Semester Overview and Summation

12/16/11

During the course of this semester I undertook a Directed Readings Seminar with two members of the faculty at the University of North Carolina at Chapel Hill, Dr. James Umbanhowar and Dr. Charles E. Mitchell. Under their guidance and direction I critically examined approximately two sources of literature from the field ecology each week, wrote a combination objective and subjective blog about each, and then met with one of my advisors to discuss the work and its context within the larger field of ecology. The blogs for these papers are given as a transcript below, however the original sources can be found at the website address given in the title of this report.

The range of topics covered stayed mainly within the fields of invasive species ecology and disease ecology, from which both theoretical and experimental studies were analyzed. Generally, the method of article choice for the following week was based on intriguing topics that were embedded in the current weeks’ discussion. We began with an overview of the models used to map the spread of invasive species over time and space. From here we were able to expand into a variety of different types of models used in the ecological sciences, including traveling waves, stratified diffusion, and even the classic SIR models (Susceptible-Infected-Recovered). Several case studies were analyzed for classic epidemiological cases, including measles, Dutch Elm Disease, conjunctivitis of birds in the northeastern United States, influenza, and cholera.

From the experimentally-based literature sources we covered a variety of system choices and pathogen types. Marine diversity of pathogens and their relevance to the resource cycling of primary producers was looked at, along with the interaction of different kinds of pathogens within a single host, whether that host population was buffalo herds from Africa, or bacteria in culture.  We also spent some time investigating the role of lifestyle choices in viruses, whether a lytic (kill first) or lysogenic (incorporate into host genome) lifestyle could be favored in certain environments over others. We ended the semester with an exploration of the role of certain kinds of nutrients on pathogen dynamics.

In summation, a broad range of topics was covered during the course of this seminar. The subject material was chosen from both subfields of invasion and disease ecology. For the most part however, the string of literature sources was woven together from week to week to allow flexibility in topic choice, but also to allow growth and exploration of the more difficult questions presented within the ecological sciences.

Elser, J.J. et al. Ecology Letters. (2007).

"Global analysis of nitrogen and phosphorus limitation of primary producers in freshwater, marine, and terrestrial ecosystems".

Reviewed: 12/02/11

Past research has demonstrated the importance of nitrogen and phosphorus as limiting nutrients across a wide variety of habitats. The relative merits of each one as the primary nutrient of limitation however has been debated across systems. Does the biological demand for N and P depend on the system of study, namely terrestrial, freshwater and marine, or is the biological machinery necessary for photosynthesis and autotroph-ism similarly affected by nutrient additions or limitations across the globe? A meta-analysis comprised of a little more than 1000 separate experiments was the basis for this study. Experiments were drawn from a wide variety of habitat types across each system, and from multiple latitudes. Above- and below-ground experiments were also used for the terrestrial systems. The results of each study was converted into a log-transformed response ratio that looked at the effect of N, P, or N+P addition on some metric of community production or biomass. Only studies that manipulated both N and P within the experimental design were included in the meta-analysis.
Additions of nitrogen and phosphorus were found to induce a significant, non-zero, positive response across all system types. The community response to P additions, averaged across all habitat subtypes, did not significantly differ across the systems, though the response to N alone, as well as to N+P, did differ. Marine systems received a particularly large boost from additions of N relative to P. A synergistic effect was noted from the dual addition of N and P across all systems, whereby the addition of both limiting nutrients induced a larger response than the sum of each nutrient effect alone. The reason for this is unclear and may depend on the habitat of study. Say if for example bacterial autotrophs are better able to cope with reductions in N as long as they are not experiencing a simultaneous decrease in P.
Terrestrial and Freshwater systems were both shown to be equally limited by N and P, though marine was not as previously stated. Within systems however, the equivalence of N and P as limiting nutrients was not always true at the habitat subtype level. Grasslands were shown to be equally limited by both nutrients, while forests responded more readily to phosphorus additions.
The similarities in nutrient limitation across systems highlights the need for researchers to consider both major nutrients in their assessments of ecosystem dynamics, while the variation seen within habitat leads to the notion that every system of study should be assessed independently if possible in order for adequate conclusions to be drawn. The source, cycling, and use of nutrients within each system was not assessed in this article. Though these three dynamics may be of more relative importance within a system depending on the biological demand for a certain quantity, and quality, of nutrients. There are global scale differences in how nutrients are turned over within systems and where they come from. The merits of this study comes from its ability to draw large scale conclusions about community response to key nutrient additions, however a similar broad scale look at the internal dynamics of these nutrients within communities would also be beneficial to future assessments, particularly as they relate to global change.

Cronin, J.P., et al. Ecology Letters. (2010).

"Host physiological phenotype explains pathogen reservoir potential".

Reviewed: 12/02/11

The framework for approaching disease should not always be focused at the level of the individual or population of hosts only. The capacity any given individual has for disease directly affects how that disease might be transferred to other potential hosts within its community. The authors of this study set out to assess the reservoir potential of 6 different grass species, important to California grasslands, as they relate to the the viral pathogen Barley Yellow Dwarf Virus-PAV (BYDV-PAV) and the aphid vector Rhopalosiphum padi. Reservoir potential has been linked to three measurable epidemiological traits: the susceptibility of any given host to transfer of virus by the vector, the competence of the host to pass on the virus to a feeding aphid after the disease had become internally systemic, and lastly the host ability to support vector populations.
During the first Greenhouse experiment physiological traits were measured for the 6 different grasses, independent of viral infection, under conditions of low and high nitrogen. Principal Component Analysis (PCA) was able to condense the results of all five traits down to two primary principal component axes (PC1 and PC2). PC1 explained 50% of the variance in the results and was linked with a beforehand hypothesized continuum of 'Quick-Return' and 'Slow-Return' phenotypes, QR and SR respectively. The QR-SR continuum is a classification continuum that posits that quick growing host species will be more poorly defended but faster growing, while slow return species will allocate less overall to rapid, short-term growth but will have high defenses to enemies. The link of PC1 with this continuum was important for the researchers as it cohesively combined a complex array of traits into one definable axis of study.
Under the two nitrogen regimes, those grasses grown under higher nitrogen were consistently shifted more toward a QR phenotype, except for a single grass host.
The second part of the experiment was designed to test whether the conglomerate of physiological traits was sufficient to explain the three epidemiological parameters previously outlined, or whether host lifespan, phylogeny, and provenance (native vs. exotic) were also required. Nested models were used to test this theory by systematically dropping explanatory terms from the model, and using AIC for comparison. Host physiological traits, in the form of PC1, were consistently necessary to explain host reservoir potential. QR type hosts are more efficient as reservoir hosts, meaning that can support high levels of aphid vectros, become infected more easily, and transfer pathogens more easily. The authors propose host physiology as primary in importance for predicting epidemiological parameters, however the phylogenetic history and lifespan/provenance of a host is still relevant to the discussion, as shown by their significant inclusion in two of the paramters: vector population size and host susceptibility.
This study looked at five traits and ran them through a PCA, however future studies should expand beyond the nitrogen centered framework used here. Multiple nutrients are responsible for the dynamics seen in terrestrial systems, (eg Nitrogen and Phosphorus, as wel as other micronutrients). In this experiment nitrogen was shown to shift grasses towards being a better host. If phosphorus addition or faster growth do to rising CO2 levels do the same, then this will have important implications for global change analysts and the disease emergence in the future. Inclusion of more broad-scope traits would impove the results of this analysis.

Frost, P.C., Ebert, D., & Smith, V.H. Ecology. (2008).

"Responses of a bacterial pathogen to phosphorus limitation of its aquatic invertebrate host'.

Stoichiometric conditions of the food, whether living or not, are known to have strong effects on the organism doing the consuming. Nutrient quality has the potential to drive patterns in enemy fitness as well as to reciprocally affect the tolerance of the host or prey. Three main response variables were analyzed during the source of this experiment, whereby invertebrate Daphnia magna hosts were fed on specific nutrient-levels of food and dosed with a set number of spores of the highly effective microparasite Pasteuria ramosa.  The theoretical queries at the base of this experiment are whether nutrient poor conditions will limit the pathogen as well as the host, or whether under nutrient poor conditions, the pathogen will become preferentially more efficient at utilizing the limited nutrients, thus having a higher virulence on its host.
The infection rate of the bacterial pathogen was assessed by manipulating the nutrient conditions of the food for Daphnia during the infection period, but thereafter maintaining constant nutrient conditions across all treatments, in order to assess only the ability of the pathogen to infect. A linear relationship between phosphorous content of host food and infection rate was observed, with a higher degree of infection for high phosphorus conditions. Based on previous work the authors believe this result if most likely due to reduced growth of the bascterial spores within the host under low phosphorus conditions rather than due to reduced feeding habits or contact rates.
In contrast to the methodology used to assess infection rate, spore production of the pathogen was measured by maintaining constant nutrient conditions of the food during the infection period, but thereafter altering the food content by treatment. In general more spores were found in hosts fed on phosphorus rich foods, though the relationship was non-linear. This pattern seems to be largely driven by the reduced size of the host fed on nutrient poor foods, however the density of spores within the host was non-constant across treatments. this may be interesting for future work as it could help determine if the pattern of reduced spore counts is in fact fully linked with reduced host size. An interaction may exist whereby larger hosts may still contain a proportionately larger number of pathogens in nutrient rich conditions. An experiment with a higher number of treatments, or hosts that are measured for spore containment more often during the potential growth period, could reduce the irregularities within the results and indicate a more concrete relationship between pathogen density and nutrient conditions in this study system.
The final portion of this study hoped to look at the question of nutrient effects on host reproduction. The difference in reproduction at all nutrient conditions was assessed for both infected and uninfected individuals. not surprisingly, infection reduced host production, period. However, this decrease was more dramatic in hosts fed on a low phosphorus diet, indicating that the virulence effects of the pathogen on its host was in fact higher under nutrient-stressed conditions.

Pradeep Ram, A.S. & Sime-Ngando, T. Environmental Microbiology. (2010).

"Resources drive trade-off between viral lifestyles in the planton: evidence from freshwater microbial microcosms"

Reviewed: 11/18/11

The two possible lifestyles of viruses living in aquatic systems has often been considered as a trade-off. Each lifestyle presenting its benefits and costs under certain environmental conditions, and both lifestyles having persisted across evolutionary time because of this very antagonism in the trade-off. The investigators of this paper chose to look at nutrient conditions might be responsible for the conversion of a lytic cycle pathogen into its lysogenic state. They tested the hypothesis that the addition of organic and inorganic nutrients decreases the presence of the lysogenic lifestyle overall. The experiment was conducted in a laboratory setting on samples collected from a freshwater lake in France.
Mytomycin C is an antibiotic that crosslinks DNA and can initiate a repair pathway within cells. It was this chemical that was used to induce prophages to leave the lysogenic stage. This is a common experimental technique used to determine proportion lysogenic stage (based on difference from lytic). More evidence needs to be collected on its accuracy, but overall it seemed to be a better estimating method than the TEM-based counts used as the alternative by the researchers.
Viral abundance increased under conditions where its host was fed on high nutrient based foods. This result was particularly true for inorganic, as well as organic, carbon additions. This increase however, seemed more closely linked to the benefit that the nutrient additions provided to host growth rates and abundance. researchers also measured the burst size, or internal reproduction of the virus within their hosts. The magnitude of this response was again linked to increased carbon conditions.
A ratio of lytic to lysogenic frequencies showed that a higher proportion of lysogens were found in ambient nutrient conditions, as well as for samples that had been experimentally manipulated to contain reduced viral to host ratios. The authors propose that more lysogens can be found in virus-reduced samples because the direct competition between hosts increases, creating poorer host conditions for a potentially lytic-stage virus. This finding was also proposed to be a result of lower contact frequency between host and pathogen stimulating a waiting-type lifestyle (lysogeny), until higher contact rates could be achieved.
Analysis of the Pearson product-moment correlation coefficients shows a very clear antagonism between the frequency of lytic viruses and that of lysogenic ones. This supports the idea that these two lifestyles do in fact represent a distinct trade-off in life-history metrics. The other key result from this experiment, as prevously stated, showed that nutrient additions beyond the ambient increased the proportion of lytic-lifestyle viruses largely as a result of increased bacterial population numbers. However, the study did not demonstrate that decreasing the nutrient conditions within the samples could lead to higher counts of lysogeny. This could be achieved in the future by placing the host species into a broader range of nutrient conditions by chemically manipulating the waters found naturally in the freshwater lake used in this study.

Faruque, S. M. et al. PNAS. (2005).

"Seasonal epidemics of cholera inversely correlate with the prevalence of environmental cholera phages".

Reviewed: 11/10/11

Cholera epidemics in and around Dhaka, Bangladesh occur seasonally, typically twice a year. Cholera is a human disease that is caused by pathogenic strains of Vibrio cholerae, however the bacteria is a normal component of aquatic ecosystems. Aquatic transmission of the disease-causing bacteria was first noted approximately one hundred and fifty years ago and while many environmental and biological parameters have been associated with the temporally varying disease surges, none have been conclusively linked to the cause or finish of the epidemic (other than the obvious requirement of water). Bacteriophages have been shown to be linked to transmission of toxigenicity in V. cholerae. Data obtained from plaque assays, bacterial cultures, and stool samples randomly obtained from local hospitals were used to demonstrate that the abundance of cholera-inducing bacterial strains was inversely correlated with increases in their own pathogens' numbers.
If the presence of a host-specific bacteriophage was noted within any given water sample collected from local aquatic systems, than its target host was significantly less likely to be found. The percentage of co-occurrences of virus and target host was lower than one that could have been predicted by chance alone.
Cross comparison of monthly collection and analysis for phages in water samples with stool samples showing cholera disease in humans did in fact show an oscillating relationship between the bacteria strains and their viruses. Two strains of bacteria are primarily responsible for the disease in Bangladesh, and six phage types, which can actually be grouped into 4 genetically distinct groups, are associated with them. However, the life modes of these viral types are not all homogenous. The authors propose that the difference between lytic and lysogenic capable phages may be driving a lot of the seasonality of the cholera epidemics.
The model they present begins with epidemics arising during periods of low lytic phage concentrations as described above. Modularity in epidemics may come about from the presence of lysogenic bacteria because lysogeny can build up in bacterial populations via prophages. Prophages make the lysogenic bacteria resistant to superinfection by other viral types and concurrently drive other bacterial strain populations down because they do not have the resistance to the lytic-cycle-dominant phages still present in the system.
This difference in lysogeny or lytic cycle phages, if they are capable of only one cycle or both and what would induce them to choose lysis over lysogeny, is here shown to directly link to the basic pattern of the cholera epidemic.
Other studies have provided evidence on the elimination of a previously dominant V. cholerae strain due to differential infection patterns of a lysogenic virus. It seems that more information on what environmental conditions are necessary to induce a lysogenic pathway in the virus would be useful for researchers hoping to identify natural resevoirs for the virus, or inversely the bacteria. Nutritional treatments could easily be applied to cultures of bacteria and virus in a laboratory setting. Similar methods used to test for prophages as were used in this study (methods such as Southern blots and DNA probes) could potentially provide a lot of information on this globally pervasive disease and the bacteria that causes it.

Suttle, C.A. Nature Reviews., (2007).

"Marine viruses - major players in the global ecosystem".

Reviewed: 11/10/11


Viruses are the most abundant player in the oceans when it comes to quantity of genetic information. Viruses in general are a unique class of organisms to consider due to their ability to infect hosts at multiple trophic levels. They have the potential to exert controlling forces on autotrophs and the heterotrophic grazers that feed on them. The author of this review presents information on different aspects of viral ecology as they relate to the specifics of a marine system, as well as the molecular techniques that have been developed to quantify their abundance.
It appears as though marine virus ecology might be fundamentally different from its terrestrial counterpart. It seems to me as if marine viruses can be thought of as existing in one gigantic pool, floating and dispersing after lytic events of their host species. Whereas as in terrestrial systems we usually think about viruses as being vectored or transmitted in some more organized fashion. Along with this idea is a lack of understanding about the way that viruses are transmitted in the ocean. A significant amount of data, involving genetic sampling in many diverse aquatic habitats around the globe, seems to show that their exists hotspots for certain virus families in differential parts of the ocean. It is possible to identify commonalities in different viral lineages as well. The VHSV virus is associated with a disease in trout farms of Europe, but has also been identified in marine fish and in some lakes in North America.
Interest in amassing more data on the specific roles of viruses in the ocean can be linked to their role in turnover and shuttling of carbon and other limiting nutrients as they infect and lyse their hosts. Particulate and dissolved organic matter arising after these events increases the amount of respiration done by decomposers in the photic zone.
The author also presents an interesting analysis of the spectrum of r and K selection in both the host species of the ocean and the viruses that infect them. While it appears that the abundance of marine prokaryotes and eukaryotes is weighted towards k strategists, who are slow growing and resistant to infection, the abundance curves and r-K spectrum is the opposite in the viral community. The most abundant viruses appear to genrally fall under the header of r-selected species, those with rapid replication and generally more virulent. This contrast of host and pathogen has important implications as it indicates that the rarer host species, those that are more r-strategists and are the most susceptible to infection, are controlled by a highly abundant, rapidly-replicating pathogen community. This does not mean that r-selected host species never undergo periods of release where they rapidly reproduce and expand in concentration, but it does imply that viruses are an important control to bring the overall marine ecosystem back to a more equilibrium state. It would be interesting to attempt to quantify both the affect that viruses have on the grazer populations ability to control other dominant eukaryotes or prokaryotes and how viral effects on these lower trophic order species affects the grazers who might feed on them.