Download Jaume Bibiloni Isaksson

Microbial community structure and photoheterotrophic activity across
different Australian oceanic environments oceanic environments
Investigator
PhD Candidate Jaume Bibiloni Isaksson
Supervisors
Dr. Justin Seymour – C3 Plant Functional Biology and Climate Change Cluster, UTS
Dr. Mark Brown School of Biotechnology and Biomolecular Sciences, UNSW
D. J. Des Marais
Science, 8 September 2000
Classification of Phototrophic Organisms
http://www.seagrant.umn.edu/newsletter/2005/10/all_plankton_grea
t_and_small.html
Photoheterotrophic bacteria
1. Proteorhodopsin bacteria (PRB) contains proteorhodopsin
2. Aerobic anoxygenic phototrophic bacteria (AAnPB) contains
bacteriochlorophyll a
Proteorhodopsin
• Proteorhodopsin (PR) are retinal-binding integral membrane proteins
belonging to the rhodopsin superfamily
Fig. 2 Secondary structure of proteorhodopsin. Béjà et al. (2000)
Proteorhodopsin
• PR is a light-driven proton pump that may enhance ATP production by
heterotrophic bacteria that otherwise rely on organic material oxidation
for energy.
• A single amino acid substitution in PR protein sequence bacteria absorb
different wavelengths of light: 490 nm (blue) to 520 nm (green)
Fig. 3 Proteorhodopsin and possible relation to proton pumping (Walter et al., 2007)
Bacteriochlorophyll a
Aerobic Anoxygenic Photoheterotrophs
Why are photoheterotrophs important?
• PR genes have been identified in a wide variety of cultured and
uncultured bacterioplankton, such as α and γ-Proteobacteria,
Flavobacteria, Actinobacteria, and Archaea.
• PR in Pelagibacter ubique, a cultured representative, the most abundant
bacterial group inhabiting the upper ocean marine, clades SAR11
•
•
•
up to 70% of the bacteria in the Sargasso Sea
7 to 57% North Atlantic Ocean
13% of the bacteria in the Mediterranean Sea
Contain PR
• AAnPB have been identified in a wide variety of cultured and uncultured
bacterioplankton, such as α, β, and γ-Proteobacteria.
• Roseobacter group belong to AAnPB, a cultured representative, 1 in 5
bacteria cells inhabiting coastal waters.
• Also important in DMSP degradation (cleavage/demethylation). Results
liberation of climate-influencing dimethyl sulfide, thus key in marine
sulfur cycle.
• (not all Roseobacter synthesize Bchla).
•
•
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~ 10 to 20 in mesotrophic estuaries
positively correlate with Chla in variety of environments
up to 25% in hyperoligotrophic South Pacific Ocean
AAnPB
• Both AAnBP and PRB are incapable of photoautotrophy (do not have
enzyme RubisCO) and rely on heterotrophy of their cellular energetics
• Sunlight provide additional energy to cell, reducing the need for respiratory
oxidation of organic substrates
• The ability to use light energy seems to allow more economical utilization
of dissolved organic matter, thus photoheterotrophic bacteria may play a
unique role in the microbial carbon pump (MCP).
Objectives
i) Identify major bacteria and archaea groups including PR and Bchla groups
ii) Estimate the ratio of PR and Bchla genes expression and abundance to
bacterial populations
iii) Examine how the abundance, diversity and activity of different PR and
Bchla types varies temporally in different oceanographic coastal region, which
are suffering from the impacts of climate change
iv) Perform laboratory growth experiments to test the dynamics of
photoheterotrophy under different light and nutrient condition
Hypotheses
H1: PR and AAnBP diversity, abundance and activity will vary throughout
the sample period/location, since significant physicochemical changes in
seawater will provide more suitable conditions for different types of bacteria
H2: PR-bearing bacteria abundance will become more abundant during
summer (Austral) period, since PR bearing bacteria may help to provide
energetic and physiological advantages under in more oligotrophic
conditions
Experimental procedures
Sampling and environmental parameters
Monthly samples (surface samples)
•Port Hacking Mooring (IMOS platform) (2011-2012) Temporally.
•Maria Island, Port Hacking, Stradbroke Mooring stations (2012)
Spatially/temporally
•Data is available via the IMOS portal http://imos.aodn.org.au/webportal/
Future sampling (different depths)
•North Australia research voyage (July 2013) Spatially
• East Australian current research voyage (April 2014) Spatially
•South Australia research voyage (Sept 2014) Spatially
•Environmental data will be collected in situ.
Broome
Brisbane
Stradbroke
Freemantle
Sydney
Port Hacking
Tasmania
Maria Island
Experimental procedures
Molecular experiments
• DNA/RNA extraction (Standards Kit extraction)
• PCR amplification of 16S rRNA, PR and pufM genes
• 454/Illumina pyrosequencing of 16S rRNA, PR and pufM genes to
assess diversity
• Determination of ratios of 16S rRNA (all bacteria, SAR11 clade)
and PR (SAR11 clade, Flavobacteria) and pufM gene
abundance/expression via real-time quantitative PCR
• Screen for PR and Bchla genes in seawater isolates
Data Analysis
•454/Illumina pyrosequencing data with QIIME
•Relationship between abundance, diversity and physicochemical
parameters using PERMANOVA in PRIMER+
•PR/pufM sequence compilations and analysis using ARB software
•Network analysis
Two major questions to be answer in this project
• How do Australian marine microbial communities (i.e.
photoheterotrophs) and their biogeochemical function vary in
space and time?
• Will shifting ocean circulation patterns alter microbial
community structure and function in ways that will have
potential feed-back effects on ecosystem stability?
People in our Lab
Dr Justin Seymour - Leader and supervisor
Dr Mark Brown – Co-supervisor (UNSW)
Dr Tom Jeffries - Post-doc
Lauren Messer - PhD student
Project is funding by an ARC grant from Australia government