Proteorhodopsins in Southern Ocean Bacteria

Federal Geographic Data Committee (FGDC) Metadata:

• Identification_Information
• Data_Quality_Information
• Spatial_Reference_Information
• Distribution_Information
• Metadata_Reference_Information

Identification_Information:

Citation:

Citation_Information:

Originator: Unknown

Publication_Date: Unknown

Title: Proteorhodopsins in Southern Ocean Bacteria

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 ths 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 Antractic 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: In Work

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 not yet publicly available.

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

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 focussed 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

Spatial_Reference_Information:

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

Metadata_Reference_Information:

Metadata_Date: 20100415

Metadata_Review_Date: 20121105

Metadata_Contact:

Contact_Information:

Contact_Person_Primary:

Contact_Person: DAVE 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