The interactions between plants and microbes
Similar to the countless ways that microbes are an important component of human bodies, the microbiomes of plants play a crucial yet understudied role in how plants interact with their environment. From conferring disease resistance to increasing the uptake of critical nutrients and even to regulating the genetic expression of their plant hosts, microbes and plants are inseparable.
I am particularly drawn to questions about how plants “select” their microbial counterparts and, in turn, how these bacteria and fungi shape plant fitness through stress tolerance and pathogen resistance. I am also interested in going deeper down the rabbit hole and investigating the roles that the genetic expression profiles of the host and the microbes interact with each other.
The factors that influence microbial community composition
Since so little is known about the detailed ecological requirements of most microbes, the variables that constitute a suitable habitat are best not assumed. In fact, it is probable that a large portion of the factors that shape microbial diversity occur at scales that have not yet been addressed. Using a combined approach of observational and manipulative experiments, we should be able to tease apart some of the minute variables that influence microbial occurrence. These may include the obvious such as pH, moisture, oxygen levels, etc. They also most likely include the less-intuitive such as species co-occurrence, cation exchange capacity, and even the transcriptional state of nearby macro-organisms.
It remains a challenge to observe all of the potential factors that may be causal but high-throughput sequencing of environmental mRNA can give us a much finer resolution (on the temporal scale) image of what all three domains of life are “up to” at a given instant. If we start in the lab, manipulating one or a few environmental variables, we will have a better idea of what to look for in situ.
The links between microbial genes and the global greenhouse effect
New technologies are allowing us to have unprecedented glimpses of the mechanisms behind large-scale processes. By directly sequencing nucleic acids from the environment we are able to determine who is there and what they are doing. This is a huge step forward since traditional microbiology depends on slow and difficult (impossible?) culturing of organisms. If we can obtain a snapshot of what genes are actively being transcribed we can begin to make connections between easy-to-observe patterns in biogeochemical cycling (such as methane emission) and the biochemical potential of ‘unknown’ microbial communities. These same techniques can enable us to anticipate the functional changes that a shifting climate will impose on microbes and allow stronger predictions about large scale processes.
I am interested in utilizing metagenomics and metatranscriptomics as tools for interrogating microbial communities, particularly in climate-sensitive environments. Rather than strictly sequencing the environment and looking for patterns, I believe that these tools can be usefully applied to manipulated systems to obtain mechanistic explanations for observed phenomena. For example, one of my current projects uses metagenomics to determine the interactive effects of predation and warming on a soil microbial community with concurrent tracking of carbon dynamics. In this way, for example, I hope to link community composition to the obvious increases in respiration associated with increasing trophic complexity.