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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.


The family Halobacteriaceae currently possesses about 40 recognised genera and 144 species, with new genera and species being added every year. These organisms are also called haloarchaea, halobacteria or extremely halophilic Archaea. The Clade 1 haloarchaea are shown in the phylogenetic tree reconstruction below (generated on a Mac using ARB). Email me if you want the full tree. The most famous HaloTreemember of the family is Haloquadratum walsbyi, because its cells are square shaped, and because it dominates the microbial populations of salt lakes. A group of 4 cells is 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 ┬Ám, and normally have gas vesicles to regulate their buoyancy in the water column. First discovered by A. Walsby in 1980, they often represent from 40-80% (or more) 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.


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).

The term Archaeovirus, a name I quite like, has been proposed in the recent study by Krupovic et al. (2012). This can be used to cover all viruses of Archaea.


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]





Mar, '14. Genome sequence of Haloarcula hispanica strain N601 (Genome Announc.)

Dec, '13. Transfer of Halosarcina limi and Halosarcina pallida to the genus Halogeometricum (IJSEM 63:3915)

Oct, '13. Not only are the haloarchaea of Deep Lake able to form biofilms, but they exchange a lot of DNA.See PNAS (cited 5)

Jul, '13. Halohasta is a new, validly published genus of the family Halobacteriaceae. Halohasta litchfieldiae, is named after Carol Litchfield.

Apr, '13. A newly described archaeovirus, PH1, is shown to be very similar to SH1. We propose a new virus family and two genera to encompass PH1 and related viruses. (cited 3)

Feb, '13. Sadly, Carl Woese, the 'father of the third domain of life', has died. His work directly led me to study Archaea

Feb, '13. CRISPRs provide a 'Ring of Confidence' for haloarchaea! See Biochem Soc Trans. vol 41(1)

Jan, '13. Cyanobacterial bloom at Lake Albert, Wagga. I couldn't resist taking a sample!

Nov, '12. More on haloarchaeal CRISPRs! The immune system of halophilic archaea, by Maier et al., in Mobile Gen. Elements

Sept, '12. Biofilm formation by haloarchaea (Fröls et al., 2012). Wow, so many different haloarchaea can form biofilms! Even isolates from Deep Lake, Antarctica. *background to this work. (cited 10)

July, '12. A fascinating study of protospacer adjacent motifs (PAMs) in CRISPR immunity of Haloferax J Biol Chem. (cited 29)

May, '12.Two new species of Halobellus are described in IJSEM. Hbs. limi is from Taibei, China, and Hbs. salinus is from Australia (see Burns et al., 2004). (cited 4)

Apr, '12. Sadly, Dr Carol Litchfield passed away. A well known 'halophile', she helped many other scientists, and will be sorely missed. (obit., service, library collection, GMU)

Sep, '11. An intriguing study on bacteriorhodopsin regulation by Valery Tarasov et al. (2011) in BMC Mol. Biol.

Jun, '11. After 3 years in Germany studying the genomics of Haloquadratum, I have a major publication in PLosONE. (cited 28) *about this work.

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

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

Nov 15 '10: I have a Micro-Commentary on CRISPRs in Molecular Microbiology, highlighting an important study by Gudbergsdottir et al. regarding the dynamics of CRISPR elements 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 are some pictures from my archive, celebrating the 'good old days' in the rota lab. (Obit)

Apr '10: A structural study of a haloarchaeal alkaline phosphatase is published in the J. Molec. Biol. No homologues are known in other haloarchaea, so it looks like a HGT event, probably from Bacteria. (cited 8)

Apr '10: Two new taxa of haloarchaea. We describe a new genus (Halonotius), and a new species (Nmn. moolapensis) . The latter is currently being sequenced. (cited 12)

Dec '09: Australian haloarchaea In 2007, we looked at the diversity of haloarchaea across Australia. [pdf] the results were surprising.. (cited 21)

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

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