Tag Archives: nutrient transfer

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

In an unpredictable environment, trees network for stability

In the highly variable ridge, slope and valley mosaic that forms the Luquillo Mountains of northeastern Puerto Rico, Dacroydes excelsa, commonly known as Tabnuco, dominates the landscape. Though tropical forests are generally quite diverse and seen as ideal environments for plant growth, life in this rainforest can actually be quite challenging. Powerful hurricanes pass through the Caribbean annually and hit the Puerto Rican mainland every few years. Large swatches of the Luquillo forest were flattened several years back when hurricane Hugo struck in 1989.  Aside from directly damaging or wiping out forest stands, hurricanes cause landslides that severly erode the already shallow, nutrient depauperate soils.

On steep, harsh slopes that experience such frequent disturbance, what allows one tree species to gain a competitive advantage over the hundreds of others struggling to survive? Rather than compete fiercely for limited resources only to be at the mercy of the next devastating hurricane, Tabunuco trees have adopted an alternative strategy- cooperation and resource sharing through root grafting.

Root grafting, the joining of neighboring tree roots to produce a network, is a phenomenon that scientists have been aware of for decades, though the extent of its occurrence and the benefits that it provides trees are largely unknown. In Tabunuco forests, however, root grafting is widespread and many of its benefits obvious.

Tabunuco trees grow in dense stands and will graft roots with neighboring trees as they mature, forming unions that comprise anywhere from two to over a dozen trees. A clear advantage of this strategy in an environment that experiences powerful storms is structural stability. Trees that have entered unions increase their base of support and are less likely to be uprooted during a wind event or landslide. In increasing their wind-firmness, individual trees boost their survival chances during a storm. Fewer uprooting events also reduces the probability of a major landslide and helps ensure the retention of the surface organic matter that contains most of the forest’s available nutrients.

Root networks can also improve soil conditions during the off-season. Densely packed surface roots form “organic benches” which trap leaves and other decaying plant matter rather than allowing these important nutrient sources be washed downslope. Roots aerate the soil, facilitating decomposition and nutrient flow. They also “prime” the surrounding soil for productivity by releasing sugary compounds that stimulate beneficial microbial activity (the interaction between plants and microbes in the root zone known as the “rhizosphere” is another fascinating topic entirely, which I will do attempt to do justice to in the future).

Scientists are now discovering previously undetectable advantages of Tabunuco grafting that underscore the high degree of sophistication and evolutionary purpose in the development of these networks. It is now known that root networks can actually serve as conduits for the transfer of carbon and essential nutrients between trees. This can provide an immense competitive advantage over non-networked trees. Tabunuco trees that receive the most sunlight and produce the most carbon through photosynthesis can transfer carbon to neighboring Tabunucos to ensure the long-term health and survival of the community. Individuals of less common species, such as the Caribbean palm and Colorado tree are excluded from Tabunuco networks and must compete for growth given only the resources available in the vicinity of their roots.

Though in Tabunucos root grafting precludes the need for inter-tree competition, it is theoretically possible that trees could use grafting for more selfish purposes. Ecologists have speculated whether trees can gain a competitive advantage over their neighbors by leeching a neighbor’s nutrients, much as the fungal organisms that associate symbiotically with plant roots can become greedy and actually sap nutrients from their host under stressful conditions. Root networks may even serve as a conduit for disease or herbicide transfer, allowing trees that produce or tolerate a harmful compound to efficiently clear out their competitors.

Basnet, K., F.N. Scatena, G.E. Likens, and A.E. Lugo. 1992. Ecological consequences of root grafting in tabonuco (Dacryodes excelsa) trees in the Luquillo Experimental Forest, Puerto Rico. Biotropica 25:28-35.

enzymes in the environment

enzymes are the catalysts of life. they are the link between higher forms of biological structure- cells, organisms, ecosystems- and the physical universe. they form such links by allowing incredible reactions to occur, reactions that strip complex molecules down into simple components that our cells can harvest energy from, reactions that detoxify harmful substances, reactions that take nonliving compounds and turn them into something organic. they have ugly names. ribulose-1,5-bisphosphate carboxylase oxygenase is a name that most eyes would glaze over while reading, but what if i told you that RuBisCO (it has a nickname!) is the only thing on earth that can add electrons to carbon dioxide? if that doesn’t seem to impressive, look out your window. not a single tree, flower, blade of grass, animal or human being (or man-made structure, for that matter) would exist if RuBisCO had not evolved to turn carbon dioxide into sugars.

there is a less appreciated truth about enzymes that i find to be equally intriguing, almost poetic. enzymes not only build and maintain life, they destroy it. or, to be a bit more accurate, they recycle its components. enzymes are largely responsible for decomposing organic matter, breaking down trees and blades of grass and human beings into the tiny carbon-rich compounds that RuBisCO created. in fact, if you take a small handful of soil from your garden, you are holding billions of free floating enzymes. they have been constructed by plants and microbes and were released into the environment to acquire something that their creator needs (i hate to use the word “creator”, when writing about science, if you have a better word, please do share). most often, this is an essential nutrient or a small sugar that can be used for energy. imagine if you could take your stomach out, and send it off to wendy’s to eat a chicken sandwich for you. not the prettiest analogy, perhaps, but this is in essence this is what microbes and plants do in the soil.

while intellectually it may be somewhat interesting to imagine billions of microbial exo-stomachs scouring the earth for their lunch, why should anyone really care about enzymes in the environment? well, truth be told, very few people do. but i’m going to tell you why an increasing number of environmental scientists are taking an interest in enzymes, not only in order to understand a process, but with the growing realization that understanding how enzymes shape our planet may be essential to averting looming environmental catastrophes.

as the agents responsible for the breakdown of organic, carbon containing compounds (and this is true in soils and aquatic ecosystems), enzymes are gatekeepers. they regulate how quickly carbon is broken down and taken up anew by living organisms. if you want to think realistically about any form of carbon sequestration in soils (an idea that has exploded in popularity in the last several years), or understand how global warming is altering ecosystems and the balance of carbon and nutrients within them, you simply cannot ignore enzymes.

the fact is, much as we would like to find a way to store the huge amounts of  carbon our activities are releasing into the atmosphere back in the earth, adding carbon feeds the soil. and just as human populations increase during times of food surplus, microbial populations explode, produce more enzymes and cycle that carbon at a faster rate.

another aspect of enzyme behavior that makes global climate change scenarios even stickier is that enzymes are very, very sensitive to changes in their environment. the activity and efficiency of enzymes in the environment is closely linked to temperature, moisture, and pH conditions. my own research on soil enzymes from northeastern forests is showing that even a few degrees of temperature increase can cause a dramatic increase in the rate of the carbon-cycling reactions that these enzymes perform. droughts, on the other hand, can quickly kill demolish enzyme communities and cause carbon cycling in a system to drop off.

the behavior of enzymes in the environment, we are discovering, is far more complex and nuanced than the story i’ve outlined here. moreover, ecologists know that enzymes must be understood within a broad context. the plants, animals and environmental processes that interact to form complex ecosystems, which enzymes regulate on a very fundamental level, must be somehow integrated if we are to fully understand how these tiny reaction machines keep our earth running.

Maybe we should reconsider raking our leaves

I recently learned a fascinating fact about leaf raking that should be painfully obvious to a forest ecologist- it’s bad for trees! Every spring, deciduous trees produce leaves that they use throughout the growing season for photosynthesis and sugar production.  Plants concentrate essential nutrients such as nitrogen, potassium, calcium and magnesium in their leaves, as these nutrients are all required in relatively high amounts to perform photosynthesis.

As winter approaches and the growing season ends, trees withdraw many of the proteins and nutrients they have stockpiled in leaves back into their woody tissue, so that these nutrients can be recycled to make new leaves the following year. However, most trees are able to do even better than this- after their leaves have fallen, the nutrients that couldn’t be recaptured in time are decomposed into the surface soil surrounding the tree, and will be available for uptake through the roots several years later. This regular flux of plant essential nutrients back to the soil through leaf litter means that plants depend on those same nutrients, year after year, to grow new leaves.

In fact, if you look at the typical architecture of a deciduous tree, it is no accident that probably appears like two umbrellas attached together at their handles. The top umbrella is the above ground parts of a tree from the base of the trunk to its canopy. The bottom umbrella is inverted and planted into the ground. It is composed of a main taproot that drives straight down into the earth, and lateral roots that branch out horizontally. Of these lateral roots are branching networks of finer and finer “root hairs” and associated fungi that are able, through their enormous surface area, to mine the soil underneath a tree for nutrients. Everything that is dropped from the top umbrella should theoretically be recoverable by this root system.

I’d imagine most of you can already see where this is going, but I find that sometimes simple truths are quite elusive. When we rake our leaves in the fall to maintain our clean, grassy lawns, we are removing loads of nutrients that our trees are expecting to get back! We are creating an artificially open, leaky system, that trees have spent millions of evolutionary years refining. A recent paper in a relatively esoteric research journal, “Nutrient Cycling in Agroecosystems” (who reads that??) attempted to quantify the impact of historic leaf raking on old agricultural towns in central Europe. The fascinating bit of historical information in this paper is that centuries ago, medieval farmers actually knew that leaves were a great nutrient source- farmers removed leaves from nearby forests specifically to use as fertilizer on their fields. This paper claims that the result of historic leaf raking is that the “majority of central European forests were severely depleted of nutrients…when modern long-term rotation forestry became the dominant form of forest land use”.

So next fall, when you’re pulling out your rakes or enlisting your kids to do so for a few dollars, think carefully about your trees. In all likelihood, the average patch of suburban lawn is already so nutrient depauperate from numerous land use changes (deforestation, asphalt paving, over-fertilization, the cultivation of a monoculture of non-native grasses, to name a few) that removing a few leaves isn’t going to make a big difference. But if I’ve learned anything from Malcom Gladwell, it’s that little changes that add up to produce big effects, and if medieval Europeans were knowingly removing nutrients from their forests, I figured modern suburbanites should at least be aware.