I have a watch that I often wear. This watch has an old TV test pattern on the dial. [TV test pattern? Showing my age, I need to explain to those younger than 35… Back in the day, television only broadcast from morning till around midnight. It then closed down (with the goodnight kiwi segment). Before and after the content there was a test pattern broadcast that could help calibrate your telly and test the signal (maybe?).]
One other feature of this watch is the strap. One half of the strap is black and the other is white. When I look at my watch on my wrist I almost always only see the black side. So in my mind it is a watch with a TV test pattern and a black strap. That’s ‘normal’ to me.
Occasionally, I catch a glimpse of the white side (or I see it in a photo). It always gives me a bit of jolt. That different view completely changes the way I think about the watch. It becomes a watch with a TV test pattern and a white strap. That’s ‘abnormal’ to me.
People observing me, if they think about it at all, just see a patterned watch with different coloured straps. And that’s ‘normal’ to them.
One thing that I like about the watch strap is that it reminds me that interpretation of what we observe can be very dependent on how we go about perceiving things. This is always useful for a scientist. Depending on the approach, different scientists may see and collect data on very different things from the same system.
A case in point. Recent PhD student, Arsalan Emami-Khoyi, did his research on New Zealand fur seals. We were interested in the genetic diversity of this species. NZ fur seals have been through a very small population phase and then rebounded to fairly decent numbers. We were interested in whether the DNA could tell us about how large the population was in the past, what it declined to, the genetic variation present today, especially around Banks Peninsula, as well as looking at which other mammals seals were related to.
Obtaining samples from live fur seals is a little challenging. They are big and bitey. We trialled several ways of getting seal DNA. We tried firing small hollow-tipped darts on cords into their blubbery sides to pull out a tiny piece of skin (worked sometimes but meant we had to get fairly close. Even using riot shields to keep the seals at bay was not always successful!).
We wiped down sites where they had been resting, assuming that skin would haverubbed onto the resting rocks (worked sometimes). We swabbed their mouths, as there are a lot of host cells in there (worked OK but got us very close to the bitey end). Finally, we went with grabbing seal pups when they were only a few kgs and taking a small tissue sample from a flipper (worked very well – small and bitey is easier to deal with).
From these samples we learnt a lot about New Zealand fur seals. And there I thought we were finished. Until Arsalan had a watch moment. He looked at the situation from a very different perspective. A micro perspective.
We had a bunch of swabs from the mouths of seals, mostly older pups. The DNA approach we used was sensitive enough to pick up the DNA from the various organisms that live in the mouth of the seals. So by switching the focus we could survey the mouth bacteria of seals. This would seem like an obvious thing to do for a microbiologist but not so much for a vertebrate biologist.
Arsalan has published this survey in Marine Mammal Science with his supervisors, Adrian Paterson and James Ross of Lincoln University, as well as other experts. He detected DNA signatures from the mouth swabs and matched them to existing bacterial DNA databases.
The mouth is continually exposed to the environment and is a gateway to the stomach and the internal areas of the seal.Several nasty bacterial species lurk in the mouths of fur seal pups. These species are a major cause of deaths in young seals in their first year of life. Other bacteria work with their seal host in symbiotic partnerships.
Around 100 species were found overall. Many species identified are helpful for the seal in normal conditions but can become a problem if the seal develops lesions or cuts (such as Campylobacter). Many appeared to be similar to bacteria found in the marine environment and these species likely colonise seal mouths from the surrounding habitat. Others are likely to be passed down from mother through bacteria that live around the lactating areas.
Amongst this diversity were species that would cause problems if humans (or other organisms, including other seals) were bitten. These include the bacterial species Chryseobacterium (generally keep wounds open and not healing), Cardiobacterium (causes peritonitis where internal membranes are inflamed) and Flavobacterium (causes septicaemia or blood poisoning).
Seals have been proposed to be a potential host for the bovine Tb causing Mycobacterium species. We detected none of these species.
From a study on population structure and history where we mainly worried about avoiding the bitey end of NZ fur seals, we now have a great deal of knowledge about the amazing micro-diversity that lives in the bitey end. We also used a similar approach to examine what comes out of the non-bitey end of the seal to show us what they eat.
I’ve published papers on a wide-range of organisms but I never thought that I would do so with bacteria. Seeing things and situations from a different perspective can be very rewarding for a scientist!