Research Overview

Our lab studies the g
eneration 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 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.

Microbial biogeography

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.

Our recent work in the area of biogeography is twofold. First, we are aiming to test the importance of dispersal for microbial composition and functioning in the field. To do this, we are quantifying and manipulating dispersal in leaf litter decomposer communities. Our first publication on this work showed that reducing dispersal altered the abundance, diversity, and composition of the communities (Albright and Martiny 2018).

Second, we are investigating the biogeography of "microdiversity" (diversity within a 16S-defined taxon). While conserved regions such as 16S can capture a large breadth of the microbial diversity, these regions, by their very nature, limit the detection of finer-scale genetic variation. We are currently working to resolve the diversity of an abundant surface-soil bacterium (Curtobacterium) to detect ecological and evolutionary processes occurring at a much finer genetic scale (Chase et al. 2017). Our latest study revealed the existence of six ecotypes with differential abundances along a climate gradient, suggesting fineā€scale niche partitioning (Chase et al. 2018).

Microorganisms and global change

survey litter Oct2015
How will microbial communities respond to current global change? What will the ecosystem consequences be? These two questions motivate much of our lab's work and present an urgent challenge to our field (Cavicchiolo et al. 2019). However, these questions highlight many unanswered, fundamental questions. For instance, a pervasive idea in microbiology and ecology is that much of microbial diversity is functionally redundant. Indeed, 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. Certainly, some microbial groups show a high degree of metabolic flexibility and physiological tolerance to changing environmental conditions. And rapid evolutionary adaptation might allow sensitive microorganisms to adapt quickly to new conditions.

As a result, the functional redundancy of microorganisms is a central assumption in many ecosystem and global models. 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 2013). Only in this way can one directly measure the relative effects of compositional variation versus the environment on ecosystem processes.

Our current work deploys microbial “cages” to manipulate microbial composition (while preventing migration into and out of the cages) and alter the environment by placing the cages in different locations. In collaboration with several labs at UCI, we have found that changes in microbial composition exposed to drought changes leaf litter decomposition and litter chemistry (Martiny et al. 2017). And recent work demonstrates that the decomposition response to climate change depends on the microbial community (Glassman et al. 2018).

Bacteriophages and coevolution

Bacteriophages (viruses that infect bacteria) are extremely abundant and diverse in environments from the ocean to the human gut. As with other microorganisms, we know little about the mechanisms by which bacteriophage diversity varies over time and space. However, bacteriophages provide an excellent system to study how coevolution contributes to microbial diversity (Martiny et al. 2014).
In collaboration with Marcia Marston (Roger Williams University), we have been investigating marine cyanophages that infect photosynthetic cyanobacteria and in particular, Synechococcus, which is thought to be responsible for up to 30% of the oceans’ primary productivity. Thus, cyanophages provide an amenable system for studying marine viruses, and the results are likely to have direct implications for marine ecosystem functioning.

We investigate cyanophages in two broad ways. First, we have characterized the biogeography of cyanophages along the Pacific and Atlantic coasts and recently reported the existence of viral ecotypes that each have distinct temporal or spatial patterns of abundance (Marston and Martiny 2016). Second, we have been conducting laboratory coevolution experiments to investigate the network of interactions between cyanophages and their hosts, building on our past work in this area (Marston et al. 2012).