Australian Environmental Microbiology
The Project:
Goal/Deliverables:
Effective “genomics” encompasses not only genome sequencing, but intelligent analysis of the data (bioinformatics) and comprehensive functional (“phenomic”) assessment (e.g. proteomics, transcriptomics, metabolomics, gene knock-out). Resources in genomics would immediately benefit the following areas:
1. Cold
adaptation: Discover how Antractic lake communities
(metagenome) and individual microorganisms
(Methanococcoides burtonii, Methanogenium frigidum,
Halorubrum lacusprofundi) adapt, and have evolved to
form the Earth’s enormous, cold biosphere.
2. Living with limited nutrition:
Discover the precise molecular strategies of how
microorganisms compete for the limited supply of nutrients
in natural environments, using two model marine organisms
with different life-styles, Sphingopyxis
alaskensis and Photobacterium angustum.
3. Life in hot acid: Discover how
Acidianus sp. JP7 can thrive at pH 0.3 and 50-80C,
and is capable of extremely efficient bioleaching, by
oxidizing ferrous iron, sulfur and mineral sulfides; the
type of organism thought to be prevalent when life first
evolved on Earth.
4. Life and competition on
surfaces: Discover how biofilm formation is controlled
in the marine environment through genomic studies of two
unique anti-fouling organisms (Roseobacter
gallaeciensis and Pseudoalteromonas tunicata)
and metagenomics of surface communities.
5. Evolution of natural
communities: Discover how microorganisms evolved from
ancestors which emerged 3.8 billion years ago, and what
controls the evolution of natural communities, in order to
forecast the effects of present day environmental change on
the genetic blue prints and adaptative responses of life on
Earth.
6. Biodegradation: Discover how a
novel consortium of three microbes (Parvibaculum
lavamentivorans, Comamonas testosteroni and
Delftia acidovorans) can degrade linear
alkylbenzenesulfonate; an environmentally damaging compound
of laundry detergents.
7. Microbial waste water treatment:
Discover how microorganisms in activated sludge can degrade
and remove waste compounds (e.g. phosphorus) in
water treatment systems, by performing metagenomics of
unculturable organisms from environmental samples.
8. An untapped resources: Australia
has expansive, diverse and unique ecosystems. Additional
programs representing all States of the Nation that would
immediately benefit from enhanced resources for genomics
include studies of hypersaline lakes, soils, the Great
Artesian Basin, and marine environments that span from the
Coral Sea to Antarctic ice.
Why sequence/study thegenome?
Microbial genomes are small, and can be
sequenced for a relatively low cost. The novel genes for
each unique specimen can be identified rapidly, and a broad
range of functional studies performed immediately, to
uncover critical answers in fundamental areas of
bio-discovery through to innovative development of
bio-applications. The same genomics principles apply to
sequencing entire microbial communities (metagenomics),
while magnifying the scope for discovery through the
expanded diversity and richness of new genomic data.
Australia’s environmental microbiology community has
demonstrated a capability to engage in genomics, despite
the lack of an Australian mechanism to support genome
sequencing. While this has been character building for
individuals involved, it is not a sensible way for
Australia to be attempting to pursue scientific excellence.
A key to deriving success with genomics that is offered by
Australia’s environmental microbiology community is
not only expertise in “omics” and chosen
fields, but a capacity to effectively interface with
scientists from a range of other disciplines (e.g.
geochemistry, meterorology, paleontology) to derive a
systems biology view of ecosystems and how they are placed
in a global perspective.
What is the benefit to Australia?
Demonstrating a national capacity to perform
genome sequencing of individual microorganisms and
communities will be a cost effective way of generating an
Australian profile, in what is otherwise, an international
“genomics era” of science. This will underpin
functional studies for which Australia has an established
(e.g. proteomics) and growing (e.g.
metabolomics) international reputation, foster student
training and mutually beneficial scientific exchanges, and
establish a credible future for Australian biological
sciences. Programs of microbial gene discovery create real
potential for bio-application, with obvious areas relating
to bioactive compounds used for the prevention and
remediation of biofilms, cold-active and heat stable
enzymes for biocatalysis and cleaning of medical
instruments, enhanced metal recovery from bioleaching,
modifying civil and industrial processes for enhanced
removal of unwanted waste products, and so forth. The
provision of reasonable funds for genomics of environmental
microorganisms will enable Australian’s to control,
or be significantly more active in benefiting from this
national biological resource.
Contact Information:
The spokesperson for a large team of
Australian researchers behind this collective project is:
Assoc. Prof. Rick Cavicchioli
School of Biotechnology and
Biomolecular Sciences
The University of NSW (UNSW)
Sydney NSW 2052 Australia
Tel. +61-2-9385-3516
Fax. +61-2-9385-2742
Email. r.cavicchioli@unsw.edu.au
http://www.babs.unsw.edu.au/research/ehm/lab_cavicchioli.html
