Updated: All up and running (almost)

After a long period of having issues with our power supply it seems like we have been able to solve this problem for the time being. It is now possible to actually see our data online now which is quite exciting. There are of course some kinks that still need to be ironed out but all-in-all everything is looking functional.

One major update we have had is the installation of a eddy-flux covariance tower (see pic below). This is a rather exciting joint venture with Cyril Marchand in New Caledonia.

Eddy-flux covariance tower

I have also had a bit of a play around with what little uninterrupted data I have been able to extract (see below). There is not a whole lot to report because of the very short time frame. One interesting thing is the stem-radius fluctuations. In terrestrial trees the stems expand from dusk until dawn and then begin shirking again when the sun comes out. In my trees there is a lag after dawn where the stems expand until 10-11am and only then begin shrinking. This is quite unusual and I have as yet not got a concrete explanation. One potential reason might have something to do with tide but I will need a longer time series and accurate tidal timing and height measurements.

Update: I forgot to mention that the period of stem-radius increase on 2-Aug and 3-Aug is most like to do with bark swelling caused by the rainfall event indicated by the grey bars on the bottom panel.

Daily cycles of physiological and environmental measurements

Daily cycles of physiological and environmental measurements

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EcoTas13 poster

I recently presented a poster at the EcoTas13 conference in Auckland. The conference was extremely stimulating and I walked away filled with new ideas. Expect some decent updates based on some of those ideas. For now just look at my poster.

EcoTas13 poster

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Pretty [science] pictures

I have arrived in Basel for some professional development related to my PhD . Travelling time was almost 40 hours with three stops. I felt quite good despite the 11 hour time difference between Auckland and Basel. As I wrote previously I am learning some new techniques for my work. I will also be giving a talk on my mangrove work at the Botanical Institute of Basel. In preparation for the talk (and a poster for a conference) I put together some figures of a three day time-series of some data we have collected. Being a newish R user I found it highly frustrating at times, particularly getting around the way that R deals with time. After many hours of trial and error, and the patient assistance of some colleagues, I finally got what the figures pretty close to how I wanted them.

It depicts three environmental/climatic variables and three plant water-use measures. There is a really nice tight coupling between all of the variables that can be explained within current understanding of tree physiology. During the day (white areas) when it is warm, humidity is low and the sun is shining, sap-flow is elevated, tree stems shrink and leaves lose turgor. Heat, dry air and sunlight promote transpiration which results in the observed sap-flow rates. At the same time, water stored in the stem is transpired which causes the stems to shrink. Leaves lose turgor, or become flaccid, because they are losing water to the atmosphere (transpiring). At night time (shaded areas) when it is cool, humid and dark transpiration very low or non-existent. Therefore, there are depressed sap-flow rates, an expansion of the stem and increased leaf turgidity.


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Smashing plant bits

I am going to Switzerland next week for my PhD work. I will be learning some new techniques and collaborating with with Günter Hoch at the Botanical Institute, University of Basel. The work involves analyzing non-structural carbohydrates (NSCs) in my mangroves (see section 3. CO2 and plant-animal interactions in a previous post for a very brief explanation of the significance of NSCs). I will discuss NSCs in more detail once I have some data. For now I just want to do a little ‘show and tell’ what I did yesterday preparing my samples for the NSC analyses. I smashed ‘plant bits’ into fine powder using a ball mill. Ball mills operate on a simple but highly effective mechanism. You fill a jar with heavy balls, put your samples in with the balls. This jar then goes in a machine that rotates around an axis at high speed (400 rpm in my case) while the jar itself spins simultaneously. The animation below shows the outcome of this action. This high speed spinning pulverizes the sample you put in.

Action of a ball mill. Source: http://en.wikipedia.org/

So what did I pulverize? Mangrove branchlets, leaves and pneumatophores. It only took a minute and a half to turn a leaf into dust smaller than 100 µm. It was really impressive. The branchlets and pneumatophores took longer (5-10 min) because they are quite fibrous, but super cool nonetheless. Definitely better than using a mortar and pestle that’s for sure. I took some before and after pictures of the leaves to see how effective this tool was. Excuse the picture quality, I am still learning how to drive my new phone.

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It has begun

As of today I am officially a PhD candidate at AUT University with the Institute for Applied Ecology New Zealand. I have, however, done a bit of work prior to official enrollment to get ahead a little. What this has involved so far is reading (never ending) and the setting up my research site – what I like to call my outside office for the next few years.   I am pretty excited about my research site. It looks really sciencey. Best of all it actually is pretty sciencey. The central part of the system consists of three different types of sensors for measuring continuous and instantaneous water relations in trees (mangroves in my case). I will expand further on these measurements and sensors in a later post once they are up and running but for now enjoy the pictures of the first stage of set-up. It consists of a custom made aluminium scaffolding structure from Safeway Scaffolding (if you are in New Zealand and need a custom structure make sure you go and see Philip, he’s great). The structure will form the central hub for my sensors including, water-relations and environmental, as well as the power generator.

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Updated: CO2 and Plants

CO2 levels in Earth’s atmosphere have just reached 400ppm. This is more than a third higher than what it was in pre-industrial times (about 270-280ppm). It is clear that CO2 has an impact on climate and it is more than just the mean values that will change, but also greater variability around the mean.  Also, it is more than just the impact that CO2 has on warming the atmosphere that is interesting. There are numerous direct impacts on other parts of the ecosphere. One area of interest to me is the direct influence that elevated levels of CO2 have on plants. The initial instinct is to assume that because ‘plants eat CO2‘, elevated levels of CO2 will have positive effects on plant growth – this is called CO2 fertilization. There are numerous greenhouse studies with short-lived herbaceous plants that support the CO2 fertilization hypothesis. However, when different systems have been looked at the results vary.  Körner (2003) provides a nice review of the impacts that elevated CO2 has on plants. The paper is presented in three themes: (1) the interaction between CO2 enrichment and nutrients; (2) water and CO2 enrichment and (3) how CO2 enrichment influences plant-animal interactions.

1. CO2 and nutrients

The biomass of plants is made up of predominantly carbon based compounds. Therefore, as I mentioned before we might imagine that more CO2 means more growth. But, we also know that photosynthesis (the process that fixes carbon) requires several other components. That means that regardless of how much CO2 increases, growth rates can be limited by other factors. This is nicely demonstrated in studies in natural systems (forests and grasslands) that have experimentally increased CO2 in conjunction with fertilizer additions versus those that have just used CO2 enrichment: productivity is typically increased significantly in the CO2 plus fertilizer studies but, either increased marginally or not all in the CO2 only studies. This suggests that many systems are not CO2 limited and that it is other factors that are limiting to growth. This might include nitrogen, phosphorous and water. One thing to take note of is that the Körner (2003) paper talks almost exclusively about direct CO2 effects of plants. If we consider indirect effects through changing climate the picture is a bit different. For example, one study that looked at long terms changes in tree growth in tropical forest in relation to CO2 increases and climatic variation found growth was influenced by dry-season rainfall and night-time temperature but not by annual CO2 levels (Clarke et al. 2010).

2. CO2 and water

Plants are the highway for CO2 entering and water leaving terrestrial systems. As much as 70% of water that enters the atmosphere and almost all the carbon in terrestrial systems passes through trees. At the centre of this are the little pores (stomata) on the leaves of plants, which I like to call the gatekeepers. What some studies have found is that under elevated levels of CO2 stomata reduce their aperture. What this does is allow the same amount of CO2 in but less water out. That means that trees are taking up less water from the soil which can result in water logging. The follow on effect of this is that the water logged soils can favour the competitive abilities of some species over others. In grasslands, and other herbaceous communities with short turnover times, the community composition can change remarkably fast. Interestingly, stomatal closure varies among species with some species not responding at all. Therefore, it is difficult to make general predictions about the effect of CO2 on water dynamics of different systems.

3. CO2 and plant-animal interactions

Trees fix carbon as structural compounds for building biomass (cellulose and lignin) and for use in energetic metabolic tasks. In addition, plants typically contain storage compounds, often called non-structural carbohydrates (NSCs). In times of growth, NSCs are depleted from the storage pool and in times when growth is limited (e.g. water or nutrient shortage) NSCs accumulate in the plant tissues. This happens because carbon supply from photosynthesis and carbon demand for growth is not always in sync. What has been found in CO2 enrichment studies is that carbohydrate concentration often increases in tissues but protein concentration decreases. This change in ratio of carbohydrate to protein can then change the feeding behaviour of herbivores (e.g. caterpillars). And again, as with species responses in stomatal closure, herbivore species have been found to respond differently to food plants grown in elevated CO2. This makes general predictions difficult to make given our current knowledge.

So what do we learn from Körner (2003)? Elevated CO2 has direct impacts on plants. These impacts are not as intuitive as we may think they are. Different plant species respond differently to elevated levels of CO2. The responses have broad reaching follow on effects on whole communities of plants and animals. We also get the picture that the CO2 issue is a complex one and difficult to make generalizations on – at least at the moment and so more work needs to be done.


I have just read a paper (Jasechko et al. 2013) that looked at transpiration vs total evapotranspiration (the combination of transpiration and evaporation) and found that transpiration contributes as much as 90% of evapotranspiration. That mean that in order to understand water cycles effort should be concentrated on the biotic factors (plants), rather than the physical factors (evaporation). I really nice strong justification for my work!


Clark, D. B., Clark, D. A., & Oberbauer, S. F. (2010). Annual wood production in a tropical rain forest in NE Costa Rica linked to climatic variation but not to increasing CO2. Global Change Biology, 16(2), 747-759. doi: 10.1111/j.1365-2486.2009.02004.x

Jasechko, S., Sharp, Z. D., Gibson J. J., S. Jean Birks, S. J., Yi Y., & Peter J. Fawcett, P. J. (2013). Terrestrial water fluxes dominated by transpiration. Nature 497, 341-451.

Körner, C. (2003). Ecological impacts of atmospheric CO2 enrichment on terrestrial ecosystems. Philosophical Transactions of the Royal Society of London A, 361(1810), 2023-2041.

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Welcome to The Hip Ecologist

I have set up a new page for sharing my research and all things related to it. Stop by from time-to-time to see what I’m up to. For now check-out the institute –The Institute for Applied Ecology New Zealand – that I am associated with to get an idea of what is happening around me.

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