Tag Archives: molecular genetics

In the turbulent phyllosphere, bacteria associate tightly with host plants

Large populations of bacteria  reside on leaf surfaces, in a zone known as the phyllosphere. Dr. Noah Fierer and colleagues at the University of Colorado, Boulder used high resolution DNA barcoding techniques to create a profile of the bacterial communities on 56 different tree species. They were interested in measuring 1) intraspecific variation, or the changes in phyllosphere communities across  different species and 2) interspecific variation, the changes in community composition within a species from tree to tree. Looking at the community variation within a single tree species allowed the researchers to isolate specific environmental variables that may be influencing community structure. To understand interspecific changes in diversity along environmental gradients, Fierer and colleagues barcoded Pinus ponderosa trees taken from several locations across the world.

Dr. Fierer found that phyllosphere communities are not randomly distributed, but organized in patterns that could be predicted given the relatedness of the tree species. In other words, related bacteria inhabit related tree leaves. Moreover, they found that the interspecific bacterial diversity- the difference between Pine and Oak tree phyllosphere communities, for instance- is greater than the intraspecific variability between distant individuals of the same species. Certain bacterial taxa were more common on gymnosperms (plants that reproduce by seed) than angiosperms (flowering plants). However, within a single species such as P. Pondersoa, bacterial communities could be highly similar across thousands of miles. Given that the bacterial communities in two handfuls of soil taken 10 meters apart are likely to look nothing alike, this result suggests a strong selection for particular bacterial species inhabiting particular leaves, regardless of environmental gradients.

Terrestrial leaf surface area is estimated to exceed 10^8 km^2, making the phyllosphere one of the largest microbial habitats on earth. Phyllosphere communities face the distinct challenge of extreme and unpredictable environmental variability. Imagine if your world could go from brilliantly sunny to dark in a manner of seconds, and that such events occurred randomly throughout the day. Rainstorms are not trivial events, but epic floods that pose imminent threat to all but the most resilient individuals. Temperature change is rapid and often extreme, and gusts of wind threaten to blow you upside down or off into oblivion. One may imagine that in such a turbulent world, bacteria with very specific properties would not only inhabit, but become expert dwellers on, very particular types of leaves. Dr. Fierer’s research supports this hypothesis by demonstrating a tight coupling between bacterial species and leaf properties associated with different tree species.



Hybridization of the New Zealand kaki- good, bad, or simply unnecessary?

Hybridization of closely related species to due land use and climate changes is accelerating. While hybridization often results in offspring sterility and thus reduces the fitness of parent species, in some cases viable hybrids are produced and the benefit or cost of this to the original species must be judged on a case by case basis. One of the world’s rarest birds, the New Zealand black stilt or kaki, has recently begun breeding with a self-introduced cogener, the pied stilt or poaka.

One of the world's rarest birds, the kaki is an iconic New Zealand native
The poaka, a close relative of the kaki, extends from the Philippenes and Indonesia across Australia and now into New Zealand

A recent molecular analysis of hybrid DNA confirmed that birds classified as hybrids on the basis of adult plumage are indeed genetically related to both parent species. Hybridization is both extensive and bidirectional- both sexes of both species will breed with the opposite sex of the other species.

An important question for scientists studying hybridization is whether introgression is occurring. Introgression, the introduction of genes from one distinct species into another, occurs via the backcrossing of hybrids to individuals of the parent species.  To make this concept clearer, imagine two farmers from two different towns. One farmer specializes in growing cucumbers, just like everyone else in his town. The other farmer, in the tradition of his town, grows only pumpkins. Now, if the children of these two farmers meet in college and decide to get married, they may well decide to start their own farm and choose to raise both cucumbers and pumpkins. Some years later, one of the children from this “hybrid” farm decides to start her own farm, but realizes that she’s really only interested in growing pumpkins (they make such tasty pies!). However, the cucumber-growing town has a much better craft beer selection, so of course she must live there. This third generation child has, in a sense, caused an introgression event to occur- she has brought a skill only available in one town into another due to the fortuitous marriage of her parents.

Why does introgression matter? In species that engage in hybridization, it can be an important mechanism for the transfer of new genes into either original species, thus maintaining a healthy level of genetic variation. In fact, “genetic rescue”  of an endangered species through intentional hybridization has become a population conservation strategy for preventing imminent extinction. Hybridization between individuals in a small population with reduced genetic diversity and a population of unrelated individuals increases the “genetic load” of the small, low diversity population.

Now, back to the mysterious kaki bird. Despite widespread evidence of hybridization, there is no evidence of introgression between hybrids and either parent species. This may be the first study to document a general lack of introgression, despite a history of extensive hybridization.

Okay, so a few weird hybrids aren’t backcrossing to the parent kaki species, so what?
Some conservationists think that introgression may be just what is needed to keep this rare species alive. Once abundant and widely distributed across New Zealand, the kaki is now critically endangered and currently restricted to the Upper Waitaki River Basin of the South Island. Intensive efforts to conserve the iconic bird have caused the population to nearly quadruple, from a scant 23 adults in 1981 to 98 adults in 2010. This population size is, however, far from ideal, and introduced mammalian predators are now representing a major threat to further species recovery.

Given that introgression may provide the fresh genetic load needed to keep the kaki species alive, researchers studying the kaki began searching for an explanation for this unusual lack of backcrossing. It turns out that the survival rate of fledgings born from hybrid female x kaki male pairs is significantly lower than the survival rate of either the normal kaki x kaki pairing, or hybrid x hybrid crosses. Coupled with an extremely small hybrid population size, which leads to less predictability in survival rates, the reduced fitness of hybrid female x kaki male pairings is not terribly surprising.

If genetic rescue will not offer relief to the kaki, are we nearing the end of the road for this marginalized species? The authors of this study don’t think so. The flip side to intentional hybridization is reduced breeding opportunities between kaki birds themselves (maybe they don’t need our help after all!). Although inbreeding and reduced genetic diversity are expected due to the low kaki population size, there is little genetic evidence for high inbreeding among kaki birds. Kaki exhibit relatively high fitness when compared to other New Zealand endemics that have suffered comparable reductions in population size. Rather than encourage further hybridization, the authors advocate active conservation strategies that promote the formation of “pure pairs” and maintain a balanced adult sex ratio in order to keep survival chances high.

Steeves et al. 2010. Genetic analysis reveals hybridization but no hybrid swarm in one of the world’s rarest birds. Molecular Ecology 19: 5090-5100

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

microbiologists watch evolution in action

rapid advances in molecular genetics are now allowing scientists to watch, and even manipulate, evolution. this may seem hard to reconcile with the idea that evolution is a very gradual, long-term process, whose effects are seen only on timescales of thousands or millions of years. the misconception here is that time governs the rate of evolution. time in the abstract is relentless and constant, moving forward endlessly. this conception of time does not take the broad range of life strategies that evolution has produced into account.

in fact it is generation time that governs rates of evolution. human beings, who tend to have several children over the course of a multi-decadal life, have relatively slow generation times. it can take millions of years for noticeable evolutionary shifts to occur in a population that grows and reproduces slowly, simply because the genetic mutations that lead to evolution are very rare, and advantageous mutations take a long time to become established in a population.

it has long been known that microbial evolution occurs rapidly- noticeable genetic shifts can be observed in a manner of days or weeks. the evolution of pathogen resistance to pesticides or medicine occurs through natural selection for a rare genetic mutation that allows survival. because microbial populations often grow exponentially and generation time can be as short as twenty minutes, rare genetic mutations can sweep through a population and become ubiquitous rapidly. this is evolution in action!

historically, experiments in microbial genetics have focused on determining the function of an existing gene. this is generally accomplished by creating a strain with a defective, mutant version of the gene of interest, and observing how its function differs from the normal gene. studying defective mutants, however, does not provide insight into how gene pools can be improved.

now scientists are growing microbial cultures whose entire genetic makeup is known, and performing experiments that test evolutionary theory. any number of questions are being asked- how do the bugs evolve in response to an environmental change? a new food source? the introduction of a genetically different strain? for example, if a microbial population that requires oxygen to breathe is suddenly placed in a low oxygen environment, will genetic shifts occur that allow the microbes to use oxygen more efficiently? this certainly seems to be the case with humans- human populations that have existed for centuries at high altitudes, where oxygen is scarce, exhibit slight alterations in genes that encode hemoglobin, the protein that binds oxygen and transports it throughout the body. controlled evolution experiments allow replication, which means that scientists can now ask how frequently a positive evolutionary outcome, such as increased oxygen efficiency, occurs.

though such experiments may only provide a simplistic illustration of evolution, the mechanisms leading to genetic changes in microbial populations are remarkably similar to the basic mechanisms governing genetic change in higher organisms, including humans. insights developed from these experiments may be a first step towards unraveling the complex chain of events that has created the extraordinary diversity of adaptive traits across all types of life.