When do phages shape microbial communities? Assessing how changes in abiotic and biotic conditions impact the importance of phage
Lead Research Organisation:
UNIVERSITY OF EXETER
Abstract
Bacteriophage - viruses that infect bacteria - are the most abundant life-forms on Earth, and are thought to be important in controlling microbial communities and - through this control - key ecosystem functions such as carbon and nutrient cycling and preventing bacterial disease. However, the evidence of the role phage plays in microbial communities remains mixed, is mainly correlational, varies between environments, and is almost non-existent in soil. The overarching aim of this project is to better understand the ecological conditions under which phage exert control on microbial communities. This is essential to understanding how microbial communities - and their associated
functions - will respond to environmental change.
I predict that phage impact on microbial communities will be strongest under conditions that maximise encounter rates between susceptible bacteria and phage. For example, during algal blooms and cholera epidemics - textbook examples of phage control - phage infections cause sudden reductions in the density of susceptible hosts
and increase the diversity of the bacterial community. In contrast, the increased bacterial and phage diversity and spatial structure of soil microbial communities likely result in reduced encounter rates, which may mean phages have a lower impact in soils. Furthermore, microbial communities may be less impacted by phages if all bacterial taxa can be affected by phages simultaneously. To complicate things further, soil conditions drastically change through time and space, thereby likely altering encounter rates and the impact of phages on soil communities. For example, we predict that phage impose stronger control in warmer and wetter soils where encounter rates are typically higher. Temperature and soil moisture are also two key factors that are likely to become more extreme and variable with climate change both globally and in the UK.
To properly investigate the causal impact of phage, I will dis-assemble and then reassemble natural bacterial compost communities with, and crucially without, host-specific phages. I will measure whether increasing phage diversity reduces the overall impact of phage by comparing the composition and functioning of microbial communities grown in the absence and presence of single or multiple phages. Next, we will determine how temperature and soil moisture change phage-mediated impacts. Sequencing will uncover how the bacteria and phage have adapted to their environment and each other through the course of the experiment. Finally, I will combine my data with models of bacteria-phage dynamics to examine how general my results are, and compare these with identified patterns of phage impact on bacterial abundances in published datasets of natural microbial communities. By concentrating on ways in which conditions alter encounter rates, our work will be applicable across a wide range
of environments.
This work is crucial to understanding when and where phage control bacterial communities, whether this control is likely to be impacted by climate change, and the importance of phage in climate predictions. Furthermore, it will provide key information for the conditions under which phage application may be appropriate for microbiome
engineering.
functions - will respond to environmental change.
I predict that phage impact on microbial communities will be strongest under conditions that maximise encounter rates between susceptible bacteria and phage. For example, during algal blooms and cholera epidemics - textbook examples of phage control - phage infections cause sudden reductions in the density of susceptible hosts
and increase the diversity of the bacterial community. In contrast, the increased bacterial and phage diversity and spatial structure of soil microbial communities likely result in reduced encounter rates, which may mean phages have a lower impact in soils. Furthermore, microbial communities may be less impacted by phages if all bacterial taxa can be affected by phages simultaneously. To complicate things further, soil conditions drastically change through time and space, thereby likely altering encounter rates and the impact of phages on soil communities. For example, we predict that phage impose stronger control in warmer and wetter soils where encounter rates are typically higher. Temperature and soil moisture are also two key factors that are likely to become more extreme and variable with climate change both globally and in the UK.
To properly investigate the causal impact of phage, I will dis-assemble and then reassemble natural bacterial compost communities with, and crucially without, host-specific phages. I will measure whether increasing phage diversity reduces the overall impact of phage by comparing the composition and functioning of microbial communities grown in the absence and presence of single or multiple phages. Next, we will determine how temperature and soil moisture change phage-mediated impacts. Sequencing will uncover how the bacteria and phage have adapted to their environment and each other through the course of the experiment. Finally, I will combine my data with models of bacteria-phage dynamics to examine how general my results are, and compare these with identified patterns of phage impact on bacterial abundances in published datasets of natural microbial communities. By concentrating on ways in which conditions alter encounter rates, our work will be applicable across a wide range
of environments.
This work is crucial to understanding when and where phage control bacterial communities, whether this control is likely to be impacted by climate change, and the importance of phage in climate predictions. Furthermore, it will provide key information for the conditions under which phage application may be appropriate for microbiome
engineering.
People |
ORCID iD |
| Meaghan Castledine (Principal Investigator / Fellow) |