Friday, March 29, 2013

Getting to the Roots (and Fungi) of Carbon Sequestration

This week, I found a paper that I’m calling the best of both worlds. Well, for me at least. This paper combines my past (and lingering) interest in island biogeography with a current interest in climate change and carbon storage.

If you have been reading my blog long enough then you already know my love of islands. They are just so darn useful. In the past, I have focused on oceanic islands, but lake islands are also really neat. These types of islands typically form when lower lying land areas fill with water, effectively cutting off higher areas from the mainland and making them into islands. As such, these islands usually already contain forest as opposed to an oceanic island that emerges from the ocean and must be colonized. A new study, published in journal Science, looks at a fire-driven boreal forest chronosequence on forested lake islands in northern Sweden. Such a chronosequence allows the study of soil carbon sequestration over time scales of centuries to millennia.

This new study looks at roots and their associated fungi (mycorrhizae) as sources of this stored carbon. I’m not going to spend the space to describe mycorrhize, but will, instead, send you over to my Free Market Fungi post for more information, if you need it. It is known that 16 percent of the global carbon stock is sequestered in soils. To date, most carbon studies of this type focus on aboveground leaf litter as the fundamental determinants of this carbon accumulation. But a large portion of photosynthetically fixed carbon is actually directed belowground to the roots and, subsequently, the mycorrhizae. Now, let’s add fire. It has been shown that when a forest doesn't burn, the soil and ecosystem carbon accumulate unabated, and in a linear fashion. Add this information together and it becomes a big deal when it comes to correctly allocating carbon, calculating the long term sequestration rates, and predicting how forests will respond to climate change and other environmental shifts.

The study sites were in two adjacent lakes, Lake Hornavan and Lake Uddjaure, in northern Sweden. The islands in these lakes were formed after the most recent glaciation and come in a variety of sizes. In terms of fire, larger islands burn more frequently because they are larger targets for lightning strikes. As a result, several of the large islands in these lakes have burned in the last century, whereas some of the small islands haven’t burned in at least 5000 years. This lack of fire leads to very thick humus layers (or organic layers towards the top of the soil column) on smaller islands, up to 1 meter thick!

The researchers divided islands into three size classes of 10 islands each: large (over 1 ha), medium (0.1-1.0 ha), and small (less than 0.1 ha). They took soil samples from these islands to look at the organic soil profiles and found that large islands accumulated 6.2 kg of C per square meter belowground with a mean time since fire of 585 years, medium islands accumulated 11.2 kg of C per square meter with a mean time since fire of 2180 years, and small islands 22.5 kg of C per square meter with a mean time since fire of 3250 years. Then they looked at the carbon dynamics across this chronosequence by analyzing bomb 14C. This allowed them to determine the age since fixation of soil carbon. Then they fitted a mathematical model to measurements of carbon mass and age distribution across the soil profiles for six of the islands (3 large, 3 small). This model revealed that the distribution of carbon mass and age could only be predicted when they included carbon from roots. This root-derived carbon accumulation was found to be larger on small islands (70 percent, that's a LOT!) than large islands (47 percent). They were able to explain the entire carbon sequestration difference on small islands from these root-derived inputs. The model also showed that small islands store a major proportion of their soil carbon in the deeper soil layers, those over 100 years old. However, below 20 cm depth, the root-derived carbon inputs were shown to be low and to decompose slowly. So the root-derived carbon input into the upper layers probably contributes to the long-term buildup of humus that is seen on these islands. But, as usual, that's not the end of the story.

We know that fungi play very important roles in forest ecosystems, both as decomposers and in root-assoicated carbon transport and respiration. So the researchers also profiled the relative abundance of major groups of fungi by depth in the soil profiles. They found that the upper soil layers are dominated by free-living saprotrophs (fungi that obtain their nutrition heterotrophically from non-living organic materials), and greater depths were dominated by mycorrhizal and other root-associated fungi. Their model suggests that these mycorrhizae live at the spots where the largest difference in carbon sequestration between the island size classes exists, which also tends to be the areas of highest root mass. When they ran tests for fungal biomass throughout each soil profile they found greater mycelial (the vegetative part of a fungus, consisting of a mass of branching, threadlike hyphae) production on large islands, but less mycelial necromass (dead stuff) on small islands. This suggests that the large production is counterbalanced by faster decomposition of mycelial remains. “Correspondingly, the 14C model indicated faster decomposition of root-derived [carbon] on large islands, despite inputs being conservatively constrained to be equal across all islands.”

I found these conclusions to be interesting because of the amount of soil carbon from roots and mycorrhizal fungi, especially on small islands. And although they saw less carbon accumulation on large islands, these islands have a greater root density and so should have more carbon allocation to roots and the associated fungi. Did you catch the contradiction? Well, in response to increased carbon dioxide, there will be an increase of carbon inputs to the roots which will accelerate the turnover of soil organic matter. This counteracts carbon accumulation and enhances nitrogen cycling through the microbial pools, an effect these researchers observed when they tested the C:N-ratios in the humus of large islands. This is much lower on small islands, possibly because of impared mycorrhizal nitrogen mobilization and the accumulation of nitrogen in fungal remains. This leads to progressive nutrient limitations, then leads to changes plant productivity, leading to changes in community composition, which leads to changes in total belowground carbon allocation, that leads to changes in fungi.

Definately starting to grasp the importance of the belowground dirty stuff. There’s a whole lot of carbon down there that we need to start looking at, accounting for, and seeing where it goes. We know that changes in the environment such as climate change, soil fertilization, fire suppression, and forest management make big differences to the aboveground stuff. It only makes sense that the belowground stuff is impacted as well.

ResearchBlogging.orgClemmensen, K., Bahr, A., Ovaskainen, O., Dahlberg, A., Ekblad, A., Wallander, H., Stenlid, J., Finlay, R., Wardle, D., & Lindahl, B. (2013). Roots and Associated Fungi Drive Long-Term Carbon Sequestration in Boreal Forest Science, 339 (6127), 1615-1618 DOI: 10.1126/science.1231923

If you would like some follow-up reading I suggest:

Treseder, K. K. (2013-03-29) Fungal Carbon Sequestration. Science, 339(6127), 1528-1529. (DOI: 10.1126/science.1236338

Also check out the write-up in Nature "Fungi and roots store a surprisingly large share of the world's carbon"

(image via Forest Keepers)

Tuesday, March 26, 2013

The Mockingbird Problem

In the past, I've had this exact problem with a mockingbird. Currently, I'm having a problem with a Carolina wren that isn't aware that it isn't supposed to be singing outside my bedroom window at 3 a.m.

(via Bird and Moon)

Monday, March 25, 2013

Bad Habits (in Lab)

Ummm...I might be guilty of some of these....

Friday, March 22, 2013

They're All Alike: The Giant Squid Conundrum

I wasn’t going to post on another paper this week but then two things happened: I saw the video of the first giant squid filmed in its natural habitat (those scientists get so excited!), and I saw the study about giant squid diversity. I posted the first above and now we'll take a look at the second.

The giant squid (Architeuthis spp.) is one of the largest invertebrates and lives in the deep sea. It was first described as Architeuthis dux in 1857 by Danish naturalist Japetus Steenstrub, but since then, as many as 21 nominal species of Architeuthis have been described. The descriptions of this creature have primarily come from remains found washed up on beaches, found floating on the ocean surface, caught by deep-sea trawling activity, or in the stomachs of sperm whales (Physeter macrocephalus). It wasn’t until 2004 that a live specimen was observed in its natural habitat, and earlier this year that the first video footage was published (although not the in-the-natural-habitat version above). It is estimated that female squid reach a total length of 18m (59ft) and males reach slightly smaller sizes. The giant squid is globally distributed, with the exception of polar regions. They feed primarily on fish and smaller cephalopods. Studies of carbon and nitrogen isotope profiles of the upper beaks suggest ontogenetic diet shift earlier in life (smaller to larger prey items), and carbon isotope composition remains constant in food sources indicating that the squid inhabit relatively small, well-defined and productive areas. The predation of adult squid by sperm whales suggests that squid population size must be large enough to support such a large whale population, although this has never been proven.

There are some rather obvious difficulties in studying giant squid using conventional, observational techniques. So other techniques must be utilized. Enter, DNA. Recent advances in DNA sequencing techniques have made it easier, quicker, and more economical to sequence long stretches of DNA. The role of DNA sequencing is becoming more and more important in phylogenetic and population biology studies. It allows you to assess the number of species, examine the amount of genetic variation, and describe population structure.

In a new paper in the Proceedings of the Royal Society B: Biological Sciences, researchers collected 43 Architeuthis soft tissue samples from the carcasses of dead animals across their known range. They extracted DNA samples from the specimens to analyze the mitochondrial genomes (mitogenomes) and levels of nucleotide variation. They generated mitogeome datasets using several strategies, depending on the quality of the DNA in each sample. I’m not going to go into their sequencing methods – if you are a molecular biologist then you already know them, and if you aren’t then I’ll just bore you. To look at the population level of the genetic variance, they wanted to compare their samples with the fossil record of coleoid cephalopods. This is challenging considering the extremely limited fossil record for these organisms. So they used four different mutation rates to tentatively estimate a time of expansion and upper and lower bounds for the time of divergence of Achiteuthis from other squid families.

They were able to complete 37 complete and 6 partial mitogenome sequences. Remember up at the top of the post where I said “21 nominal species of Architeuthis have been described?” One pretty strong conclusion of this study is that there is only one species of Architeuthis that exists, namely Architeuthis dux (Steenstrub, 1857). The researchers found the haplotype diversity of these giant squid to be high at the mitogenome level, but the level of nucleotide diversity in these sequences was found to be extremely low, with only 181 segregating sites of a 20,331 base pair long sequence. Only the basking shark (Cetorhinus maximus) has a similarly low diversity, which is the result of a recent bottleneck. This diversity for giant squid is much lower than is seen in other squid, 44 times lower than Humboldt squid (Dosidicus gigas) and 7 times lower than the recently restricted population of oval squid (Sepioteuthis lessoniana). The high haplotype to low nucleotide diversity relationship is interesting because it shows that out of a very diverse phyla of animals, the giant squid is the odd one out. Looking at the species across its range, there was no evidence of any phylogeographic structure, which is odd considering the global distribution.

So how do you explain the low genetic diversity in comparison to the global distribution (and potentially large population size)? The authors hypothesize that it could be a low rate of mitochondrial DNA evolution, something that has been observed in other marine organisms. But a low mutation rate does not explain why mitogenome duplications maintain near 100 percent identity. The authors suggest that “perhaps the duplicated sequences form stable secondary structures, which are somehow selectively beneficial, thereby causing mutations to be under negative selection,” which would lead to “a decreased rate of divergence in the duplicated regions relative to the rest of the genome, which does not appear to be the case.” Alternatively, it could be a recent selective sweep such as a bottleneck. Bottlenecks are events that greatly reduce the size of a population, usually resulting in a large reduction in the genetic diversity of that group. If this bottleneck were followed by an expansion in the number of individuals in that population then you would see that low diversity spread amongst a large population. Modeling and analysis of data support the latter hypothesis over the former.

Unfortunately, genetic data alone can’t provide an answer as to why this might have happened. Whatever event it was, climatic or biological, it would have had to been wide ranging enough to affect a global population. Perhaps it was a sudden inflation of a population that was historically smaller. It is known that cephalopods tend to be subdominant predators, and as such, are affected by the changes in population of predators and competitors. If this small size was due to restraints on predators and/or competition and that restraint were released then you would expect such an inflation in squid numbers. Considering the effect of industrialized whaling in the 1700s to late 1800s, this is a likely explanation, but still too recent to explain it entirely. This change in predators and/or competitors could have been the result of climatic effects such as the last ice age changing. Such changes could have altered the abundance and distribution of competitors such as predatory fish. Or perhaps, rather than a bottleneck, A. dux existed historically as a single, small, geographically isolated population that then expanded globally. This expansion would have had to been in a non-ordered fashion with either nomadic adults or dispersing juveniles and small pelagic paralarvae capable of using currents to travel long distances. But if they can disperse really far then why would they have been restricted historically? The authors hypothesize that a global population existed for a considerable time, and that an average of just one individual exchanged between two populations per generation will be enough to prevent genetic differentiation between them. They believe that the wide ranging dispersal of paralarvae and juveniles on the currents of the upper layers of the oceans could achieve this. These young life stages float along with the currents feeding on zooplankton and such until they reach a sufficiently large size, after which they descend to the closest nutrient-rich deep habitat where they remain until maturation.

I think that’s a pretty good explanation. What about you?

ResearchBlogging.orgWinkelmann, I., Campos, P., Strugnell, J., Cherel, Y., Smith, P., Kubodera, T., Allcock, L., Kampmann, M., Schroeder, H., Guerra, A., Norman, M., Finn, J., Ingrao, D., Clarke, M., & Gilbert, M. (2013). Mitochondrial genome diversity and population structure of the giant squid Architeuthis: genetics sheds new light on one of the most enigmatic marine species Proceedings of the Royal Society B: Biological Sciences, 280 (1759), 20130273-20130273 DOI: 10.1098/rspb.2013.0273

ScienceNOW article: "Giant Squid Worldwide Are One Species"
ScienceDump: "The search for the giant squid"
Vido via Nature's: "Giant squid filmed in its natural environment"

Thursday, March 21, 2013

The Rose Shank

(via Alex Culang and Raynato Castro's website Buttersafe)
note panels moved vertically for space requirements

Wednesday, March 20, 2013

Tuesday, March 19, 2013

The Character of Elements

Kaycie D. received her BFA from the Milwaukee Institute of Art and Design with a major in Animation and a minor in Illustration. For her senior thesis project she decided to take on a massive character design project that she called “Elements - Experiments in Character Design.” Her goal for this project was to design a character based on each of the known chemical elements in the Periodic Table. The project premiered at her school's Senior Thesis Exhibition from April 2011 - May 2011 for 72 of the elements, and she completed the remaining 40 elements in November of 2011.

I'll whet your appetite with a few of my favorite of Kaycie's Elements. You can see the rest over at her KCD blog and her tumblr page.

(via io9 and The Mary Sue)

Monday, March 18, 2013

Biological Beta Testing: Altitudinal Edition

Spatial patterns in biodiversity have always been a popular topic in ecology, and understanding these patterns helps us to address the looming threats to biodiversity.

Did you notice how I made the word ‘patterns’ plural? There isn’t a whole separate field of biogeography for nothin’. Biological diversity is difficult (some say impossible) to measure using a single metric. How do you count things? Simply by the number of species? How about rare versus common species? What about species turnover? What geographic scale are you using? How and/or do you define boundaries? Would you like me to keep going or do you get the point?

Lately I’ve noticed a surge in the number of studies that look at diversity gradients that occur along latitude and altitude. We visited the topic of latitude and diversity back in October of last year with the “Dinosaurs, Diversity, Distribution, and the LBG” post. Essentially, latitudinal gradients (LBG or LDG) occur when species richness (a simple count of species) is highest in the tropics and declines polewards (warm areas are more hospitable and produce more food). Altitudinal, or elevational, gradients are nearly as ubiquitous as latitudinal gradients, and they have many of the same characteristics. As you go up in elevation (as on a mountain) the temperature gets colder and habitat areas and the communities they support become smaller and more fragmented. Gradients such as these are overall patterns. Now mix them with diversity indices. In 1960, R.H. Whittaker described the terms alpha diversity (α-diversity), beta diversity (β-diversity), and gamma diversity (γ-diversity). Basically, the total species diversity of a geographic area (γ-diversity) is determined by the mean species diversity at the local, within-site or within-habitat scale (α-diversity) and extent of change in community composition between sites (β-diversity). These definitions have been much argued over (see Tuomisto 2010), and we won’t get in to that. We are going to focus on beta diversity (β-diversity), also called species turnover or differentiation diversity. It is a measure of how different sites are from each other and/or how far apart they are on a gradient of species composition. Factors that drive β-diversity are very important, very poorly understood, and very much argued over. Is it dispersal limitation? Habitat specialization? Environmental heterogeneity? The studies published so far seem to lean toward multiple processes operating at various scales. *sigh* Isn’t that always the way? Observational and experimental studies have shown that impacts on β-diversity vary with productivity. So it would make sense to test this in relation to altitudinal and elevational gradients.

A new study to be published in Global Ecology and Biogeography looks at how local community processes may create an altitudinal pattern of β-diversity. Their study site was the Shiretoko National Park in north-eastern Hokkaido, the northernmost island of Japan. In addition to being one of the richest temperate ecosystems in the world, the area is characterized by sharp altitudinal changes in forest structure and productivity as a result of strong winds on the western side of the mountains. The researchers chose this western side to measure the diversity of woody plants and mites (Oribatida) in mature stands where they set up seven plots (each containing 10 subplots) at different altitudes. For the woody plants they recorded the number of individuals taller than 0.5 m, measured the girth at breast height (GBH), estimated the total basal area (BA), recorded canopy height (CH) of the stand, measured the diameter and length of all coarse woody debris (CWD), measured understory light, took soil cores to extract the mites, removed roots from the soil samples, measured the thickness and dry mass of the soil surface litter (A0 layer), collected leaf litter, measured water content and pH of the litter, and the carbon-to-nitrogen (CN) ratios of the litter and soil. They then calculated the β-diversity of the two organism groups for each altitude. So as to take into account the dependence of β-diversity on gamma diversity (γ-diversity), they used null modeling. This type of modeling “randomly shuffles individuals among subplots while preserving γ-diversity, the relative abundance of each species per plot and the number of individuals per subplot” which enabled them to estimate how much observed β-diversity differed from expected β-diversity. They also calculated a β-deviation value for each altitude. This is equivalent to a standardized effect size, indicating the magnitude of the deviation from what you would expect of a random (stochastic or by chance) assembly process.

First we’ll hit the results for the oribatid mites. These results showed the altitudinal gradient of β-diversity to be less evident than it was for the plants, and β-deviation showed no altitudinal gradient. That said, they found β-deviation to always be greater than expected in all locations for both woody plants and oribatid mites. In woody plants, the magnitude of β-deviation increased with altitude, suggesting that deterministic processes dominate in low-productivity, high-altitude stands, the role of these processes increasing with decreasing productivity in plant communities. The authors conclude that their results support the hypothesis that “the mechanisms underlying community assembly (e.g. niche versus neutral) play an essential role in creating biogeographic patterns of β-diversity.” They found that niche-based processes (species correlate with environmental variables, the conditions in which the species can persist) govern high-altitude stands, particularly when they included the plants growing in lower layers in the analysis. They found similar results when they calculated β-deviation along a stand-structure gradient with basal area, not altitude, particularly when small understory plants were included. This suggests that “given the altitudinal changes in stand structure, the role of understory plants in deterministic assembly becomes more dominant with altitude.” So those little guys really make a difference! Why? Well, considering that light is a precious commodity, low-elevation, structurally well-developed stands have higher competition for available light, especially for those little understory guys. This fierce competition isn’t so fierce in the higher altitude sites where the upper canopy isn't there to usurp all of the light for itself. This favors a greater, more diverse understory in higher elevations. Again, the authors speculate that this greater high altitude diversity is due to fine-scale niche partitioning, which allows more individuals to exist together.

Okay, so that is a pretty good explanation for the high altitude communities. Now what is going on at low altitudes? Well, there you have to take the site’s history a little more into account. What made these stands so “structurally developed” and generated this stochasticity? Consider this: The canopy trees of these forests colonized before the understory individuals, negatively affecting understory species by reducing the availability of space and resources. You then see a relative dominance of these big-ole-bully trees (that’s a technical term, you know) and a one-sided competition scenario.

Did I scramble your brain and make you hate biogeography yet? Can you see any sort of overall conclusion here? Lemme help you out…

β-diversity is dependent on community processes and shaped by local factors within the landscape. The species in a place use what is in a place.

Do you agree?

ResearchBlogging.orgMori, A., Shiono, T., Koide, D., Kitagawa, R., Ota, A., & Mizumachi, E. (2013). Community assembly processes shape an altitudinal gradient of forest biodiversity Global Ecology and Biogeography DOI: 10.1111/geb.12058

(image via

Friday, March 15, 2013

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