In the driest place on Earth, Chile's Atacama Desert, rocks serve as "islands of life" where microbes thrive, whereas nearby soil is mostly barren. (Credit: Jocelyne DiRuggiero)
Our understanding of the microbial world is in the midst of a revolution, led by efforts to characterize the human microbiome and understand how it impacts our health. But scientists are probing hundreds of earthly environments—animal, vegetable and mineral—to determine what is there and what it is good for. What do these diverse microbial communities have in common, and can studying rock-dwelling microbes teach us anything about those living in our gut? We asked microbiologist JOCELYNE DIRUGGIERO, PhD, Associate Research Professor in the Department of Biology at Johns Hopkins University, who has been studying some of the most resilient microorganisms on Earth for several decades, to explain the connections.
JOCELYNE DIRUGGIERO: There are ecological principles regarding the functioning of microbial communities that will apply to all types of communities. By studying relatively simple communities, such as those of extreme environments where the diversity is much lower, we can start testing those ecological hypotheses in a more tractable system. However, extrapolating from extreme environments to the human microbiome in terms of specific groups of microorganisms is difficult because the community members can be very different.
TKF: Where are the intersections between research on microorganisms in extreme environments and in the human body?
DIRUGGIERO: In both of these environments, we are investigating microbial communities—the structure and composition of these communities, how the microorganisms make a living, how they interact with each other and with their environments. In both cases, we want to understand how these ecosystems function and how they might impact their hosts—rocks in the Atacama Desert or the human body.
Another intersection is that the molecular methods we’re using are very much the same. We are just extracting DNA from different substrates. The bioinformatic challenges for analyzing the large amount of data we’re generating in both research fields are also similar.
But each environment does have its own challenges. In the case of the Atacama Desert, it is the scarcity of water and nutrients to support microbial communities; and in case of the human gut microbiome, for example, it is the fierce competition between microorganisms, the immune system, and sometimes antibiotics ingested by the host.
TKF: We know that the microbiome influences how the brain works. How do microbes living in extreme environments influence those environments?
DIRUGGIERO: Microorganisms are essential for the evolution of the Earth, its minerals, its major geochemical cycles and its atmosphere. This is also true for extreme environments where microorganisms can be essential for the 'primary production' of a system, in other words for producing organic carbon for the whole community to use; they may interact with the rocks they inhabit, resulting in weathering of the substrate; and they may provide the essential nutrients that allow plants to grow in a desert, for example, nitrogen that can be assimilated by the plants.