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Global Microbiome in a Changing Planet

What is the compelling question or challenge?

How do microbes regulate the health of ecosystems ranging from the scale of individual plants, animals or humans to the scale of the entire atmosphere and ocean?

What do we know now about this Big Idea and what are the key research questions we need to address?

It has been recently established that microbes greatly impact human, animal, and plant health through the microbiome (the complex community of microbes that inhabit macro-organisms). Just as microbes regulate the health of our bodies, they regulate the health of our planet. Environmental microbes play a profound role on our planet regulating climate, the location and amount of precipitation, global temperatures, the composition of our atmosphere, melting rate of glaciers, the productivity of plants in soil, patterns of global carbon and nitrogen cycling, and many other processes. Many studies have documented the effects of microbes in individual systems, yet our understanding of connections across systems and scales is extremely limited. Understanding which environmental microbes influence our human microbiome and health, and how they do it, is of critical importance; similarly, understanding how the microbiomes of our built environments, our livestock, and even our own bodies (as represented by waste streams containing microbes and microbially-derived chemistry that impact the environment) is equally vital.

1. How do environmental conditions shape our human microbiome and how in turn does this affect human health? Are people living near the oceans healthier than those living inland? Does exposure to soil microbes regulate immunity and even behavior? How far are harmful and beneficial microbes transmitted?

2. What are the sources of airborne microbes—ocean, terrestrial, etc. and how do they affect clouds, climate, and precipitation? How do these different sources harm and/or benefit human, plant and animal health?

3. Given that humans consume the majority of net primary production in many areas and have fundamentally altered patterns of nutrient cycling on a global scale, are there approaches to modify human, livestock, agricultural, and/or planetary microbiomes to mitigate this impact and improve sustainability?

4. How will a changing climate (i.e. warmer oceans, increased wildfires) impact microbes which in turn impact human and planetary health?

The oceans represent a major repository of Earth’s genetic and microbial diversity. Complex microbial communities play key roles in biogeochemical cycling, ecosystem services, and agricultural and industrial productivity. Understanding microbial responses to climate change, and microbes globally transported as aerosols from the ocean and their role in nucleating clouds, will be essential to predicting the future of our planet.

Use of microbes, including eukaryotic algae and cyanobacteria, for biofuels in complex communities could tremendously reduce human impacts, as could engineering microbiomes to improve crop drought tolerance and feed conversion in aquaculture and in terrestrial feeding operations.

In order to fulfil these goals, we need a transdisciplinary approach that enables better readouts of microbial taxonomy and microbial functions across different scales, improved modeling approaches, elucidation of new ecological and evolutionary principles that hold true across time and space, and data science and theoretical approaches that help guide understanding of when results from one system or scale will apply to another, and specialized approaches are required. Improved methods for handling highly multivariate sparse compositional datasets, and improved methods for measuring microbial functions on scales from the individual chemical bond all the way to the entire planet, and on timescales from femtoseconds to billions of years, will be needed to understand, predict, and ultimately control microbial impacts on Earth’s biosphere.

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