Microbial ecology from single cells to the ocean transcriptome

Elizabeth Ottesen
Postdoctoral Research Associate
Massachusetts Institute of Technology

Date: Thursday, December 10, 3:40 - 4:40 p.m.
Location: 1210 Chemistry
Host department: Ecology and Evolutionary Biology


Abstract

Microbial ecologists work on scales that range from the biology of individual strains to the impact of microbial communities on the biochemistry of the ocean and the global carbon cycle.  I’ll be talking about two projects that approach microbial communities from very different directions. The first focuses on a single group of organisms, the CO2-reductive acetogens, within a symbiotic assemblage, the termite hindgut community. The second takes a wide-angle view, using next-generation sequencing technology to enable community-wide surveys of microorganisms from the ocean.

In order to learn more about the biology of homoacetogenic bacteria within the termite hindgut, I developed the use of microfluidic digital PCR to simultaneously amplify multiple genes from individual bacterial cells within environmental samples.  This allows retrieval and sequence analysis of multiple genes associated with a single genome.  I used this technique to identify (based on 16S rRNA sequence) bacteria that bear key genes involved in homoacetogenic C1 metabolism. On a broader scale, this technique is designed to allow the exploration of metabolic capabilities of individual uncultured microorganisms.

Metagenomic time-series study of a seasonally anoxic marine ecosystem

Abstract

Research Assistant
University of Wisconsin-Madison

(This seminar is scheduled during the Tuesday lunch seminars)
Date: Tuesday, Dec. 1, 2009

Time: 12:10 - 1:10 p.m.

Location: 2009 Ruthven Museums

Abstract
Microbial systems can serve as models to test ecological theory established in larger systems, but it is yet unclear which ecology "rules" apply to microbes. Here, we used aquatic bacterial communities to investigate the application of disturbance theory to microbes. Mixing acts as a disturbance to aquatic microbes because it disrupts vertical chemical and physical gradients that structure bacterial communities and influence biological dynamics.

We mixed a temperate, dimictic bog lake during summer stratification. We achieved complete lake mixing by mechanically oscillating large volumes of water at the deep hole of the lake. An instrumented buoy measured near real-time environmental physics and chemistry. We collected bacterial community (fingerprinting and next-generation sequencing) and water chemistry samples from discrete depths to investigate microbially mediated terminal electron substrates and products (e.g. iron, sulfide, methane) changes during the experiment.

Prior to treatment, the hypolimnion was anoxic and near 5 C. Over the course of the mixing experiment, the hypolimnion gradually eroded into the epilimnion until mixing at 19 C. Though the lake slowly re-stratified, the hypolimnion temperature remained high throughout summer. Oppositely, DO depleted in the hypolimnion within days following mixing, and remained low until fall turnover. The bacterial communities in the epilimnion and hypolimnion converged at mixing, and then diverged along separate seasonal trajectories. Though communities were generally not resistant to mixing disturbance, the surface and bottom bacterial communities were differently resilient, as observed by metrics of diversity and community structure. Our results support ecological framework that habitat heterogeneity and disturbance maintain diversity, and the use of microbial model systems for advancing both micro- and macro-scale ecology theory.

Geographical genomics of human gene expression variation

Greg Gibson
Professor and Director of the Center for Integrative Genomics
Georgia Tech University

Date: Thursday, November 19, 3:40 - 4:40 p.m.
Location: 1210 Chemistry
Host department: Ecology and Evolutionary Biology

Abstract
Genome-wide association studies with transcript abundance in peripheral blood samples or derivative cell lines have demonstrated a preponderance of regulatory polymorphisms, also known as eSNPs, which impact the expression of several percent of all genes. Several of these highlight associations that contribute to a variety of disease conditions, but the question arises as to how the associations are affected by the environment. We have addressed the robustness of eSNP associations to decanalization of the transcriptome in the face of different biotic and abiotic challenges faced in different geographic locations.

I will describe a gene expression GWAS that controls for population structure and lifestyle, in a comparison of Arab and Amazigh individuals from a city and two villages in southern Morocco. Approximately 400 genomewide significant associations are observed in leukocyte samples obtained from 194 individuals, the vast majority in cis, and all are consistent across the three sample locations and after controlling for ethnicity and relatedness, despite substantial divergence in the structure of the transcriptome in rural villagers. No evidence for large-effect trans-acting mediators of the pervasive environmental influence is found and instead genetic and environmental factors appear to act in a largely additive manner. I will discuss the implications for the origins of complex disease in human societies undergoing profound transitions where genotype-by-environment interactions might be expected to influence disease risk.

The bioeconomics of invasive species: examples from the emerald ash borer and zebra mussel invasions

Jonathan Bossenbroek
Assistant Professor
University of Toledo

Date: Thursday, November 12, 3:40 - 4:40 p.m.
Location: 1210 Chemistry
Host department: Ecology and Evolutionary Biology

Abstract

In a bioeconomic framework to address the threat of invasive species there are two basic objectives: 1) to provide estimates of the regional economic impact an invasive species will potentially inflict upon a region; 2) to provide policy-makers with quantitative guidance for cost-effective alternative strategies to control, prevent, or slow the spread of the species. Within this framework I will address the spread of dreissenid mussels to the western U.S. and the spread of emerald ash borer in Ohio and Michigan.

Recently, dreissenid mussels were discovered in the lower Colorado River. This infestation constituted the first population of dreissenid mussels west of the 100th Meridian and has the potential to increase their rate of spread in the western U.S. First, we forecasted the potential spread of dreissenid mussels throughout the entire United States by predicting the overland movement of recreational boaters with a production-constrained gravity model. Second, we used a computable general equilibrium model to determine the economic impact of a dreissenid introduction on the Columbia River basin. Our results predict that the relative probability of a dreissenid introduction to the Columbia River Basin has increased by ~25% compared to a previously published model based on the pre-Colorado invasion situation. Our economic analysis indicates that a dreissenid mussel invasion of the Columbia River Basin would result in a mean annual welfare loss of roughly $5 million.

The emerald ash borer is poised to wipe out native ashes in North America with expected catastrophic losses to the ash tree forestry. To explore the bioeconomics of this invasion, we 1) estimated the potential 2) built a dispersal model incorporating both the ability of the emerald ash borer to spread naturally and via human-mediated dispersal 3) estimated the value of the ash industry using a computable general equilibrium model (CGE) and the potential direct costs to urban areas and 4) explored the costs and potential effectiveness of eradication efforts. Our results suggests the welfare loss to both Ohio and Michigan would be over $50 million annually, and that slowing the spread optimally would have cost over $1 billion. We hope our results will provide policy-makers with quantitative guidance for management of these invasive species.

Vocal duetting in neotropical wrens: acoustic communication in the animal kingdom's most coordinated singers

Daniel J. Mennill
Associate Professor
Department of Biological Sciences, University of Windsor

Date: Thursday, November 5, 3:40 - 4:40 p.m.
Location: 1210 Chemistry
Host departments: Ecology and Evolutionary Biology

Abstract
In many tropical animals, male and female breeding partners combine their songs to produce vocal duets. The temporal precision of these displays is often so astonishing that human listeners mistake duets for the songs of a single animal. Our understanding of vocal duetting behaviour is still rudimentary, in part because many duetting animals live in tropical habitats where dense vegetation makes direct behavioral observation difficult or impossible. Here I focus on the vocal duets of neotropical wrens using both descriptive and experimental approaches.

In the first section of my talk I focus on the duetting behaviour of Rufous-and-white Wrens from the humid forests of Costa Rica. I use two innovative technical approaches to study vocal duets: an eight-microphone Acoustic Location System (ALS) capable of passively triangulating the position of duetting animals based on recordings of their vocalizations, and dual-speaker playback capable of simulating duets in a spatially realistic manner. Results from ALS recordings provide the first detailed spatial information on duetting animals, demonstrating that breeding partners perform duets across distances more variable than previously imagined and that duets play an important role in maintaining acoustic contact in visually occluded habitats. Results of dual-speaker playback demonstrate that duets play an important role in territory defense during aggressive confrontations with rivals, and that duetting birds use aggressive, sex-specific strategies for interacting with territorial intruders.

In the second section of my talk I briefly describe the vocal duets of three related species of wren whose voices were unknown until recently: the Pacific Coast Plain Wren of Costa Rica, the critically endangered Niceforo’s Wren of Colombia, and the recently described Inca Wren of Peru. My results support the argument that Neotropical wrens sing the most complex, coordinated songs ever described.

An integrative approach to the study of metazoan systematics: assembling the tree

Date: Thursday, October 29, 3:40 - 4:40 p.m.
Location: 1210 Chemistry
Host department: Ecology and Evolutionary Biology

Gonzalo Giribet
Professor of Organismic and Evolutionary Biology, Curator of Invertebrates
Museum of Comparative Zoology, Harvard University

Abstract

Speciation genetics as recorded in the genome composition of hybrids

Date: Thursday, October 22, 3:40 - 4:40 p.m.
Location: 1210 Chemistry
Host department: Ecology and Evolutionary Biology

Alex Buerkle
Assistant Professor of Evolutionary Genetics
Department of Botany, University of Wyoming

Abstract
Our efforts to associate phenotypic variation with genetic variation increasingly recognize that the function of genes is dependent on the environmental and genomic contexts in which they occur. Consequently, we seek an understanding of the developmental and physiological systems from which phenotypes emerge. Similarly, our pursuit of genes and evolutionary processes that contribute to reproductive isolation and speciation will require that these be embedded within the relevant environmental and genomic contexts. In this talk I will present relevant data from two lines of research that use the genome composition of hybrids to draw inferences about reproductive isolation and the speciation process. In natural hybrid zones we have found evidence for remarkably complex genetics of isolation in different taxa, with variability across the genome and points of contact between species. In diploid hybrid species we have estimated the time scale over which the species became isolated from ancestral taxa and have developed methods to detect genomic regions that were shaped by selection and contributed to isolation in the nascent species. The research employs analyses that integrate over the many processes that shape the composition of hybrid genomes.  

Whereas these approaches lack the experimental control of more typical mapping experiments, they have the advantage of embedding the genetics within the natural context within which species' boundaries arise and are tested by hybridization.

Tracking virus-host interactions: an evolutionary genetics approach to viral pathogenesis and population dynamics

Date: Thursday, October 15, 3:40 - 4:40 p.m.
Location: 1210 Chemistry
Host department: Ecology and Evolutionary Biology

Mary Poss
Doctor of Veterinary Medicine
Professor in Biology and Veterinary and Biomedical Sciences
Penn State University

Abstract
Viruses are versatile organisms with a unique ability to respond rapidly to changes in their environment. The environment, however, includes cells, tissues, complex organisms and populations of these organisms. Changes that impact virus fitness at any of these levels can elicit a response that is often reflected in the viral genome. Thus, detailed analyses of viral genomes, coupled with knowledge of the cellular, molecular and population biology of the host, can provide important insights into dynamical interactions at multiple biological scales. This seminar will present research from my lab discussing our approach to studying host biology from the perspective of a virus.

Warren Herb Wagner Guest Lecture in Plant Evolution

Horizontal gene transfer gone wild in mitochondrial genomes: whole-genome transfer, chimeric genes, and compartment-specific mechanism

Date: Thursday, October 8, 3:40 - 4:40 p.m.
Location: 1210 Chemistry
Host department: Ecology and Evolutionary Biology

Jeffrey Palmer
Distinguished Professor and Chair, Department of Biology, Indiana University

Abstract

In this talk, I will show that mitochondrial genomes are surprisingly active in horizontal gene transfer (HGT). One, enormous plant mitochondrial genome is far richer in foreign genes than even the most HGT-rich bacterial genome. Among other things, this genome has incorporated entire mitochondrial genomes from distantly related donors. Analysis of this and other mitochondrial genomes of plants and fungi leads us to propose a molecular/cellular model explaining why mitochondrial genomes are so active in HGT. Reasons why HGT is especially prominent in mitochondrial genomes of plants will also be presented, as will mechanisms by which genes move from one plant to another. Many horizontal transfers in plants and fungi give rise to chimeric mitochondrial genes in which pieces of foreign genes are pasted into native copies. Often these occur in very short patches, leading us to suggest that many, apparently de novo mitochondrial mutations may in fact be the result of unrecognized microchimeric HGT. 

**CANCELLED**
Small fungi with big impacts: ecology and evolution of fungal endophytes in grasses

Date: Thursday, October 1, 3:40 - 4:40 p.m.
Location: 1210 Chemistry
Host department: Ecology and Evolutionary Biology

Jennifer Rudgers
Godwin Assistant Professor
Department of Ecology and Evolutionary Biology, Rice University

Abstract
Microbes feature as some of the most abundant and important mutualists with plants. In grasses, systemic fungal endophytes can ameliorate both abiotic stress (e.g., drought) and biotic stress (e.g., herbivory), and thereby promote host performance. I have used this system to address several ecological and evolutionary questions about the dynamics and consequences of symbiosis. First, to what extent do mutualistic symbioses affect community structure? Field experiments have revealed strong, cascading effects of these mutualisms on plants, arthropods, and other microbes. Effects are not easily predicted from the responses of individual community members, and detection requires a community-level perspective. While it remains unclear how widespread the community and ecosystem consequences of grass-endophyte symbioses may be, recent studies spanning several native grass and fungal species suggest these symbioses may commonly produce strong ecological impacts. Second, how can endophyte symbioses inform our understanding of the evolution of mutualisms? Is phylogenetic evidence consistent with co-speciation? Is there evidence for mutualism breakdown? How have evolutionary conflicts been resolved, and what factors may help stabilize mutualism?

Phylogenetic tests of plant defense theory

Anurag Agrawal

Assistant Professor

Department of Ecology and Evolutionary Biology, Cornell University

Date: Thursday, September 24, 3:40 - 4:40 p.m.
Location: 1210 Chemistry
Host department: Ecology and Evolutionary Biology

Abstract
Plant defense theories have long been proposed to predict patterns in the expression of defensive strategies against herbivores. Despite convergence and macroevolutionary patterns being an explicit part of defense theories, phylogenetic analyses have not been widely employed to disentangle specific predictions concerning 1) investment in resistance traits, 2) tolerance to damage, and 3) plant growth rate. Using a molecular phylogeny of milkweed I will test some of these predictions and also attempt to unravel some of the multiple evolutionary drivers of plant traits. Consistent with classic coevolutionary theory, the historical pattern of defense evolution in the milkweeds shows an escalating ability to regrow following damage, but declining investment in the two most potent anti-herbivore resistance traits (cardenolides, latex).  This pattern implicates specialist herbivores in driving the evolution of tolerance over resistance. Trichomes, however, show a phylogenetic pattern more consistent with this trait being an adaptation to arid environments.

Nitrogen deposition effects on forest carbon storage: a review and new estimates

Date: Thursday, September 17, 3:40 - 4:40 p.m.
Location: 1210 Chemistry
Host department: Ecology and Evolutionary Biology and Department of Anthropology

Christine L. Goodale
Assistant Professor
Department of Ecology and Evolutionary Biology, Cornell University

Abstract
Human activities have greatly accelerated emissions of both CO2 and reactive nitrogen (N) to the atmosphere. Because N availability often limits forest productivity, it has long been expected that anthropogenic N deposition is stimulating forest carbon (C) sequestration. However, quantitative estimates from models and plot-level studies vary dramatically, and observational evidence has been lacking for deposition-induced stimulation of regional forest growth. The responses of forest soil C storage and solute C loss are even less well-understood. I will present recent work reviewing historical estimates of the importance of N deposition as a mechanism of terrestrial C sequestration, along with new evidence of the effects of N additions on forest growth, soil decomposition, and loss of dissolved organic carbon.

We find that N additions have markedly reduced rates of decomposition at four of six long-term experiments in the Northeast, but that effects on DOC (dissolved organic carbon) losses across a dozen long-term experiments appear driven more by soil response to acidification than to N itself. Lastly, we find that N deposition has affected tree growth, survival, and C storage across the northeastern and north-central USA during the 1980s and 1990s, with varying consequences for both growth and mortality of different tree species, perhaps due in part to differences in tree mycorrhizal association. Aboveground biomass increment increased by 56 (40-78) kg C per kg N deposition, amounting to a 36 (27-46) percent enhancement over pre-industrial conditions. These observations indicate that atmospheric N deposition is a substantial contributor to global C sequestration.