Tag Archives: carbon fixation

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


Shade leaves: nature’s most efficient light harvesters

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Not all leaves are created equal. Within a single plant, a spectrum of light availability exists- some leaves are positioned to receive maximum sunlight every day, while others, by luck of the draw, are primarily shaded and experience full sun only in short, erratic bursts.  The sun leaves, by virtue of their superior position, are equipped with the capacity to capture the most light and perform the most photosynthesis. They tend to have more cell layers, larger numbers of the enzymes involved in capturing CO2 and converting it to sugar, and a larger volume of space to perform carbon-fixing reactions than their less-exposed neighbors.

Though it may seem that shade leaves get a raw deal, they are in fact uniquely adapted to a low light environment. Seemingly minor biochemical changes allow shade leaves to be far more efficient light harvesters, maximizing the amount of sunlight captured during those rare moments of exposure.

Chlorophyll is the main light-harvesting pigment in most plants, capturing light radiation primarily in the red and blue parts of the visible spectrum. These light waves are between 400 and 700 nanometers in length and are known as photosynthetically active raditaion (PAR). When PAR is absorbed by chlorophyllous tissue, radiation of longer wavelengths in the 680-760 nanometer range is re-emitted in a process known as fluroescence.

Measuring the kinetics of chlorophyll fluorescence has proved a useful tool in discerning the different photosynthetic capabilities of sun and shade leaves. To do so, a plant physiologist may incubate identical leaves in contrasting light conditions and measured fluorescence levels when a “saturating” pulse of white light is applied in each case. It turns out that the dark incubated leaves respond far more dramatically to a brief pulse of light than that already light-exposed leaves.

The pulses of light used in such laboratory experiments are in fact comparable to the erratic “sun flecks” that understory leaves may experience over the course of a day. Much as a starving animal will metabolize and release energy more slowly than a well-fed one, shade leaves take the limited light resources available and make far more out of these brief, shining moments than sun leaves would ever be able to.