Australian microbial and environmental genomics
1. Funding, projects and collaborations
Table 1. Australian-lead genome projects of environmental microbes
| Organism | Genome size | Status | Primary Funding Source |
Funding amount (estimate) |
Sequencing Collaborator |
| Methanogenium frigidum | 3 Mb | 90% complete | Moore Found. | $60 000 | Venter |
| Methanococcoides burtonii | 2.5 | Complete | DoE | $150 000 | JGI |
| Halorubrum lacusprofundi | 4.3 | 99% complete | DoE | $186 000 | JGI |
| Sphingopyxis alaskensis | 3.4 Mb | Complete | DoE | $168 000 | JGI |
| Photobacterium angustum | 5 Mb | 99% complete | Moore Found. | $100 000 | Venter |
| Pseudoaltermonas tunicata | 4.9 Mb | 99% complete | Moore Found. | $98 000 | Venter |
| Roseobacter gallaeciensis | 4 Mb | 99% complete | Moore Found. | $80 000 | Venter |
| Ruegeria R11 | 5 Mb | 90% complete | Moore Found. | $100 000 | Venter |
| Parvibaculum lavamentivorans | 5.5 Mb | 90% complete | DoE | $210 000 | JGI |
| Comamonas testosteroni | 5.5 Mb | 90% complete | DoE | $210 000 | JGI |
| Delftia acidovorans | 5.5 Mb | 90% complete | DoE | $210 000 | JGI |
| 48.6 Mb (total) | $ 1572 000 (total) |
In addition to the genome sequencing of individual microorganisms (Table 1), several large scale project are underway that characterise important microbial communities via genome sequencing approaches (metagenomics) (Table 2).
Table 2. Metagenome projects of important Australian microbial systems
| Microbial Community | Sequencing estimate | Primary Funding Source |
Funding amount (estimate) |
Sequencing Collaborator |
| Marine planktonic and surface-associated microbes | 1600 Mb | Australian Research Council + Venter | $1600 000 (ARC)
$2100 000 (Venter) |
Venter |
| Antarctic Lake microbes | 500 Mb | DoE + Venter | $650 000 (DOE)
$150 000 (Venter) |
JGI
Venter |
| Enhanced Phosphorous Removal Sludge microbes | 180 Mb | DoE | $360 000 | JGI |
| 2280 MB (total) | $ 4860 000 (total) |
In total more than $ 6.2 Mio of funding for microbial and environmental genomics were awarded to Australian microbiologist with more than 75% of the funding coming from overseas.
2. Short term benefit.
List of Publications (Australian scientists highlighted in bold)
Burke CM, Thomas T, Egan S, Kjelleberg S (2006) Tambjamine biosynthesis in the marine bacterium Pseudoalteromonas tunicata (submitted Applied and Environmental Microbiology)
Martin HG, Ivanova N , Kunin V, Warnecke F, Barry K, McHardy AC, Yeates C, He S, Salamov A, Szeto E, Dalin E, Putnam N, Rigoutsos I, Kyrpides NC, Blackall LL, McMahon KD, Hugenholtz P (2006) Metagenomic analysis of phosphorus removing sludge communities. (submitted to Nature Biotechnolgy)
Kunin V, Martin HG, Warnecke F, Peterson SB, Ivanova N, Blackall LL, McMahon KD, Hugenholtz P (2006) Metagenomic analysis of two activated sludges reveals high global dispersal rates and ecosystem vulnerability (submitted to Science)
Thomas T, Egan S, Burg D, Ng C, Ting L, Cavicchioli R (2006) The integration of genomics and proteomics into marine, microbial ecology. Marine Ecology Progress Series, (in press)
Goldberg SM, Johnson J, Busam D, Feldblyum T, Ferriera S, Friedman R, Halpern A, Khouri H, Kravitz SA, Lauro FM, Li K, Rogers H-Y, Strausberg R, Sutton G, Tallon L, Thomas T, Venter E, Frazier M, Venter JC (2006) A Sanger/Pyrosequencing Hybrid Approach for Generation of High Quality Draft Assemblies of Marine Microbial Genomes. Proceedings of the National Academy of Science U S A (in press)
Saunders, N. F. W.,
Ng, C., Raftery, M., Guilhaus, M., Goodchild, A. and
Cavicchioli, R. 2006. Proteomic and computational
analysis of secreted proteins with type I signal peptides
from the Antarctic archaeon Methanococcoides
burtonii. Journal of Proteome Research
(in press)
Cavicchioli, R. 2006. Cold adaptation in Archaea:
lessons from genomics and proteomics. 6th
International Congress on Extremophiles, Brest,
Brittany, France, September 17-21.
Cavicchioli, R. 2006. Pioneering Understanding of
Cold Adaptation in Archaea (the Third Domain of Life):
Unique Microorganisms from Lakes in the Vestfold Hills.
Scientific Committee on Antarctic Research (SCAR)
XXIX, Hobart, July 11-15.
Cavicchioli,
R. 2006. Cold adaptation in Archaea: an
Australian led, international program of discovery.
Presentation for the 2005 Frank Fenner Research Award.
Australian Society for Microbiology: Annual Scientific
Meeting and Exhibition, Gold Coast, July 2-6.
Anderson, I. J., Whitman, W. B., DasSarma, S.,
Cavicchioli, R., Olsen, G. J. and
Kyrpides. N. C. 2006. Archaeal Diversity Sequencing
Project: Preliminary Results. 106th
General Meeting of the American Society for
Microbiology, Orlando, Florida, May 21-25.
Cavicchioli, R., A.
Goodchild, N.F.W. Saunders, C. Ng, D. Burg, L. Giaquinto,
D. De Francisci, M. Katrib, M. Raftery, M. Guilhaus, P.M.G.
Curmi, D. Nichols, H. Ertan, K. Sowers. 2006. Cold
adaptation in Archaea. International
Conference on Alpine and Polar Microbiology,
Innsbruck, Austria, 27-31 March.
Saunders, N.F.W., Goodchild, A., Raftery, M.,
Guilhaus, M., Curmi, P.M.G. and Cavicchioli, R.
2005. Predicted roles for hypothetical proteins in the
low-temperature expressed proteome of the Antarctic
archaeon Methanococcoides burtonii. Journal of
Proteome Research 4: 464-472.
Goodchild, A., Raftery, M., Saunders, N.F.W.,
Guilhaus, M. and Cavicchioli, R. 2005. Cold
adaptation of the Antarctic archaeon, Methanococcoides
burtonii assessed by proteomics using ICAT.
Journal of Proteome Research 4: 473-480.
Thomas T, Egan S,
Saunders N, Longford S,
Taylor M, Tujula N,
Burke C, Yung PY,
Holmstrom C, Cavicchioli
R, Steinberg P,
Kjelleberg S (2005) Genomic analysis of
marine prokaryotes associated with eukaryotic host
surfaces. GSAC 2005: Genomes, Medicine and the
Environment. Hilton Head, South Carolina, October
17-19.
Cavicchioli, R.,
Goodchild, A., Saunders, N.F.W., Raftery, M., Guilhaus, M.
and Curmi, P.M.G. 2005. Insight into cold
adaptation in archaea from an integrated genomic/proteomic
approach. 11th International Congress
of Bacteriology and Applied Microbiology at the
International Union of Microbiological Societies
(IUMS), San Francisco, 23-28, July.
Goodchild, A., Saunders, N.F.W., Ertan, H.,
Raftery, M., Guilhaus, M., Curmi, P.M.G. and
Cavicchioli, R. 2004. A proteomic determination of
cold adaptation in the Antarctic archaeon,
Methanococcoides burtonii. Molecular
Microbiology 53: 309-321.
Goodchild, A., Raftery, M., Saunders, N.F.W., Guilhaus, M.
and Cavicchioli, R. 2004. The biology of the cold
adapted archaeon, Methanococcoides burtonii
determined by proteomics using liquid chromatography-tandem
mass spectrometry. Journal of Proteome Research 3:
1164-1176.
Cavicchioli,
R. 2004. Insight into cold adaptation in archaea
from an integrated genomic/proteomic approach.
12th Annual International Meeting on
Small Genomes, Lake Arrowhead, USA, 26-30 September.
Cavicchioli,
R. 2004. Insight into cold adaptation in archaea
from genomic and proteomic studies. 5th
International Congress on Extremophiles,
Chesapeake Bay, Maryland, USA, September 19-23.
Cavicchioli,
R. 2004. Insight into the biology of a cold
adapted archaeon from genomic and proteomic studies.
10th International Symposium on
Microbial Ecology (ISME), Cancun, Mexico, August
22-27.
Saunders NFW, Thomas T,
Curmi PM, Mattick JS,
Kuczek E, Slade R,
Davis J, Franzmann PD,
Boone D, Rusterholtz K, Feldman R, Gates C, Bench S, Sowers
K, Kadner K, Aerts A, Dehal P, Detter C, Glavina T, Lucas
S, Richardson P, Larimer F, Hauser L, Land M,
Cavicchioli R. (2003) Mechanisms of
thermal adaptation revealed from the genomes of the
antarctic Archaea Methanogenium frigidum and
Methanococcoides burtonii. Genome
Research 13: 1580-1588 [first high impact publication]
Only a fraction (appr. 10%) of
the genomic data listed in Table 1 and 2 have been
analysed, and just this year two of the genomes were
completed. We are in a tremendous position to reap the
benefits of all the data, and a number of very important
publications will be produced in the next few years. There
is clearly a unique short-term opportunity to grow
Australian microbial research to generate considerable
long-term benefits.
3. Long-term benefits:
1. Novel biocatalysts
The international market for enzymes is worth billions of dollars, and many biotechnological processes rely on efficient bio-catalysts that operate around ambient temperature. Enzymes from cold-adapted microbes have been shown to possess superior properties for these applications. The genomic information of Methanogenium frigidum, Methanococcoides burtonii, Halorubrum lacusprofundi and the metagenome of the Antarctic Lakes provides a natural resource for harvesting many useful enzymes that will have enormous biotechnological and biomedical value.
2. Novel Bioactives
Microbes associated with marine surfaces have been shown to be a rich source of novel bioproducts and many novel antimicrobial and antifungal compounds have been discovered. The genomes of Pseudoalteromonas tunicata, Roseobacter gaellaeciensis, Ruegeria R11 and the surface-associated metagenomes will provide an endless arsenal of bioactives to fight the rising flood of multi-antibiotic resistant pathogens and open unique biomedical applications.
3. Bio-fouling in the marine environment
Surfaces in the marine environment become quickly covered in a layer of fouling organisms such as fungi, macroalgae or barnacles. This process termed bio-fouling is mediated by bacteria and costs the shipping and aquaculture industry worldwide several billion dollars in damaged marine, structures. The genomes of Pseudoalteromonas tunicata, Roseobacter gaellaeciensis, Ruegeria R11 and the surface-associated metagenomes will reveal the mechanism of bio-fouling and will allow for the development of intelligent, cost-effective and environmental-friendly control measures. Bio-fouling also occurs on any surface that is in contact with water (such as drinking-water pipes or medical instruments) and technology transfer to these systems might create further long-term benefits for Australia.
4. Improved waste-water treatment
Phosphorous removal is an essential part of waste-water treatment and failure of the process results in poor-quality water for users and the environment. The metagenome of a waste-water treatment sludge will allow the development of effective methods to manage and control phosphorous removal resulting in dramatically improved and consistently improved water quality and an overall improvement to consumers and the environment.
5. Biodegradation of detergents
Laundry surfactants become degraded in the environment via a microbial process. However, the process sometimes fails and causes foaming in rivers and other water systems. The microorganisms Parvibaculum lavamentivorans, Comamonas testosteroni and Delftia acidovorans are unique in mediating effective biodegradation and hence, their genome information will allow us to better understand and control the process.
6. Carbon-cycle in the ocean
The ocean represents an important carbon-dioxide sink and contains much of the fixed organic carbon in the world. Sphingopyxis alaskensis and Photobacterium angustum are important marine organisms that use different strategies for carbon conversion. Their genomes will provide the blue print for understanding the role of microbial processes in controlling the global carbon cycle, and in particular, carbon dioxide sequestration.
7. Maintaining the health of Australian ecosystems: leading the world
Deriving an integrated understanding of microbial ecology is essential to empower members of Government and other decision makers with informed choices to enable the need for domestic and industrial programs to be balanced with the responsibility for preserving the health of the world’s ecosystems. Australia has the opportunity to take a leading role in this international arena.
