Unearthed! The Amazing Microbiome Exposed: The Arising Researcher

Abstract

Science is at a threshold where the intertwined relationships between microorganisms and their impacts on the macroworld are challenging how we think about systems biology, ecosystem functions, and even how we define individual organisms. Over the last decade, an increasing amount of research is showing that microbial processes drive macro-ecological systems. I first began thinking about the interactions between plants and their microbiomes while I was trying to come up with a Masters research project in the summer of 2003. It was a challenge to narrow down an area related to microbiome in plant communities, which includes so many different disciplines. I finally settled on plant–microbe interactions and the regulation of plant trait expression, which cascade through ecosystems. I owe a debt of gratitude to John Klironomos for shining his flashlight into the “black box” of soil microbial communities with some very elegant “feedback” experiments with plants. In his 2002 paper, “Feedbacks with soil biota contributes to plant rarity and invasiveness in communities” (Nature 417:67–70), John paved the way for microbial perspectives to be applied to the macro-ecological phenomenon of plant invasion ecology. He showed that soil biota were regulating plant biodiversity and coexistence; microbes got put on the map as potential drivers of plant community assembly, rarity, and invasiveness. His paper was instrumental in helping many look beyond soils as a black box, and it inspired me in my own research. I have long been fascinated with microbiology and hold a deep respect for the discipline that studies the oldest life forms on earth: prokaryotes. I was exposed to many courses that dove deeply into the diversity of microbial functions, highlighting their fascinating genetic structures that allow pretty much anything to serve as a terminal electron acceptor, unlike animals that only use oxygen, O2. Simply put, microbial diversity of function was born out of the long evolutionary history the organisms have had in shaping and surviving this planet for the last 3.5 billion years. Microbial diversity in action, transforming nutrients is happening all around us: the soil biogeochemistry in our yards and gardens, fields, and forests. It is not hard to see how microbial communities that are largely responsible for soil nutrient dynamics shape the macroscale distributions of plants. For me, when I started my Masters research studying the impacts of an invasive grass on native plant communities, my natural preoccupation with microbiology kept telling me to look at the invasion process from a microbe-centric, rather than plant-centric perspective. John's work on soil feedbacks gave me the grounding to argue strongly for the role of microbes in these larger ecological patterns that I was convinced were related. Moving from just plant–plant interactions to a wider view that included plant–soil interactions made sense, because in essence soil is the functional legacy of microbes. The black box of soil still persists due to the challenge of studying things that cannot be seen with the unaided eye or cultured in the laboratory. However, advanced molecular tools have opened the door to the world of soils and related areas, such as what we think constitutes the plant genome. The microbiome is an extension of the plant genome, and this has huge implications for how we think about solving real-world problems. I was inspired by John's research and look forward to how my work on microbially mediated feedbacks between plants and soils will contribute to our understanding the role of the microbiome in plant invasions. How we view macroprocesses in plant science will continue to evolve as new microbial light continues to shed into the dark world of soils.