New study explores the complex dynamics of bacterial communities

Miniature worlds called microcosms are used to study complex ecosystems under controlled laboratory conditions.

Predicting and controlling microbial ecosystems has long been a challenge due to their complexity and dynamic nature.

Now, in a new study published in Nature Communications, researchers including Professor Tom Bell, Department of Life Sciences, Silwood Park, have discovered fresh insights into how bacterial communities operate, paving the way for better control of microbial systems and allowing us to optimise ecosystem services.

The research was the result of a collaboration between experts in microbial ecology and computational biology from the Spanish National Centre for Biotechnology, ETH-Zürich, Manchester Metropolitan University and the University of Exeter as well as Imperial. 

The interdisciplinary team explored how bacterial communities hosting hundreds of species can follow similar paths under standardised conditions, despite their inherent variability. Their study also highlighted unexpected tipping points in these ecosystems, where initial small differences can lead to more much larger changes later. These findings have significant implications for industries that rely on microbiomes and efforts to control microbial ecosystems for environmental and human health.

Key Challenges in Microbial Ecology

Microbial ecosystems are highly diverse and play a key role in ecological functions, from nitrogen fixation in agriculture to waste degradation in industrial processes. However, understanding how these communities change over time and impact broader ecosystem functions remains a challenge.

Current approaches to microbial ecology often focus on either the environmental conditions shaping microbial communities or the functional roles specific microbes play, but bridging the gap between community composition and ecosystem function remains elusive.

Alberto Pascual-García of the Spanish National Centre for Biotechnology said: ‘The inherent complexity of microbial ecosystems has always posed a challenge for scientists. Microbial communities are not static; they’re in constant variation, influenced by a variety of factors. Our research aims to uncover patterns of predictability and reproducibility in this variation and to develop protocols and theory to manipulate and control these systems.’

The team created a ‘frozen archive’ of hundreds of naturally occurring bacterial communities, reviving and culturing the samples in a standardized, complex resource environment. As these communities live in cavities in the roots of beech trees, they used the simple approach of growing them in a “tea” made from the leaves of the tree. This allowed them to observe how the communities behaved under the same conditions over time.

By controlling the environment, the team could focus solely on the intrinsic properties of the microbial communities, using advanced DNA techniques and measurements to track changes in the communities' makeup and function.

This allowed them to build a clear picture of how the communities grow, stabilise and respond to initial compositional differences.

Tipping points in microbial dynamics

One of the study’s key findings is that when bacterial communities are placed in the same environments, they tend to follow similar patterns. This includes both the composition of the microbial community and its functional outputs, such as breaking down substances.

"The phenomenon of tipping points was particularly surprising. It underscores that while microbial ecosystems can be predictable under some conditions, they’re also subject to complex, nonlinear dynamics. This dual nature is both a challenge and an opportunity for those working to harness microbial communities for biotechnological applications." Professor Thomas Bell Department of Life Sciences, Silwood Park

The findings suggest that, under controlled conditions, complex microbial ecosystems can be predictable, potentially having uses in industrial and ecological applications.

Importantly, the researchers also discovered that even in a controlled environment, small differences in the initial composition of microbial communities can lead to different outcomes. These small changes are amplified over time, causing the communities to follow different paths.

Professor Bell said: ‘The phenomenon of tipping points was particularly surprising. It underscores that while microbial ecosystems can be predictable under some conditions, they’re also subject to complex, nonlinear dynamics. This dual nature is both a challenge and an opportunity for those working to harness microbial communities for biotechnological applications.’

Implications for ecosystem services and beyond

In agriculture, where microbial communities affect soil fertility and crops, understanding these dynamics could help create more sustainable farming practices. In human health, where the gut microbiome is recognized as a key player in disease and wellness, these insights could lead to better probiotics or microbiome-based therapies. For industries using microbes, such as wastewater treatment or biofuel production, these results provide a roadmap for improving microbial systems.

The study concludes that predicting microbial ecosystems requires a detailed understanding of the complex factors that influence them. It also raises intriguing questions about how microbial communities might react to changing environmental conditions such as those found in natural ecosystems. Future research will need to explore whether predictability still holds up in less controlled settings, where factors like temperature fluctuations, nutrient availability, and interactions with other organisms come into play.

The research represents a big step forward in understanding the dynamics of microbial ecosystems, providing insights from fields from agriculture to medicine to environmental management. As scientists continue to unravel the complexities of microbial life, the potential to harness these tiny but mighty organisms for the greater good grows ever more promising.