In a world where constant adaptation is crucial for survival, freshwater bacteria face a paradox: they are pressured to stand still, making them vulnerable to the rapid shifts brought by climate change.
Are freshwater bacteria capable of adapting to the rapidly changing conditions brought by climate change? The stalling of adaptive processes in freshwater bacteria threatens their ability to adapt to climate change, highlighting the need for targeted studies and enhanced monitoring efforts to ensure ecosystem resilience.
Adrian-Stefan Andrei
Bacteria: Masters of adaptability
Bacteria exemplify nature’s extraordinary capacity for adaptation. These microscopic life forms flourish in various environments, from the mundane to the most extreme. They can thrive and endure in conditions where their presence is least foreseen: from the frigid expanses of the Arctic to the intense heat of hydrothermal vents, and from the ocean’s abyssal depths to the lofty heights of the atmosphere. This impressive adaptability relies more on their ability to exploit a wide array of nutrients to fuel a rather conserved central metabolism than on their diverse metabolic capabilities.
Central to nutrient acquisition are proteins situated outside the bacterial cell. These proteins, which can cross bacterial membranes, attach to the cell wall, or stay in the space between membranes, make up the secreted proteome. They play a key role in helping bacteria adapt to their environment by recognizing and taking in nutrients, communicating with other bacteria, attaching to surfaces, and sending signals. These proteins allow bacteria to sense and respond to their physicochemical environment quickly and efficiently.
Credit. Author.
Freshwater bacterial diversity
In our work, we employed an unconventional approach to studying the adaptive capabilities of bacteria thriving in freshwater environments by examining the evolutionary pressures on genes encoding both the secreted and cytoplasmic proteomes.
We collected samples over time from five European lakes with different nutrient levels. These samples were sequenced, producing about 11 billion reads and 3.31 Tb. We created a comprehensive database of around 5,500 freshwater bacterial genomes using advanced genomic techniques. This database was divided into bacteria with average to large and small genomes.
Credit. Author
Challenging evolutionary models
According to adaptive models of bacterial speciation, the bacterial-secreted proteome is expected to evolve faster than the corresponding cytoplasmic one. The secreted proteome represents the primary interface in which bacteria interact with their surrounding environment.
We observed that species with average to large genomes adhered to the dominant paradigm of evolution through environmental adaptation. These species exhibited more diversity in the genes encoding secreted proteins than those encoding cytoplasmic ones. In contrast, species with small genomes displayed an opposite pattern, with secreted proteomes less diverse than their cytoplasmic counterparts.
To understand the emergence of this contrasting gene diversity pattern, we analyzed the evolutionary pressures acting on the genes coding for secreted and cytoplasmic proteomes. Our analyses revealed that the differing diversity patterns in the secreted proteomes of the two genome size categories were due to variations in selection pressures. Specifically, the selection pressure was significantly lower on the secreted proteome of medium to large genome-size bacteria, while it was notably higher in species with small genomes.
Gene snatchers
Our analyses revealed fascinating insights into how bacteria handle their genetic material. Bacteria with medium to large genomes acquire genetic material from a wider variety of other bacteria than those with smaller genomes. This new genetic material is mostly preserved in the secreted proteins of large-genome species, boosting their genetic diversity.
Interestingly, our findings also show that bacteria with larger genomes have more functionally redundant proteins in their secreted proteomes than in their cytoplasmic ones. In contrast, small-genome bacteria have more unique proteins in their secreted proteomes. This redundancy in larger genome bacteria likely enhances adaptability by keeping extra copies of genes and functions. This provides a safe space for secreted proteins to evolve and diversify. Conversely, the lack of redundancy in the secreted proteomes of small-genome bacteria may limit their ability to evolve, posing a potential challenge to their adaptive capacity.
Lifestyle strategies
Our research reveals how bacteria adapt to their environments based on the size of their genomes. Bacteria with larger genomes thrive in nutrient-rich conditions because they can quickly respond to nutrient concentration changes and grow rapidly. They have redundant proteins, which act as a “backup” system, helping them adapt and evolve.
In contrast, bacteria with smaller genomes are better suited for stable, nutrient-poor conditions. These bacteria grow slowly but efficiently, focusing on consistent growth. They have fewer redundant proteins, limiting their ability to adapt to new conditions but making them very efficient at using available nutrients. Their proteins are highly optimized, so further changes are neither beneficial nor necessary.
Studying the genetic makeup of abundant freshwater bacteria has provided insights into how different bacterial species evolve and adapt. We found that some bacteria, especially those with small genomes, experience long periods of no evolutionary change in their genes coding for secreted proteomes, known as “adaptive stasis”. This lack of change is due to a shortage of redundant proteins, which restricts their ability to innovate and adapt to changing conditions.
Credit. Author
Diversity threatened by climate change
Freshwater lakes play a crucial role in ecosystem functioning and global carbon cycling due to their high biological productivity and microbial activity.
However, our research shows that many common freshwater bacteria, especially those with small genomes, have reached a point where they no longer adapt to new conditions. This makes them vulnerable to climate change. Rising temperatures and environmental changes may disrupt the bacteria communities, which are crucial for nutrient cycling and maintaining water quality. Understanding the limits of how these bacteria can adapt is crucial for protecting these ecosystems and managing our water resources as climate change continues to impact them.
Collaborative efforts to protect freshwater ecosystems
To safeguard our freshwater ecosystems, coordinated action from all sectors is essential. Research institutions must pioneer advanced methods to assess the impact of climate change on microbial biodiversity, with funding agencies prioritizing these critical initiatives. Governments should promote international collaboration, forging partnerships between scientists and regions most affected by climate change and water scarcity. Meanwhile, industry bodies must embrace sustainable water management practices to protect ecosystem health and quality. Only through these collective efforts can we confront the challenges posed by climate change to our precious freshwater resources.
🔬🧫🧪🔍🤓👩🔬🦠🔭📚
Journal reference
Serra Moncadas, L., Hofer, C., Bulzu, P. A., Pernthaler, J., & Andrei, A. S. (2024). Freshwater genome-reduced bacteria exhibit pervasive episodes of adaptive stasis. Nature communications, 15(1), 3421. https://doi.org/10.1038/s41467-024-47767-7
