An Ancient Armsrace: Bacteria and Bacteriophages in Sediment Cores – Part I

My field work experience is limited to sticking tubes into the ground to collect soil samples, ususally from underneath shrubs next to my office or in some random field (while it rains). However, last Thursday field sampling was a whole lot cooler. Although the principle was again ‘sticking tubes into mud’, the field site, weather, gear was much more exciting than usual and I had some great company as well.

Britt Koskella and myself are starting up a project to track coevolution between parasites and their hosts sampled through historic time. Parasites are ubiquitous in nature and the arms race between hosts and parasites is believed to be a key factor influencing population dynamics, genetic diversity, the evolution of virulence and the evolution of sex. Just like plants and animals, bacteria suffer from infection by parasitic viruses (‘bacteriophages‘). Lytic phages bind to a receptor on the bacterial cell surface, inject their genetic material into the cell and take over the bacterial cellular machinery to make multiple copies of them which are released through lysis of the bacterium. This process has received extensive experimental attention using the Pseudomonas fluorescens and phage Φ2 model system developed by Angus Buckling and co-workers. (Both Britt and myself did a postdoc with Angus at Oxford and followed him to Exeter where he now is a Professor of Evolutionary Biology.)

The beauty of experimental evolution is that new resistant and infective mutants evolve on a time scale of days, and that bacteria and phages can be stored in the freezer, allowing parasites to be paired to hosts from the past, present and future and vice-versa. Although highly elegant, these lab experiments are not a complete substitute for the study of populations ‘in the wild’. Inspired by a paper resurrecting the water flea Daphnia and their microparasites from lake sediment to pair real-life populations through evolutionary time, Britt and I plan to do the same for bacteria and phage trapped in lake sediment. When we succeed in isolating bugs from these cores, we could potentially track coevolutionary dynamics spanning centuries (we are also planning to track bacteria and phage throughout the season by conventional sampling).

We got in touch with palaeo-limnologists Richard Jones and Christopher Caseldine from Exeter University’s Department of Geography and were lucky to be able to join in on their one day expedition to pretty Loe Pool. Richard, Christopher and their team (Lucy, Zoe, Mark and Richard) collected two 3 meter sediment cores using a Mackereth corer for their own research projects. After that, the team helped Britt and myself to collect three smaller cores. Below some pictures!

The large Mackereth corer is launched from two zodiacs tied together. (Britt, Lucy and myself towed this contraption out onto the lake in another zodiac.)

Pressurized air is used to push the inner coring tube into the sediment and after that to float the whole apparatus. Care has to be taken at this last step; Mackereth himself was knocked out of his boat when the corer came back up below him and died of pneumonia afterwards…..

Back on land, the inner core tube is retreived and sealed.

The small corer for our own samples.

Richard holding one of the cores.

All three cores are in a cold room back on Tremough campus. With the aid of two undergraduate students, Ben and Claire (neither of them could unfortunately make it to the field), we will attempt to isolate bacteria and phage from along the sediment core.  Britt and I will try out how to slice and dice the sediment in the coming weeks using our first practice core, more serious work will start in the new term. More about that in part II!

Michiel

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5 Responses to An Ancient Armsrace: Bacteria and Bacteriophages in Sediment Cores – Part I

  1. Christina says:

    It seems very exciting to sample with the Mackereth corers! Good luck with your research! The results will be very interesting!

  2. Thanks Christina! I will post updates although it will be a while because the undergrads will start in September.

  3. mark says:

    looks like a great project. if only to see what’s resurrectable in your samples.

  4. Robin Tecon says:

    “My field work experience is limited to sticking tubes into the ground to collect soil samples, usually from underneath shrubs next to my office”
    Ah! just like me 😉
    Your planned experiments of archeomicrobiology seem pretty cool. Thanks for posting about it!

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