Key players in the microbial world

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The paper in Nature Reviews Microbiology is here:

The concept of keystone taxa was originally proposed by ecologist Robert T. Paine in 1966. In a seminal experiment, he showed that the removal of sea stars (Pisaster ochraceus, a common predator of mussels) had a drastic effect on the local biodiversity at Makah Bay, Washington1. The concept is well-established in ecology and a wide range of plants and animals have been characterized as keystone taxa. However, over time, the overuse and misuse of the term ‘keystone taxa’ resulted in confusion about the actual meaning. Thus, in our article, we proposed a definition of keystone taxa in microbial ecology. We summarized over 200 of such taxa from various ecosystems and the human microbiome. We found that various members of Rhizobiales and Burkholderiales orders were identified as keystone taxa in different studies and across different ecosystems. This is certainly encouraging because it highlights the importance of such taxa for microbiome structure and composition. While keystone taxa in plant and soil microbiomes have mainly been identified computationally using network-based scores, keystone taxa in the human microbiome is empirically established. A large number of empirical studies have reported that keystone taxa are linked to a range of processes, including inflammation, colon and gastric cancer, starch degradation and stabilization of the human microbiome. Our article explored various strategies that keystone taxa may employ to exert effects on microbiome. We also introduced the tenet of microbial keystone guilds. We further discussed the environmental and ecological factors that determine their distribution and activities in ecosystems and summarized several recent approaches that can be employed for characterization and manipulation of keystone taxa.


Microbial networks and keystone taxa

There have been a number of exciting reports on keystone taxa in recent years and the topic is receiving increasing attention. It has been shown that the effect of abiotic factors and host genotypes on phyllosphere microbial communities is mediated via microbial keystone taxa2 and that root microbial network complexity is linked to plant survival 3. A recent study also found that low-abundant keystone taxa can explain microbiome compositional turnover better than all taxa combined 4. Indeed, such encouraging reports highlight the relevance of keystone taxa for microbiome structure and functioning. Our upcoming work will continue to explore the occurrence of keystone taxa and their associations to ecosystem processes.

Identifying keystone species is difficult-but essential to understanding how loss of species will affect ecosystems.”- Power et al., 19967


1.        Paine, R. T. Food Web Complexity and Species Diversity. Am. Nat. 100, 65–75 (1966).

2.        Agler, M. T. et al. Microbial Hub Taxa Link Host and Abiotic Factors to Plant Microbiome Variation. PLoS Biol. 14, 1–31 (2016).

3.        Durán, P. et al. Microbial interkingdom interactions in roots promote Arabidopsis survival. (2018). doi:10.1101/354167

4.        Herren, C. M. & McMahon, K. D. Small subsets of highly connected taxa predict compositional change in microbial communities. bioRxiv (2017). doi:

5.        Power, M. E. et al. Challenges in the Quest for Keystones. Bioscience 46, 609–620 (1996).

Samiran Banerjee

Project Leader, Agroscope