephone: +61 3 6232 3351
Contact_Electronic_Mail_Address: dave.connell@aad.gov.au
Metadata_Standard_Name: FGDC Content Standards for Digital Geospatial Metadata
Metadata_Standard_Version: FGDC-STD-001-1998
Metadata_Time_Convention: local time
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