TemperateReefBase Geonetwork Catalogue
Proteorhodopsins in Southern Ocean Bacteria
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
Simple
Identification info
- Alternate title
- Proteorhodopsins in Southern Ocean Bacteria
- Date (Publication)
- 2014-10-09
- Edition
- 1
- Citation identifier
-
Dataset DOI
- Title
- Information and documentation - Digital object identifier system
- Date (Publication)
- 2012-04-23
- Citation identifier
- ISO 26324:2012
- Citation identifier
- doi:10.4225/15/543605EA9F101
Originator
Publisher
Principal investigator
Collaborator
- Name
- CAASM Metadata
- Status
- Completed
Custodian
- Topic category
-
- Biota
- Oceans
Extent
))
Extent
- Description
- Temporal Coverage
Temporal extent
- TimePeriod
- 2009-09-30 2012-03-31
- Title
- Utility of gel-free, label-free shotgun proteomics approaches to investigate microorganisms
- Date (Publication)
- 2011
- Citation identifier
- 90
- Citation identifier
- DOI 10.1007/s00253-011-3172-z
Author
- Name
- Appl Microbiol Biotechnol
- Page
- 407-416
- NASA/GCMD Earth Science Keywords
-
- EARTH SCIENCE > OCEANS > OCEAN CHEMISTRY > NUTRIENTS
- EARTH SCIENCE > BIOLOGICAL CLASSIFICATION > BACTERIA/ARCHAEA
- Keywords
-
- Bacteria
- proteorhodopsin
- PCR
- NASA/GCMD Earth Science Keywords
-
- SHIPS
- LABORATORY
- NASA/GCMD Earth Science Keywords
-
- AMD/AU
- CEOS
- AMD
- NASA/GCMD Earth Science Keywords
-
- OCEAN > SOUTHERN OCEAN
- GEOGRAPHIC REGION > POLAR
Resource constraints
- Use limitation
- This metadata record is publicly available.
Resource constraints
- Access constraints
- licence
- Other constraints
- These data are publicly available for download from the provided URL.
Resource constraints
- File type
- Portable Network Graphic
- Title
- Attribution 4.0 International (CC BY 4.0)
- Website
-
https://creativecommons.org/licenses/by/4.0/legalcode
Legal code for Creative Commons by Attribution 4.0 International license
- Use constraints
- licence
- Other constraints
- This data set conforms to the CCBY Attribution License (http://creativecommons.org/licenses/by/4.0/). 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.
- Language
- English
- Character encoding
- UTF8
Distribution Information
Distributor
Distributor
Distributor
- Fees
- Free
- Planned available datetime
- 2014-10-09T00:00:00
- Units of distribution
- MB
- Transfer size
- 2.8
- Distribution format
-
- Excel, PDF
- OnLine resource
-
GET DATA
Download point for the data
- OnLine resource
-
PROJECT HOME PAGE
Public information for AAS project 3127
- OnLine resource
-
VIEW RELATED INFORMATION
Citation reference for this metadata record and dataset
Resource lineage
- Statement
- 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.
- Hierarchy level
- Dataset
- Maintenance and update frequency
- As needed
- Maintenance note
- 2010-04-15 - record created by Dave Connell from a progress report submitted by John Bowman. 2011-12-19 - record updated by Dave Connell after data were provided by John Bowman. 2012-11-05 - record updated by Dave Connell to correct dodgy character in publications. 2014-10-09 - record updated by Dave Connell to publicly release the data.
Metadata
- Metadata identifier
- string/AAS_3127
- Language
- English
- Character encoding
- UTF8
Author
Sponsor
Owner
Type of resource
- Resource scope
- Dataset
Alternative metadata reference
- Title
- gov.nasa.gsfc.gcmd
- Citation identifier
- 17c96d3f-b99c-4369-a6d9-d0da78885bab
Alternative metadata reference
- Title
- gov.nasa.gsfc.gcmd
- Date (Last Revision)
- 2015-11-30T03:58:30
Identifier
- Description
- metadata.extraction_date
Alternative metadata reference
- Title
- gov.nasa.gsfc.gcmd
- Citation identifier
- 8.6
- Metadata linkage
-
http://data.aad.gov.au/metadata/records/AAS_3127
Point of truth for the metadata record
- Date info (Creation)
- 2010-04-15T00:00:00
- Date info (Last Update)
- 2017-04-26
Metadata standard
- Title
- ISO 19115-3
- Edition
- 2014
- Other citation details
- Version 1
- Title
- DIF to ISO 19115-1 Profile
Overviews
Spatial extent
Provided by
