Science on the Spectrum is moving

I was fortunate enough to have my entry into the Imperial College London student blogger's competition accepted and so now I am an official Imperial Student Blogger! Consequently I am concentrating my blog writing efforts there so will be taking a break from Science on the Spectrum.

If you are interested in following my posts as an Imperial College PhD student my new blog can be found at: http://wwwf.imperial.ac.uk/blog/studentblogs/victoria14/

Eek I’m a PhD student!

Well technically I’m a MPhil student, since you first register fro that and then apply for an ‘upgrade’ at the end of the first year. Checking some old text messages I was amused to find how they tracked the ups and downs of my application, interview and offer and gave me some reflection on the journey before I turn and look towards the path ahead.

Evidently I was very nervous about the interview:

But I wasn’t alone:

I hadn’t! In part because I’d fallen into my old trap of “ignore it and hope it goes away” but also because I had been distracted my a new job I had just started! Anyway after some interview advice / pep talk the next day was interview time which was one of the most stressful things I have done so far. I was placed second, but to my delight the first choice candidate declined and a month later I received an email offering me the PhD scholarship:

So six months later I have started my PhD. Predictably I’m stressed! It helps that I have some familiarity with both Imperial College and the Museum but the start of term at university is not an autism-friendly time, the campus was very busy with fresher’s week stands, and I didn’t feel up to looking around with all the crowds. However in the PREDICTS lab I feel I am settling in ok, I have attended lab meetings which are useful to hear what everyone has been up to and share recent papers. I am still feeling rather lost, but it is improving every day. I’m trying to remember how I felt when I first started in the soil group, did I feel lost and like I didn’t belong? I can’t remember, but if I did it must have gotten better, so logically it will again.

Sorting litter at home and abroad

Since I finished volunteering on the BESS Earthworm Project I have been continuing to work in the Natural History Museum Soil Biodiversity Group sorting leaf litter samples on my day off. After the sieved leaf litter samples have spent three days in the Winkler bags the pots are removed and the alcohol containing the invertebrates (and hopefully not too much mud and debris!) is decanted into tubes ready to be sorted by volunteers. Each litter sample is poured into a petri dish and put under the microscope for sorting. If you are lucky the sample looks like this; a nice clean sample with not too much debris where the the invertebrates can easily be picked out and counted.

A nice clean leaf litter sample ready for sorting

However sometimes the samples look like this! This one I had to split into parts and dilute in order be able to pick out the specimens from the murky alcohol. The invertebrates are identified to order level and each group counted into its own glass tubes which are labelled with the sample details and bundled together, some will eventually go on for species identification, and in the case of some tropical samples, DNA sequencing.

A soil group volunteers’ nightmare!

I started off sorting litter samples from Borneo, these are from one of my many projects run at Stability of Altered Forest Ecosystems (SAFE). This site provides a gradient of forest modification, from primary rainforest to increasing levels of logging and fragmentation, and finally oil palm plantation. I was excited to work with tropical samples for the first time although I did not find them as different from UK leaf litter samples as I expected. Many of the groups were familiar, within the beetles there were Staphylinidae which I recognised as from subfamilies Pselaphinae and Aleocharinae; but every so often though I was reminded that I was ‘abroad’ when a sample turned up exotic invertebrates such as termites, scorpions and crickets.

Meeting soldier termites for the first time in a Soil Biodiversity Group leaf sample from Borneo

I also noticed that when samples had a lot of ants or termites they had very few other invertebrates, which was a striking illustration of how much impact these two groups have on tropical forest ecosystems. Sometimes the number of ants or termites in the samples can be very high indeed, this tube from one litter sample has over 200 individuals. A current joint project with the Soil Biodiversity Group and Kate Parr’s lab is investigating how termites and ants effect other soil and litter invertebrates by excluding them experimental plots. 

Hundreds of termites sorted from a Soil Biodiversity Group litter sample

Some of my favourite invertebrates from the Borneo samples were these cute little scorpions and a fly with beautiful wing patterns. I am now back to sorting samples from the UK as we process those from the National Vegetation Classification project, which have a pleasing familiarity to my MSc leaf litter samples. Each sample has a different ‘character’ however so I never get bored, sorting Winkler samples to me as exciting as opening my stocking on Christmas morning – the old favourites are always there but you also never know what exciting new things there will be!

Scorpions and a pretty fly from Borneo leaf litter samples

A day in the woods with the Soil Biodiversity Group

I recently took a day off volunteer on fieldwork with the Natural History Museum Soil Biodiversity Group – my first fieldwork with the group since the BESS Earthworm Project, and a nice change from the pollinator and plant surveys I have been doing as part of my work at Reading University. The project I assisted on this time is the National Vegetation Classification (NVC) Project, this is a structured survey of soil and litter invertebrates across UK woodland types which began in 2002 and is now on its third round of sampling. The National Vegetation Classification categorises all UK ecosystems according to major vegetation type (woodland, grasslands etc.) which are then broken down into community types according to plant species composition. Woodlands are given the prefix W and fall into ‘wet woodland’ W1 to W7 and ‘dry woodland’ W8 to W18, this year is the turn of the dry woodlands and the study site I visited was Warburg Nature Reserve in Oxfordshire, an example of W12, a beech (Fagus sylvatica) woodland with plants characteristic of basic soils such as Dog’s Mercury (Mercurialis perennis).

Quadrat assembled – sampling can begin!

Instead of sampling from random quadrats as in my MSc fieldwork the NVC project uses a transect through the habitat with a 1m square quadrat being sampled at set intervals, alternating each side of the transect line. Other than that the method was similar, fellow volunteer and current MSc student Dan and I took turns scrapping and sieving litter from the quadrat which was then bagged up with a label to take back to the lab. Paul took the environmental readings while Kelly dug a soil pit and collected any invertebrates found into tubes of alcohol. A vegetation survey was also made of each quadrant, although being a beech woodland this was sparse and a lot less effort than my MSc project were the quadrats were often covered in vegetation!

Dan sieves leaf litter while Kelly sorts soil for invertebrates

After the cold wet days sampling in the middle of winter for the BESS Earthworm work the NVC fieldwork on a sunny day was quite a treat, finishing before lunch! Then it was back off to the Natural History Museum to process the leaf litter samples. The sieved leaf litter is placed into mesh bags which are hung inside a Winkler bag, basically a cloth funnel with a pot of alcohol tied to the bottom. These are hung up for three days and as the leaf litter dries the invertebrates move downwards into the pot where they are preserved ready for sorting and identification. Once, the Winkler bags were hung up in one of the towers either side of the main entrance of the Museum, but now they are in a much more convenient location which doesn’t involve carrying bags of leaf litter up narrow Victorian staircases!

Paul puts the sieved leaf litter samples into Winkler bags

After the three days are up the pots can be removed ready to be sorted and counted to order level by volunteers with selected invertebrate groups later identified to species level. The NVC dataset is just one example of long-term data collection by the NHM Soil Biodiversity Group, another being the monthly sampling at Whitley Wood in the New Forest, which I am volunteering on in August. I am very excited to be given the opportunity to analyse these datasets, among others, in my upcoming PhD.

Celebrating 50 Years of the Biological Records Centre

Last weekend I was at a symposium in Bath celebrating 50 years of the Biological Records Centre (BRC). The BRC collates and manages species observation data, including supporting biological recording schemes in publishing atlases, developing and hosting online resources. I have a long interest in biological recording, as a child spending most of my weekends and school holidays recording wildlife in a local woodland, but it was always on my own. It has not been until the last few years I have become interested in ‘formal’ biological recording by joining schemes and societies, much of this has been helped by the emergence of the internet in allowing me to make contact with like-minded people. Many of the talks at the symposium were of interest to me not only as a biological recorder but had some relevance to my future PhD research as the species distribution data held by the BRC have been used to understand responses to environmental change. I had my usual anxiety about attending but was at least confident I would know some delegates already, even if just through the internet, with the useful icebreaker “I follow you on Twitter” at the ready. There was an additional challenge in that I forgot to book my accommodation at the venue so ended up staying in a hostel in the city. I had never stayed in a dormitory before and was very concerned at how I would cope, but thought of it as an ‘experience’ and reminded myself of my promise to ‘be scared but do it anyway’. In the event it was not too bad, although the noise and bright light of the surrounding bars made sleep difficult, but at least it was cheap!

Saturday morning in Bath

The symposium talks were on Friday afternoon and Saturday, and covered the range of ways biological recording data  has been used to detect changes in species distribution, especially responses to climate change, and some of the problems involved in this. Biological data does not reflect constant effort, with bias in site and taxon selection etc. Data aggregation and selection, and computer modelling are some of the methods that can be used to detect the signals among the noise, all the talk of data and modelling got me very excited - I have definitely chosen the right PhD for me!

There were also thought-provoking lectures on citizen science, and on how technological developments have impacted and may impact on biological recording, including the use of molecular techniques in species identification and monitoring. 

The cake was tasty too!

The highlight of the weekend was a Sunday fieldtrip to Salisbury Plain Defence Training Estate, a military site not open to the public. It is the largest area unimproved chalk downland in north west Europe, with 20,000 hectares of Sites of Special Scientific Interest (SSSI) and Special Areas of Conservation (SAC) making it the largest designated site in the United Kingdom. Delegates with a wide range of interests in biological recording boarded two coaches for an escorted trip around the site, stopping at four areas to hunt for their favourite group(s), discuss hot topics or just admire the glorious habitat. I really enjoy trips with people who study different groups as it is a great way to discover new species. I did not go with the intention of collecting a group myself, since I knew I would not have time to process them at the moment, but contented myself observing the scenery and diversity. Observing the observers was also interesting, and fun to deduce which groups(s) they are looking for based on the techniques they use. Botanists often got down on their knees to examine plants, ornithologists and photographers were loaded with cameras and binoculars, and entomologists of various sorts had their assorted nets, pooters and tubes. Those turning over stones and grubbing about often turned out to be woodlice or centipede recorders; also in this category were several members of the Earthworm Society of Britain (ESB), because digging was not permitted due to the risk of unexploded ordinance – a sad restriction for an earthworm recorder. Despite this at least four species were recorded by rummaging in muddy puddles and turning over stones and other objects.

Keiron and Vicky from the ESB make do with turning over stones to find earthworms on Salisbury Plain

Vicky and I with the first earthworm of the day, probably Apporectodea longa, found under a rusty drum

Being a chalk download there were many woodlice and molluscs to be found under the stones, including the pill woodlouse Armadillidium vulgare, a species familiar to many for its defense of rolling up into a ball. Many of the specimens had babies, which develop from eggs in a special brood pouch on their underside.

Armadillidium vulgare with young on Salisbury Plain

Flowers and insects were everywhere, more than I have seen anywhere, and I get the feeling other chalk grasslands will never look so good again! Lepidoptera were everywhere, this thistle busy with Marbled Whites (Melanargia galathea), Burnet moths (Zygaena sp.) and assorted flies was typical. Other day-flying moths seen included the striking Forester (Adscita statices). I also saw some impressive flies including Cynomya mortuorum, my old favourite previously seen in Scotland, and the huge black parasitoid fly Tachina grossa.

Marbled Whites, Burnet moths and assorted flies nectaring on thistle

Forester on Greater Knapweed at Salisbury Plain

I met a number of new plants, including Dwarf Spurge (Euphorbia exigua), the rare Tuberous Thistle (Cirsium tuberosum) and probably my most exciting plant of the day, Knapweed Broomrape (Orobanche elatior), a plant parasitic on Greater Knapweed (Centaurea scabiosa).

Knapweed Broomrape (Orobanche elatior) on Salisbury Plain

My most exciting invertebrate of the day was neither a fly nor an earthworm however, it was the Fairy Shrimp (Chirocephalus diaphanus) which I have wanted to see since I first learnt about it when I was around 5 years old. These shrimp are found in temporary pools, their eggs lying dormant when the pools dry out ready to hatch on the next heavy rain. It is protected under Schedule 5 of the Wildlife and Countryside Act 1981 but the trip organisers, who have a licence, had collected some in a jar for us to view.

BRC 50th delegates huddle around temporary pools created by military vehicle manoeuvres to look for the elusive Fairy Shrimp

Fairy Shrimp (Chirocephalus diaphanus)

The photograph through the container using my phone really does not do them justice. They were quite big, a couple of inches long with a translucent pinkish colour, swimming using beautiful undulating motions.

So in all it was a brilliant weekend, meeting new species (and people!) and giving me lots to think about for my own research. A big thanks to the organisers, and long may the BRC continue.

A royally good earthworm meeting

A couple of weekends a go I attended a meeting organised by the Earthworm Society of Britain (ESB), this two day event consisted of a field trip to Richmond Park on the Saturday followed by a workshop on the Sunday to identify the specimens collected on the trip. Unfortunately I could only attend one day, and because Richmond Park was high on my ‘places to visit’ list and I have had no shortage of earthworm identification lately I decided to attend the Saturday event.

Richmond Park is one of the Royal Parks and the largest enclosed space in London, it is a National Nature Reserve, Site of Special Scientific Interest (SSSI) and a European Special Area of Conservation (SAC), because of this the ESB had to obtain special permission and a permit to collect earthworms. It was one of those glorious English Summer days when you can get soaked and sun-burnt in the same day! A group of 10 earthworm fans assembled at Richmond Station, clad in waterproofs before taking a bus to the park – my first ever trip on a London Bus – so that’s another ‘things to do in London’ crossed of my list! I had barely stepped into the Park when I got stuck in grubbing about in a rotten tree, finding the first earthworm off the day – and it was adult, so into a tube it went ready for Sunday, when it turned out to be Eisenia fetida.

Earthworm Society of Britain (ESB) members huddle in the rain around the first earthworm of the day at Richmond Park

The organisers had planned a range of areas to visit in the Park, aiming to visit as many habitats as possible to maximise the number of species recorded, and to cover as many grid squares as possible to increase the number of earthworm records. The first stop was some quite acidic looking grassland, where Kieron gave a crash course in earthworm surveying for those who had not done it before and introduced the ESB method and recording forms. As might be expected from the soil type, this area yielded few earthworms but other areas of neutral, improved grassland were better. We also surveyed woodland areas which again appeared to have an acid character, with lots of Rhododendron ponticum and was earthworm-poor.

Earthworm Society of Britain members survey for earthworms in grassland in Richmond Park

The best areas in terms of numbers were two wet habitats, one a small stream where we dug pits along the bank and took material from the bed itself, and a fen area. The stream produced a very special earthworm indeed: Helodrilus oculatus – an earthworm with very few records, all previously from wet deciduous woodland. This was an earthworm I was particularly keen to find, although I feel I can only half cross it off the ‘earthworm bucket-list’ since I did not see it under the microscope. Wet habitats are unrecorded for earthworms, and can have specialist semi-aquatic species, something I discovered when I targeted seeps in my MSc project and found lots of Eiseniella tetraedra which also turned up in some number in the Richmond Park fen habitat.

The small stream in Richmond Park where Helodrilus oculatus was found 

Concentrating as we were on earthworms I did not have much time to admire Richmond’s other charms and will have to make a point of visiting again when I am living back in London. We did however see some of the deer, including a mother and fawn, and saw the spot where this (in?)famous video was filmed. A visit to see the rut in the Autumn is high on my ‘things to do in London’ list!

Earthworm Society of Britain members admiring a camera-shy deer in Richmond Park 

Towards the end of the day Keiron gave a demonstration of how to relax and straighten earthworms using a plastic storage box. Putting the earthworms straight into a 80% solution of alcohol (industrial methylated spirits or IMS in this case) is a quick way to sample but causes them to twist and curl which can make them more difficult to identify. By first using a 30% alcohol solution to anaesthetise them they can be arranged in the groves of a plastic storage box (or I use drinking straws cut in half lengthwise). This helps make a nice neat reference collection, but I find it takes too much time if a lot of sites are being sampled.

Keiron demonstrates how to relax and straighten earthworms for easier identification

There was time to end the trip with a pint in a local pub before heading back to the station. The workshop the next day revealed a total of 15 species from the 7 sites were collected, all adding to the ESB data set. It is interesting to note this is the same number of species from the entire BESS project, which only sampled pasture, illustrating how sampling from a wide range of habitats can make a big difference to the number of species found. Reading the report recently circulated to members, in addition to the Helodrilus oculatus I also missed out on meeting Dendrobaena octaedra and Apporectodea icterica under the microscope for the first time! Looks like I will have to try and diversify the habitats I do my own sampling in.

The next Earthworm Society of Britain meeting is planned for the Autumn – why not join in? Membership is only £5 a year and on completion of the workshop you are given a recording pack which includes a copy of the AIDGAP Key to Earthworms.

Earthworms by numbers

Last week I finished sorting and identifying ‘my’ half of the Soil Biodiversity Group’s samples from the BESS Earthworm Project. The tubes from the last couple of fields were rather full, and because earthworms contain a high percentage of water this had diluted the alcohol, reducing its preserving qualities. The liquid in the samples was dark and pungent and the earthworms soft, this made identification more difficult as the features can be obscured and the earthworms fragile to manipulate. The final earthworm I identified from the samples was a somewhat underwhelming, squishy, headless and tailless Aporrectodea longa!

The final tube was a particularly ‘squishy’ sample

Some previous samples were more exciting however, in particular during the project I have identified by first ever Ap. limicola, Ap. caliginosa subsp. noctura and Octolasion tyrtaeum, although sadly I did not meet the Ap. icterica I was also hoping to find. Here are some of the facts and figures from my time volunteering on the BESS earthworm project:

Sorting and identifying earthworms from 14 fields from seven farms took around 90 hours, and I counted a total of 5940 earthworm specimens, 2124 which could be identified to species. I identified 16 earthworm taxa in total, with the highest number (12) occurring at the Dorset site. This was also the site with the highest number of earthworms per single pit – a whopping 110 individuals, but the highest number of species per pit was from the Dumfries and Galloway site, with seven.

The most common species in my samples were, as expected, Aporrectodea caliginosa (742) and Allolobophora chlorotica (506), but the sites differed in abundance between the two and it will be interesting to see if any environmental preferences emerge when the whole dataset in analysed. The rarest earthworms in my half of the data are Ap. caliginosa subsp. nocturna and Octolasion tyrtaeum with just a single specimen each, both from the fields in Dorset. Other uncommon species were Satchellius mammalis (4) and Dendrodrilus rubidus (3) both more commonly found in leaf litter, which is sparse in pasture.

Subjectively each field and farm had a different ‘character’ of earthworm diversity, and I am particularly looking forward to seeing what the statistics have to say about the variation between and within the different sites. Some preferences are quite obvious, Ap. limicola was found in large quantities exclusively (so far at least) from a field on a floodplain, and is known to have a preference for wet conditions (as suggested by its name, limnic = referring to freshwater). An old favourite of mine from my MSc project, Murchieona muldali, previously associated with hedgerows and field edges did seem to occur more frequently in low intensity fields with some scrub. There are so many other questions about earthworm diversity that the project will go some way to answering, like does earthworm diversity decrease with latitude? What are the environmental tolerances of each species and is there evidence for competitive exclusion? Do more fertile pastures have more individuals but fewer species? I am so excited to see the results!