#FEMSmicroBlog: Understanding the bigger picture by analyzing a microbe’s home


Soil microbes are some of the most important organisms on this planet. Their metabolic activities impact how we inhabit this planet and advance as a society. Yet, we don’t understand much about the environment in which soil organisms thrive and how their activities on the micro scale relate to the macro scale of our planet. The perspective “Micro on a macroscale: relating microbial-scale soil processes to global ecosystem function” published in FEMS Microbiology Ecology argues that we need to better understand the microbial perspective to accurately predict global processes. In this #FEMSmicroBlog, Darian Smercina explains that modelling microbial systems can help us better understand global ecosystems like biogeochemical cycles. #FascinatingMicrobes


Soil microbes – tiny but valuable players in the global ecosystem

Soils are important in many global processes and human civilization. This ecosystem is vital to human health, economies and societies providing water purification, agriculture, and climate mitigation through carbon storage.

Soils are also the filter through which all major global nutrient cycles like the carbon and nitrogen cycles pass. The importance of understanding soil processes cannot be understated. Yet, the soil is challenging to study since it is mineral-dense and chemically complex.

Within this complex soil world, microbes carry out ecologically vital processes that make Earth habitable for the rest of us. This is why soil microbes are often described as “the engines that drive global biogeochemical cycles”.

The cryptic and complex nature of the environment of soil microorganisms makes quantifying their activity very challenging. Also, the scale difference between microbes (micron scale) and ecosystems (meter) is a grand challenge for soil microbial ecology. Note that 6 orders of magnitude separate the quantitative prediction of microbial activity in relation to global cycles.


Microbial habitat and the challenge of scale

The perspective “Micro on a macroscale: relating microbial-scale soil processes to global ecosystem function” published in FEMS Microbiology Ecology explains the major hurdle to overcome this scaling challenge. Currently, we lack a strong understanding of the microbial scale and specifically the microbial habitat.

In the case of macrofauna, habitat is more obvious. Think about the habitat of a lion and you’re likely to picture the African savannah. Similarly, but not as easy to observe: microbes live within habitats that are defined by resource accessibility – much like their macro counterparts.

Similarly to other organisms, microbes live in habitats that are defined by resource and nutrient availability.

However, at the microbial scale, diffusion drives the exchange of substrates, metabolites and signalling compounds. This determines resource availability for microbes as well as an information exchange with their environment.

Thus, the current best estimate of microbial habitat size considers bacterial interaction through the diffusion of signalling compounds. Estimates range from just 12 to upwards of 78 microns but is typically observed to be ~20 microns.

Microscale in soil
Modelling microbial function and ecosystem processes. From Smercina et al.

These distances pose a challenge not only for measuring microbial function but also for scaling that function from micro to macro. A single soil sample is generally considered 2.5 cm diameter by 10 cm deep soil core. Hence, in one such sample could be nearly a billion microbial habitats.

Plus, each of these microhabitats could have unique environmental conditions and microbial community members and therefore be considered distinct. This makes quantifying and predicting functions at a large scale difficult. Thus, it is vital that we determine the extent to which distinct microhabitats exist at the microbial scale.


Understanding microbial activity in microhabitats

Carefully considering microhabitats and the microbial perspective could help us answer many questions about soil microbial ecology. For example, it would be interesting to understand which microbes in a community determine the function of that community.

One major question to better understand microhabitats is which microbial player in a community defines the function of that community.

To quantify the microbial perspective, we need controlled experiments and mathematical modelling that focuses on the microbial scale. Using new and adapted methods could help us measure microbes at their scale. In particular, we need to measure microbes and their activity systematically from “micro to macro”.



About the author of this blog

Darian Smercina is a Linus Pauling Distinguished Postdoctoral Fellow at Pacific Northwest National Laboratory. She completed her PhD in 2020 with Dr. Lisa Tieman at Michigan State University. She is interested in soil microbial ecology and biogeochemistry relevant questions. Currently, her work uses novel microfluidic systems and advanced imaging techniques to study biological nitrogen fixation as a model process for addressing questions about microbial scale processes and microbial interactions.

About this blog section

The section #FascinatingMicrobes for the #FEMSmicroBlog explains the science behind a paper and highlights the significance and broader context of a recent finding. One of the main goals is to share the fascinating spectrum of microbes across all fields of microbiology.

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