Phages – Masters of the Biosphere
Figure 1: A group of phages (green) attack an E.coli cell (yellow). Image from Science Source/Eye of Science
Bacteriophages, also referred to simply as phages, are the most abundant biological entities on the entire planet. Phages are the major predators of bacteria and that’s actually where they get their name from. Bacter, referring to Bacteria and phago meaning “eaters of”. While phages don’t technically “eat” their prey they do infect bacteria and they infect them at a massive scale. It’s estimated that Virus infections/unit time here. During infection phages can introduce bits and pieces of DNA from other environments and sometimes entire genes. The process of genetic transfer via phages is referred to as Horizontal Gene Transfer (HGT) and is one of the major drivers of evolution.
Many bacterial species don’t live solitary lives and are members of a microbial community. Microbial communities impact everything from the global carbon cycle to how you digest food therefore understanding their evolution has important implications across many aspects of our daily lives. Previously, most studies investigating the evolution of microbial communities focused on reconstructing HGT events of the past via comparing difference microbial genomes that had already been sequenced. During my post doc I wanted to understand and observe the process of HGT within microbial communities in real-time.
The first challenge of this endeavor was designing an experiment that could actually capture the process of HGT in some observable way. Why is this a challenge? Well, HGT events were expected to be relatively rare therefore we would need to sequence a lot of DNA to capture a particular event. If the microbial community contained too many species of bacteria we might not be able to detect the signal from the noise. We also wanted to apply some type of selection pressure on the microbial community towards a particular trait with the hopes of accelerating evolution. Finally, we wanted microbial diversity to be maintained over time and not have a single bacterial species become the “winner” and dominate the entire community. In the end we settled on the following experimental conditions:
Experimental Conditions
1) Founding microbial communities – Parisian compost (soil)
2) Carbon source – Cellulose
3) Experimental manipulation – +/- Mixed phage communities
We wanted to start complex and push the system towards simplicity with the hopes of staying in the diverse, but not too diverse, Goldilocks zone where we could actually observe HGT events. Therefore as a founding community we utilized soil, amongst the most diverse microbiomes in the terrestrial environment, taken from a local compost heap near the lab in Paris. To simplify this community we needed to give them a carbon source that was relatively difficult to eat and would thereby prevent the establishment of the single “winner”. Cellulose was selected as the sole carbon source for two main reasons. First, the process is known to occur slowly. Second, microbial communities in nature work together to chop off bits and pieces of cellulose by forming biofilms and we thought maybe we could foster more HGT if we were already working in a system that required cooperation. For example, if a gene emerged that was particularly good at eating cellulose in one member of the microbial community maybe that advantageous gene would also emerge in other species via HGT.
Many bacterial species don’t live solitary lives and are members of a microbial community. Microbial communities impact everything from the global carbon cycle to how you digest food therefore understanding their evolution has important implications across many aspects of our daily lives. Previously, most studies investigating the evolution of microbial communities focused on reconstructing HGT events of the past via comparing difference microbial genomes that had already been sequenced. During my post doc I wanted to understand and observe the process of HGT within microbial communities in real-time.
The first challenge of this endeavor was designing an experiment that could actually capture the process of HGT in some observable way. Why is this a challenge? Well, HGT events were expected to be relatively rare therefore we would need to sequence a lot of DNA to capture a particular event. If the microbial community contained too many species of bacteria we might not be able to detect the signal from the noise. We also wanted to apply some type of selection pressure on the microbial community towards a particular trait with the hopes of accelerating evolution. Finally, we wanted microbial diversity to be maintained over time and not have a single bacterial species become the “winner” and dominate the entire community. In the end we settled on the following experimental conditions:
Experimental Conditions
1) Founding microbial communities – Parisian compost (soil)
2) Carbon source – Cellulose
3) Experimental manipulation – +/- Mixed phage communities
We wanted to start complex and push the system towards simplicity with the hopes of staying in the diverse, but not too diverse, Goldilocks zone where we could actually observe HGT events. Therefore as a founding community we utilized soil, amongst the most diverse microbiomes in the terrestrial environment, taken from a local compost heap near the lab in Paris. To simplify this community we needed to give them a carbon source that was relatively difficult to eat and would thereby prevent the establishment of the single “winner”. Cellulose was selected as the sole carbon source for two main reasons. First, the process is known to occur slowly. Second, microbial communities in nature work together to chop off bits and pieces of cellulose by forming biofilms and we thought maybe we could foster more HGT if we were already working in a system that required cooperation. For example, if a gene emerged that was particularly good at eating cellulose in one member of the microbial community maybe that advantageous gene would also emerge in other species via HGT.
Figure 2: Experimental setup.
To kick off the experiment ten founding microbial communities were established by incubating some Parisian compost in minimal media with cellulose paper as the sole carbon source. Next, the founding communities were split into two transfer regimes: vertical and horizontal. In the vertical regime each of the ten communities were homogenized every two weeks and transferred to fresh medium with a new piece of cellulose paper. In the horizontal regime each transfer involved the founding microbial community as well as a mixed cocktail of “phage juice” from all ten bottles, thus providing the opportunity for genes to move between horizontal but not vertical communities (Figure 2). Using comparative metagenomics, we provide evidence for large-scale movement of genetic material between horizontal bottles that involves genes with various predicted functions including iron acquisition, virulence factors, transcription, and individual phage genomes. As a general proxy for community function we also measured the ammonia concentrations during the course of the two-week regime. Surprisingly, we found that the majority of horizontal communities had significantly higher ammonia production compared to their vertical counterparts.
To our knowledge this study describes for the first time the emergence of a functional impact of HGT on a complex microbial community through direct experimentation. If you are interested to learn more check out the original paper here as well as commentary that was co-published in the same issue here.
To our knowledge this study describes for the first time the emergence of a functional impact of HGT on a complex microbial community through direct experimentation. If you are interested to learn more check out the original paper here as well as commentary that was co-published in the same issue here.