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  Acridine orange stained cells of a new Haloquadratum isolate (Bajool9) from an Australian salt lake.
 
 

 


 

I am interested in the microorganisms in salt lakes. Australia's largest lakes, such as Lake Eyre, are salt lakes, and there are thousands of other, smaller salt lakes with water salinities ranging from 25% (i.e. 25g/100ml) up to saturation (~37%). Sea water, by comparison, is only around 3.6% salt. In waters with salinities from about 30% upwards, the majority of microbes are haloarchaea, members of the family Halobacteriaceae, Domain Archaea. Their viruses are thought to be 10-fold higher in concentration than the cells. Little is known about the microbes that live in our natural salt lakes, even though they grow to such high densities, around 107 - 108 cells/ml, that the water is a distinctive red colour, as shown in the picture below. While many tourist brochures and signs say the water colour is due to the green alga Dunaliella salina, this is not usually true; it is the haloarchaea that produce most of the visible pink-red colour, as their cell membranes contain carotenoid pigments. Only occasionally do blooms of Dunaliella overshadow the Archaea.

salt lake mds

Salt lakes are highly productive ecosystems with a natural biodiversity we are just starting to explore. Some lakes are used commercially for salt manufacture e.g. Lake Tyrrell, Victoria, and for biotechnology. Dunaliella salina, a green alga, is cultivated for its beta-carotene, a widely used antioxidant and food colouring agent. Nationally, this is an important industry, as Australia produces 95% of the world's supply of natural beta-carotene. There is a great potential to use salt lakes for the production of other useful compounds, but first the organisms that grow in them need to be thoroughly understood, and genetic methods developed to be able to manipulate them. My work on the dominant archaea in salt lakes is a step towards this goal.

DIVERSITY, GENOMICS AND EVOLUTION

The family Halobacteriaceae currently possesses about 33 recognised genera, and this number increases every year. These organisms are also called halobacteria or extremely halophilic Archaea. The most famous HaloTreemember of the family is Haloquadratum walsbyi, because its cells are square shaped. A group of 4 cells are pictured below, and there is also a picture at the top left of this page. These cells are like thin tiles, approx. 1.7 x 0.2 µm, and normally have gas vesicles to regulate their buoyancy in the water column. First discovered by A. Walsby in 1980, they often represent the dominant cell type in salt lakes around the world, ranging from 40-80% of the total cell population. laketyrrellDespite growing very well in nature, they were not able to be grown in culture until 2004. David Burns [website] first grew them in my laboratory in 2002 (B.Sc. hons, thesis), and the work was formally published on 21 August 2004. Being able to grow these organisms was a major step towards understanding their ecology, characteristics and evolution, and to be able to study their genetics and biotechnological potential. From diversity and cultivation studies I have moved into genomic sequencing in order to understand their genetic makeup and evolution in precise detail. more on the SHOW group.

HALOVIRUSES

Viruses of haloarchaea (haloviruses) outnumber cells 10-fold and are significant modulators of the cell population, infecting and lysing host cells. They may be useful to control particular species of haloarchaea (the same idea as 'phage therapy' in human medicine). For example, salt manufacture may be improved by suppressing certain cell types in crystallizer ponds. They are biologically interesting because they are adapted to high salt and must be able to replicate in archaeal cells. The transcription and translation systems in Archaea are primitive/simpler versions of those in eukaryotes, and their membrane lipids are fundamentally different from those in Bacteria or Eukarya. The types of viruses and their interactions with host cells will tell us a great deal about the selective pressures on cell populations in hypersaline environments, and their role in lateral gene transfer. They are also likely to provide useful genetic tools for manipulating haloarchaea. plaquesOver several years, I and my students have isolated a number of novel haloviruses (HF1, HF2, His1, His2, SH1) from australian salt lakes, and and have been studying their characteristics and genomes. All are novel, and many have unusual morphologies (e.g. the lemon-shaped His1), or uncommon replication strategies (eg. protein-primed polymerases). The 3D structure of one of our halovirus isolates, SH1, has recently been published in PNAS, and has wonderful surface spikes (for cell attachment) and a previously unknown surface geometry (T=28 dextro).

A recent review has suggested the name Archeovirus to cover all viruses of Archaea, but to me this is not consistent with the root word Archae- (as in archaeal, archaeon, archaeum, Nanoarchaeum etc.). To avoid confusion in spelling, the name should be Archaeoviruses or simply Archaeviruses.


Flamingos

Why put a picture of Flamingos here? Well, they are an elegant bird, they display haloarchaeal colours, they often frequent hypersaline lakes, and maybe they carry haloarchaea with them on their travels around the world, perhaps entrapped in salt crystals.
[Photo: MDS]

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Sep, '11. I am a co-author on nice study on Bop regulation by Valery Tarasov et al. (2011) in BMC Mol. Biol. (highly accessed, 746 views)

Jun, '11. After 3 years in Germany studying the genomics of Haloquadratum, I have a major publication in PLosONE. (822 views, 168 downloads) [*background to this story].

March, '11. Joined the editorial board of Frontiers in Extreme Microbiology.

Feb, '11. I joined the Wagga campus of Charles Sturt University, within the microbiology group of BMS. Now teaching and setting up a new research lab. Fantastic place to live and work.

December, 2010. The Oesterhelt Department has now closed. Those who have worked in the dept. will appreciate these pictures of the Halocafe and this coffee mug.

Nov 15 '10: I have a Micro-Commentary on CRISPRs in Molecular Microbiology. It highlights an important study by Gudbergsdottir et al. regarding the dynamics of CRISPR elements in the archaeon Sulfolobus.

Aug 2 '10: Dr Ian H. Holmes, the Melbourne virologist who co-discovered the human rotavirus, has died. Ian was my Ph.D. supervisor. Here is a picture from my archive, celebrating the 'good old days' in the rota lab. My sympathy to Ian's family at this sad time. (Obit)

Apr '10: A study I have been involved with here on the structure of a haloarchaeal alkaline phosphatase is now published in the Journal of Molecular Biology. There are no homologues known in other haloarchaea, so it looks like a HGT, probably from Bacteria.

Apr '10: Two new taxa of haloarchaea ! We describe a new genus (Halonotius), and a new species (Natronomonas moolapensis) of haloarchaea. The latter is currently being sequenced.

Jan '10: Halostagnicola kamekurae. It is pleasing to see that a new species of Halostagnicola has been named in honour of Dr Masahiro Kamekura. This recognises his long career in halophile research, particularly haloarchaea. Congratulations !

Dec '09: Australian haloarchaea In 2007, we looked at the diversity of haloarchaea across 3 states of Australia. Now published [pdf] the results were surprising..(more)

Dec '09: Halovirus Methods: a summary of methods for studying archaeal viruses (Archaeviruses) has just been published [pdf]

Nov '09: ARB on Snow Leopard: Here is a step-by-step guide to set up the latest, fastest, stable ARB on OS X 10.6 !! Matt Cottrell has made installation a breeze.

Apr '09: Halohandbook. Slight update from 2008, with revisions to a few sections. [here]

Oct '08: Movie of halo motility in Halobacterium salinarum. See how haloarchaea move towards and away from light stimuli, using their rigid, spiral flagella.

Sept '08: Two halovirus papers published from my lab, transcription of SH1, and transfection and transposon mutagenesis.

Mar '08: Sadly, Dick Shand passed away after a long battle with cancer. Well known for his work on haloarchaea, particularly halocins. He is greatly missed. [home page pdf; Safari webarchive]

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 


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