U.S. Department of Energy

Pacific Northwest National Laboratory

A new framework for understanding the microbial role in ecosystem function

This conceptual map shows the intersection between microbial (vertical) and ecosystem (horizontal) ecology. Note the three categories of microbial characteristics defined in the text: microbial processes, community properties, and microbial mentorship.

Researchers suggest moving away from identifying correlative relationships between microorganisms and the ecosystems they so influentially inhabit

The Science

Co-authors of a paper in Nature Microbiology, including PNNL scientist Emily Graham, propose a new conceptual research framework that would harness the ever-increasing wealth of information on microbiomes. The framework would reveal how—at the ecosystem level—microorganisms influence the ecological systems they inhabit.

Current research frameworks are often limited in their applications because they do not align with mechanistic representations in ecosystem process models. Instead, many researchers seek to identify correlations between microorganisms and ecosystem properties. The authors say current frameworks often yield ambiguous results that fail to provide new insights into processes and that blur the mechanisms by which microbiomes relate to system-level functioning.

The new framework, offered as a new approach to formalizing inquiries into microbiome science, proposes to empirically link three distinct categories of microbiome characteristics to each other and to the broader ecosystem processes they affect.

The Impact

The new conceptual framework, informed by decades of research on environmental microbiomes and ecosystem processes, offers a promising pathway to discovering empirical linkages between the microorganisms in an ecosystem and the processes of that ecosystem. The framework would also help focus future research on potential microbiome-ecosystem links that are most likely to be detected empirically.


Identifying relationships between microbiomes and the ecosystem-level processes they influence is an exceptionally hard research challenge. That is true because of increasingly rich data on microbiomes in the natural environment and the absence of a robust conceptual research framework that would help elucidate underlying causal mechanisms.

Presently, causal relationships are implied yet rarely tested, and researchers mostly rely on correlative approaches. These limit the potential to expand the influence of a single microbiome-ecosystem relationship to additional systems. Correlative approaches do not yield any information on mechanisms that can be transferred across systems.

The authors propose a new framework that targets microbial characteristics known to contribute to system-level processes of interest. The framework, intended to link measurable microbiome characteristics with ecosystem-level processes, is constructed based on three distinct categories of microbiome characteristics: microbial processes, microbial community properties, and microbial membership.

From there, the authors show how researchers can use existing methods of investigating microbial ecology to elucidate properties within each of these categories and to connect these three categories of microbial characteristics with each other.

Central to the framework is one idea: that it is particularly important to distinguish microbial community properties that can be predicted (called community aggregated traits) and those that researchers are currently unable to be predict (called emergent properties).

Collectively, the framework introduces a new research paradigm for closing the gaps between empirical investigations and the ecosystem process models they seek to inform.

March 2019
| Pacific Northwest National Laboratory