Tag Archives: Antarctica

GeoChip: linking genetics with environmental processes

Over the past decade, environmental scientists have been casting a wider net in their attempts to understand complex environmental processes on a molecular scale. Once fascinating new line of research involves co-opting techniques developed by geneticists, largely for the biomedical industry, in order to understand how genes are important regulators of earth-scale processes as carbon and nitrogen cycling.

The GeoChip is a clear example of this search for new methods to answer old questions. Microbiologists  are working on remote Antarctic islands to understand some of the simplest nutrient cycling pathways in the world. The ecosystems they study are often composed of only a handful of fungal and microbial species. These simple food chains allow resarchers to contruct basic models of how energy and nutrients (such as carbon and nitrogen) are transferred.

This is where GeoChip comes in. GeoChip is a gene microarray chip designed to identify “functional genes” involved in important nutrient cycles. It allows the identification of genes in an environmental sample that regulate carbon fixation, decomposition, and atmospheric nitrogen fixation, to name a few.  Understanding what functional genes are available in a system allows scientists to both understand the potential of that system for cycling nutrients and better predict how that system will respond to environmental change.

Imagine a glass floor divided into hundreds of indentical squares. Each of these squares contains a different fragment of DNA, reconstructed by geneticists from known DNA sequences. When scientists want to probe an environmental sample for specific DNA sequences, they “wash” their sample over the floor. Fragments of DNA will stick to their complementary sequence on the floor, causing a square to light up. Scientists can “read” a GeoChip by identifying fluroescently lit spots where environmental DNA has attached. They use this information to develop a picture of the functional genes present in that system.

In Antarctica, GeoChip is already been used to answer important ecological questions. For example, scientists are finding that genes for nitrogen fixation, the crucial ecosystem process that produces plant-useable nitrogen in the soil, occur in lichen-rich areas. Lichens are believed to be among the earliest land colonizers, and the ability of lichen-dominated systems to add nitrogen to the soil may be an important finding in reconstructing the early colonization of terrestrial systems. Other findings include carbon-fixation genes in plots that lack vegetation, indicating microbial communities that are able to perform some sort of photosythesis in the absence of plants.


Yergeau et al. 2007. Functional microarray analysis of nitrogen and carbon cycling genes across an Antarctic latitudinal transect. The ISME Journal 1: 163–179


Fossil forests reveal a subtropical Antarctica

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Antarctica today is buried under a sheet of ice up to 5 miles thick, but this wasn’t always the case.  Fossilized forest stands of the now-extinct tree known as Glossopteris have been found in northeastern Antarctica. These trees existed in stands as thick as 20,000 per acre. These fossils have been found at 20-25 degrees from the South Pole; a latitude which today receives no sunlight for half of the year.

Glossopteris fossils provide important evidence for currently accepted distribution of continental plates in the Permian period that ended 250 million years ago. Fossils have been found in regions as distant as Patagonia, India and southern Australia. In the Permian, these landmasses were joined into a southern supercontinent known as Gondwana. The mass extinction that marks the end of the Permian period is believed to have led to the disappearance of Glossopteris.

The distribution of several extinct species in Gondwana. Glossopteris distribution shown in green.

These ancient forests tell more than just continental distribution, however- they provide insight into ancient climates, and possibly even into a major event in plant evolutionary history.

Paleobotanists have reconstructed Glossopteris as a tree that tapers upward like an evergreen. However, the leaves of this tree were broad and lance-shaped, and are thought to have fallen at the end of the growing season. A much warmer climate would have had to exist for such a tree to flourish. This corroborates paleoclimate data, which places Antarctica in a subtropical climate zone during the Permian.

A specimen of Glossopteris with well-preserved reproductive structures was found in Queensland, Australia. Dating to 250 million years ago, the structures found in this specimen indicate a very simple form of pollination . The pollen tubes and ovule examined from this in Glossopteris imply a close relationship with extant seed plants such as conifers and angiosperms. Angiosperms, the widespread group of flowering plants that dominate many terrestrial ecosystems today, are not thought to have evolved until over a hundred million years later. Glossopteris may therefore represent a missing link in the early evolution of pollination biology.

An artist’s rendition of a Glossopteris tree

For anyone interested in the evolutionary history of plants, this is a great interactive timeline developed by plant biologists at Cambridge University.


1.    Nishida, H., Pigg, K.B. & Rigby, J.F. Palaeobotany: Swimming sperm in an extinct Gondwanan plant. Nature 422, 396-397 (2003).
2.    Pigg, K.B. & McLoughlin, S. Anatomically preserved Glossopteris leaves from the Bowen and Sydney basins, Australia. Review of Palaeobotany and Palynology 97, 339-359 (1997).
3. Peter Jupp on “Ancienct Destructions”