Research Overview

Our lab studies the generation and maintenance of microbial diversity and its consequences for ecosystem functioning. In the past, we have focused on characterizing patterns of microbial diversity (biogeographic patterns).
We are now turning our attention to experimentally testing the evolutionary and ecological mechanisms generating these patterns and whether this variation in microbial composition affects ecosystem functioning.

We study all sorts of microbes such as viruses, bacteria, and fungi in a variety of ecosystems. Depending on the question, we also apply a range of approaches, including experimental evolution, field experiments, and greenhouse microcosms. We often use molecular genetic approaches to characterize microbial diversity (from PCR and cloning to whole genome sequencing and functional metagenomics), with the goal of linking this genetic diversity to phenotypic traits and ecosystem functioning.

The resilience of microorganisms to environmental change

DSC_0190 DSC_0042_1024 DSC_0100 DSC_0152_1024
A pervasive idea in microbiology and ecology is that much of microbial diversity is functionally redundant. Certainly, some microbial groups show a high degree of metabolic flexibility and physiological tolerance to changing environmental conditions. Further, rapid evolutionary adaptation through horizontal gene transfer might allow sensitive microorganisms to adapt quickly to new conditions. Finally, given the enormous abundance and diversity of microorganisms, it can be difficult to imagine that biogeochemical cycling is limited by microbial abundance or genetic diversity.

A result of this paradigm is that the functional redundancy of microorganisms is a central assumption in many ecosystem and global models. Thus, this paradigm is central to our ability to predict the response of ecosystem functioning to environmental changes. Borrowing from classical ecology, we introduced a framework for considering the functional redundancy in microorganisms (Allison and Martiny 2008) and are working to test these hypotheses. To do this, one must disentangle the effects of environment and composition, which requires manipulating the microbial community, ideally under natural field conditions (Reed and Martiny 2007, 2013). Only in this way can one directly measure the relative effects of compositional variation versus the environment on ecosystem processes.

We have been developing microbial “cages” so that we can manipulate microbial composition (while preventing migration into and out of the cages) and alter the environment by placing the cages in different locations. Our current work in grasslands (in collaboration with Steven Allison, Eoin Brodie (LBL), Michael Goulden, Adam Martiny, and Kathleen Treseder), asks whether microbial composition matters for leaf litter decomposition and if so, whether this composition is resilient to global change disturbances. To address these questions, we are conducting a transplant experiment using litter bag “cages” (Allison et al. 2013). The cages are transplant within a global change experiment that manipulates precipitation and nitrogen deposition. This design allows us to partition the relative effects of microbial composition, plant litter quality, and abiotic environment on litter decomposition. We are also using laboratory microcosms to manipulate the particular composition of bacteria and fungi.

Microbial biogeography and marine viruses

Although the existence of microbial biogeographic patterns is now well established, little is understood about the mechanisms creating and maintaining these patterns. Recently, we proposed that just four processes – selection, dispersal, mutation, and drift – act on microbial assemblages on inseparable ecological and evolutionary scales (Hanson et al. 2012). This framework may help in moving microbial biogeography from a pattern-based to process-based discipline.

One group of microbes that has been a focus of our biogeographic studies are marine viruses. Marine viruses are extremely abundant and diverse. While studies demonstrate that the spatial and temporal distribution of marine viruses is non-random, we do not understand the mechanisms by which virus diversity varies over time and space.

Attaching to cell
To investigate the controls of marine virus diversity, we study viruses that infect cyanobacteria (cyanophages) as a model system. Cyanophages appear to play a central role in marine biogeochemistry; as much as a quarter of photosynthetically-fixed organic carbon may be recycled back as dissolved organic material via viral lysis. Synechococcus spp. are photosynthetic cyanobacteria, abundant in coastal, temperate, and upwelling regions and thought to be responsible for up to 30% of the oceans’ primary productivity. Thus, Synechococcus cyanophages provide an amenable system for studying marine viruses, and the results are likely to have direct implications for marine ecosystem functioning.

In collaboration with Marcia Marston (Roger Williams University), we are studying the coevolution of cyanophage and Synechococcus (Lennon et al. 2007; Stoddard et al. 2007; Lennon and Martiny 2008; Marston et al. 2012). We are also comparing the temporal diversity of cyanophage between the Pacific and Atlantic coasts (Clasen*, Hanson* et al. 2013; Marston et al. 2013). To do this, every month we monitor the abundance and diversity of cyanophage that can infect a group of Synechococcus strains. We then use these isolates to test hypotheses about the diversity patterns we detect.