The phyllosphere of Arabidopsis thaliana as a model for testing ecological theory

	Two-week old seedlings of Arabidopsis thaliana grown on sterile phytoagar.

In recent years several studies have examined whether microbial systems demonstrate the same ecological patterns documented in macro-organisms, with a particular emphasis on factors producing biogeographical patterns of microbial diversity and whether deterministic or neutral factors dominate community assembly. However, two central issues have not been addressed: (1) sampling typically occurs on length scales many orders of magnitude larger than a typical microbial cell and (2) usually only taxonomic (16s) diversity is assayed.

Our aim is to develop a model microbial system that allows us to track the parallel development of replicate microbial communities over space and time, using leaves of plants grown in a controlled environment as complex natural substrates. High-throughput sequencing data collected at multiple spatial and temporal scales will allow us to access the genetic information contained within these communities. Using this rich dataset, we will perform direct tests of the fundamental rules that govern the stability and resilence of complex microbial systems.

We are developing microbial communities found on the leaves of the model plant Arabidopsis thaliana into a model system for assaying:

1. how microbial community assembly operates at "microbial" (micrometer to centimeter) scales
2. whether taxonomic, genetic, and functional measures of microbial diversity (as assayed with high-throughput next-gen sequencing) show common successional patterns over space and time
3. the influence of niche versus neutral dynamics in community assembly
4. the influence of plant productivity on leaf surface diversity.
5. the role of commensal microbes in disease resistance in Arabidopsis.

Emelia DeForce conducting sterile sampling of Arabidopsis plants in the greenhouse.		Trays of Arabidopsis plants in a custom shade chamber in the MBL Greenhouse.

Characterization of Marine and Freshwater Photosynthetic Consortia that Accomplish Cellulose Degradation and Nitrogen Fixation

Collaboration with Dr. Jean Huang, Olin College

Nutrient cycling in the environment is carried out by complex microbial communities. Unraveling the network of organismal interactions that drive carbon and nitrogen cycling in nature is a challenging task given the taxonomic, functional, and biochemical diversity of most natural systems. This project will study a series of environmentally derived freshwater and marine photosynthetic microbial communities that grow using cellulose and dinitrogen as sole sources of carbon and nitrogen, respectively. These communities contain distinct populations that can degrade nitrogen-poor cellulose, fix atmospheric N2, and harvest light energy through photosynthesis at different light wavelengths under anaerobic conditions. The goals of this research are to generate new insights into the links between community structure, productivity, and organismal interactions that produce stable nutrient-cycling microbial systems by using biochemical, molecular, and model-based analyses. These environmentally derived consortia can provide insight into how renewable resources such as cellulose, N2, and light can be efficiently converted into cell biomass and other usable products under marine and freshwater conditions.

	The Connecticut field site shown after corn harvest (Z. Cardon).

Microbial diversity in agricultural soils

Collaboration with Zoe Cardon, MBL Ecosystems Center

How are taxonomic, genetic, and functional microbial diversity coupled (or uncoupled) in ecosystems? How do their dynamics contribute to ecosystem "function", and at what spatial and temporal scales?

We are exploring these questions in soil microbial communities using a long-term agricultural field site located at at the University of Connecticut, where corn has been grown for over 40 years. The field hosts four tillage and aboveground biomass harvest treatments started in 1968. Dramatic, treatment-specific gradients have developed in soil organic carbon pools, soil aggregation, soil faunal diversity, and soil microbial community structure. These gradients provide a natural laboratory for examining characteristics of taxonomic, genetic, and functional diversity that have emerged under yearly management pressure in a single field over decades. Additionally, the experimental design offers the statistical power of triplicate plots for each treatment.

Initial work using massively parallel tag sequencing of the V6 region of 16s rRNA has shown a dramatic difference in whole soil bacterial taxonomic diversity across treatments. We are currently focusing on soil aggregation, which has been shown to substantially augment carbon sequestration. Soil aggregates are localized microenvironments in which the arrangement of soil particles and pores, organic carbon inputs, and microbial activities all contribute to the balance of soil carbon gain and loss. As a first step towards exploring links between aggregate microbial communities and the extent of SOC storage, we are conducting massively parallel 454 tag sequencing of bacterial rRNA, Illumina metagenome sequencing, and Illumina metatranscriptome sequencing of three aggregate size fractions isolated from high SOC soils collected at the field site.