Student blogs

Last week I was pleased to have another day of fieldwork, this time in the New Forest National Park in south England. The New Forest includes one of the largest areas of pasture, heathland and forest in south east England and the site we visited is Whitley Wood, a oak-beech wood pasture woodland with grazing deer and ponies. The Natural History Museum Soil Biodiversity Group have been sampling at this site for soil and leaf litter invertebrates nearly every month since 2002.

A 100 meter transect line is laid at random in the forest and a sample is taken every seven meters. This comprises a measure of soil moisture and temperature and what plants are growing in a 1 m quadrat. Then a pit is dug and any earthworms collected and the leaf litter from the 1 meter square is sieved and put into bags to take back to the Museum. From this month onwards we will also be collecting soil samples which I will be analysing for microbial DNA, I will then use this to investigate how microbe diversity changes during the seasons and the relationship with invertebrates.

Using a syringe barrel as a soil corer I took four samples per quadrat which were then mixed together in a tube, both syringes and tubes had to be sterile to avoid contamination with microbes from other places and each quadrat had its own tube – this will also give an idea of how variable soil microbes are across the woodland.

Whitley Wood fieldwork is popular with Soil Biodiversity Group volunteers and students because at the end of the fieldwork we visit a pastry shop for lunch. Then its back to the Museum to process the samples.

To extract the invertebrates the sieved leaf litter is placed into Winkler bags, these are made up of two parts – the inner bags are made of mesh and look a bit like laundry bags, these are then suspended in a fabric funnel which is hung up in a room for three days. The top of the bag is tied up to stop the invertebrates escaping and at the bottom there is a bottle of alcohol. As the leaf litter dries out the invertebrates move down the funnel into the bottle to be preserved for later counting and identification.

Of course this time I also had my soil samples to store. The DNA extraction and analysis will require travelling to my co-supervisor’s laboratory at Imperial College Silwood Park so rather than going every month I am storing them up to process in bulk. To preserve the microbes they are stored in a freezer at -8o°C ready for when I need them.

Read Soil, microbes and pasties in full

As much as I enjoy working at my computer analysing data, it felt good to get out to get outside and collect some data of my own recently. I was sampling earthworms in Purbeck, Dorset with the help of Soil Biodiversity Group volunteers John Chesebro and Fevziye Hasan (https://twitter.com/fezidae), Rachel Efrat of the British Geological Survey (https://twitter.com/RachelEfrat) and my boyfriend Andrew.

The study site is part of a long-term study into heathland restoration. Heathlands are found in areas of free-draining infertile, acidic soils, and are dominated by shrubs such as heather and gorse. Part of this heath was converted to agricultural land in the 1950s by the application of large quantities of fertiliser to increase nutrients, and lime to increase the pH of the naturally acidic soils. Since then there has been a move to restore the original heathland vegetation, which is a habitat for rare species.

The original study compared different methods of making the soil more acidic, by removing the topsoil, adding sulphur or iron sulphates, these were then sown with cuttings from the nearby heathland. Not all the plots were successful, but it did result in a long gradient of different soil pH levels, which I am using to investigate the influence of pH on earthworms.

Earthworms are known to prefer alkaline conditions, and species vary in their tolerance to pH levels but the data we already have is confounded by being collected across different soil types and locations. At this site the plots are on the same soil type, so hopefully the data will show the pattern of earthworm abundance and species with pH which can then be compared with the overall data set to see if the patterns are similar or different.

I had a GPS device with the co-ordinates of the plots, and had chosen ones with a good range of pH measurements. Once we had found them the fieldwork was straightforward, we take measurements of soil pH, moisture and temperature and then dig a standard sized hole and collect any earthworms we find.

Any earthworms found in the soil were preserved in methylated spirits to be identified back in the laboratory.

We were fortunate to have three days of good weather, which was a novelty as my previous experiences of earthworm sampling has been in the cold and rain! The dry spring did mean the soils were not as wet as I expected however, which necessitated some changes to the sampling in order to maximise the number of earthworms sampled – hopefully it will be enough.

Read Digging for earthworms in Dorset in full

For the final day of the Natural History Museum postgraduate field trip we were off to look for aquatic invertebrates and algae, first in some freshwater and later at the coast. The first stop of the day was at the Corfe River where we had a great view of the ruins of Corfe Castle, an 11th Century fortification built by William the Conqueror (and popular destination for my childhood holidays).

Eileen and Polly demonstrated the technique of kick-sampling, where you hold a net under the water and kick the sediment for a set amount of time, this dislodges animals living on the river bed and they are then collected in the net. This method is used to test the health of freshwaters, as each animal collected is identified, counted and assigned a score based on how sensitive they are to water pollution.

Despite being the middle of winter there were still plenty of animals living in the river, including snails, freshwater-shrimp (actually a type of amphipod, more closely related to woodlice than the shrimp people eat) assorted insect larvae and we even a Bullhead fish (Cottus gobio).

Next it was off to the River Piddle (*snigger*) in Wareham. A larger river but which had unfortunately recently been partly dredged and had most of the vegetation cut back, but we did find plenty of Minnows (Phoxinus phoxinus) and I had a dig around the banks to find some earthworms to identify later.

After going back to the Old Malthouse to have lunch (and warm up) plus do a little identification of some of the specimens we brought back from the Corfe and the Piddle wet set of to the coast at Swanage to do some rockpooling.

We found two species of limpets, assorted periwinkles and topshells. There were Beadlet Anemones (Actinia equina) in several colours, you can see one below which had ‘babies’ budding off from it. There were also some tiny Shore Crabs (Carcinus maenas). We also recorded many seaweed species which Eileen helped us identify later back in the lab.

Read A break from London (with science!) part 4 – splish splashing around in full

Two attendees on the Natural History Museum field trip to Dorset were parasitologists, and they brought along some herring and a dogfish for us to dissect and look for parasites. Firstly we inspected ‘our’ fish for external parasites such as fish lice or leeches, but every fish was clean. Next we removed the gills and looked at them under a microscope to see if any parasites were attached. Again, none of the fish contained any parasites, leading to complaints of them ‘being too healthy”(!)

The next stage was to open up the body cavity and remove the organs to look for parasitic worms. I could immediately see that my herring was female, due to the large pair of roe, but at first could not see any parasites in the organs. After looking carefully I eventually found some small, white worms curled up into tight balls, which when removed with forceps into water started to uncurl and wiggle around. I eventually collected around 10 of the worms from the herring, quite a small number, so I was told. These nematode worms were probably the larvae of a nematode belonging to the genus Anisakis, a very common parasite in marine fish and mammals. It is harmless to humans when the fish has been frozen or cooked but can rarely cause an illness called anisakiasis when ingested with uncooked fish. The worms were preserved in alcohol to go of for genetic sequencing, hopefully we will later get some feedback on what they are identified as.

Read A break from London (with science!) part 3 – something’s fishy in full

Dorset is the location of some fine geological sites, known as the Jurassic Coast, and designated as a World Heritage Site so we spent a day there with Richard Twitchett, a geologist from the Natural History Museum. The evening before Richard gave an overview of some geological concepts and an introduction to the geology of the area.

The rocks of this area are the sedimentary type, which are formed by accumulation of material compacted and cemented together over millions of years. These type of rocks may contain fossils of plants and animals that died and became trapped and preserved between the layers. The exposed rocks of the Dorset coast are Jurassic (200-145 million years old) and Cretaceous (145-65 million years old) in age. The rocks of Cretaceous age would have originally lain on top of the older Jurassic ones but earth movements have titled them so they become younger as you move east along the coast – like a walk through time. This entertaining video tells the story better than I.

First of all, we stopped by the Square and Compass pub in Worth Matravers to visit it’s small museum, sadly it was closed but Richard gave us a tour of the garden furniture which are constructed from slabs of local rock, including examples of dinosaur footprints and mud cracks.

Then we were off to Lulworth Cove, with Richard refreshing our minds on the age and type of rocks in this area from his introduction the night before. Lulworth is one of my favourite sites, but I’ve mostly had the misfortune to visit in the pouring rain, luckily today was beautiful day. Coves form when there are layers of rocks with different resistances, so a sea breach, maybe through a weakness in the rock, carves out the softer rocks behind. West of Lulworth Cove is Stair Hole, a smaller example which provides a glimpse of how Lulworth Cove formed.

Stair Hole features some amazingly tilted and folded rocks (called the Lulworth Crumple), so that in some places they are completely turned over.

Next we travelled West to Osmington Mills, were the cliffs form a rock sequence called the Corallian. As we walked along the shore Richard explained the different features of the rock and what this told us about the environments they formed in.

Some layers were full of fossil shells, dumped during ancient storms. Others were finer grained mudstones with many fossil traces of burrowing animals.

After a walk back along the top of the cliffs, admiring the views we set off back to the Old Malthouse for a very different evening activity – parasitology!

Read A break from London (with science!) part 2 – a stony reception in full