Toward a Predictive Understanding of Earth's Microbiomes to Address 21st Century Challenges

Abstract

Microorganisms have shaped our planet and its inhabitants for over 3.5 billion years. Humankind has had a profound influence on the biosphere, manifested as global climate and land use changes, and extensive urbanization in response to a growing population. The challenges we face to supply food, energy, and clean water while maintaining and improving the health of our population and ecosystems are significant. Given the extensive influence of microorganisms across our biosphere, we propose that a coordinated, cross-disciplinary effort is required to understand, predict, and harness microbiome function. From the parallelization of gene function testing to precision manipulation of genes, communities, and model ecosystems and development of novel analytical and simulation approaches, we outline strategies to move microbiome research into an era of causality. These efforts will improve prediction of ecosystem response and enable the development of new, responsible, microbiome-based solutions to significant challenges of our time.

FIG 1

Microbial landmarks in the evolution of our biosphere. Adapted from original artwork of Mariana Ruiz Villarreal (https://commons.wikimedia.org/wiki/File:Timeline_evolution_of_life.svg).

FIG 2

The microbiome and our changing Earth system. Population growth, urbanization, environmental degradation, and global climate change. Human-induced soil degradation based on data from reference ; urban population by 2050 based on data from reference ; global surface warming data based on data from reference ; trends in global water extraction (dark color) and consumption (light color) by sector are based on data from reference ; food yield increases required by 2050 are based on data from reference .

FIG 3

Cross-disciplinary innovations needed to advance functional understanding of Earth’s microbiomes. HTP, high throughput; STXM, scanning transmission X-ray microscopy; CMOS, complementary metal-oxide semiconductor; microCT, microcomputed tomography; TnSeq, transposon sequencing; NanoSIMS, nanoscale secondary ion mass spectrometry; NanoSIP, nanometer-scale stable isotope probing. Credits: The STXM image was adapted with permission from Remusat et al. (133), and the global ocean model depiction was adapted and reproduced with permission from Follows et al. (161).

FIG 4

The potential impact of a unified microbiome initiative to understand and responsibly harness the activities of microbial communities.