25 January, 2018

The 2017 Research Experience Placements

The bi-directional influence of a soil organism and an insect endosymbiont on each other

Based: James Hutton Institute, Dundee

Project objectives:
Soil organisms can have surprising influences aboveground—and aboveground organisms can have equally surprising influences on soil organisms. One such soil organism, arbuscular mycorrhizal (AM) fungi can prime plants for a faster defence response when exposed to herbivores (1), and our previous research has shown that herbivores that host their own microbial partner can influence AM fungi. AM fungi are key soil organism, because of their frequent association with plants. These fungi grow inside plant roots and in soil, taking up nutrients and water for host plants and trading them for carbon from the plant (2). AM fungi associate with over 80% of plant species, and are highly susceptible to changes in the environment.

In this project we will determine whether AM fungi influence the attraction of parasitoids and aphids to plants, and if so does this vary by plant species or genotype, and 2) does an aphid endosymbiont negatively influence AM fungi in plant roots or does this depend on plant species or genotype?

Project outcomes:
The student developed, tested, and applied a program in Matlab that allowed us to video and collect data from olfactometer tests. The program tracked the movement of a wasp or aphid throughout an olfactometer set-up (also developed by the student) in the video, and recorded the amount of time that insect spent in one of four quadrats within the olfactometer during a 30 minute observation period. This program allowed us to vastly increase our olfactometer data collection, and we expect to publish the data Yorick collected from an experiment in which he applied the program.

The student rose to the challenge and, despite several unforeseen set-backs involving both programming and biological issues, was able to design successfully design a program. He expanded his computer programming skills and applied them to our system. He had the opportunity to work with the parasitoids, aphids, and plants to develop his program, and interacted with a number of other students working in our group this summer (completing biological degrees in the UK and Europe) to develop the equipment and the program. Through lab meetings and reading papers the student was also exposed to the wider area of ecological research conducted within our group.

Drought effect on Arctic, Temperate and Tropical peatlands.

Based: Bangor University

 Project objectives:
To compare the drought effect on microbial communities (structure and metabolism) and ecosystem functioning (gas interchange and pore water quality) of Arctic, Temperate and Tropical peatlands.

Project outcomes:
The student learned about different techniques in wetlands ecology, such as enzyme activities, gas interchange measures and water quality related measures. Also he learned how to deal with biological databases, getting information from them to make meaningful graphs.

The student helped setting up an experiment for Colombian and Welsh peat soils, so had to deal with common problems such as the unpredictability of the fieldwork and variability of natural samples. He also had to work cleaning and organising everything for the experiment learning how to be recursive under limited resources, a common problem in biological research. Additionally he was in charge of the experiment at some points, helping him to develop responsibility and understand the needed care for running experiments.

New approaches to mitigating phosphorus(P) losses to freshwater streams from agriculture by aggregating iron ochre and testing its suitability to trap P, for subsequent recycling to land.

Based: BGS Keyworth

Project objectives:
It is known that iron ochre waste material from the UK Coal Authority has a very large P-sorption capacity. There have been several attempts to use iron ochre to sorb dissolved phosphorus (P) in freshwater channels; this P is largely derived from diffuse agricultural sources of pollution. Recent attempts have involved combining cement with ochre to form large aggregates before placement instream to sorb P, but this material cannot then be recycled to land recovering the P because the cement has a massive structure, unlike granular soil. Alternatively, sintering of ochre has been proposed but will require large inputs of energy. The objective of this project was to investigate whether it was possible to combine iron ochre (waste from the UK Coal Authority) with a large surface area clay mineral (Fuller’s Earth) and a binding material to form aggregates. These would have: i) sufficiently large (>100 microns) to be retained in a fine mesh bag in a dry state, and ii) also in a wet state – thus mimicking placement in a stream/small channel setting. If this were possible the aggregates and their sorbed P could be returned directly to land, obviating the need for disposal (and associated costs) and recovering the macronutrient P for enhanced crop growth.

Project outcomes:
We first started trying to aggregate clay with iron ochre to form granules that will adsorb phosphorus by using Xanthan gum as a binding agent, freeze drying and an interesting freeze-thaw technique. These were unsuccessful in creating a suitable material that was sufficiently stable in water. However, there was some initial promise in creating a gum like substance that if could be contained in a porous shell of some kind could be a direction for future development. The main outcomes from this project came from the work in aggregating cement and iron ochre to create a pellet shaped material; building on existing work and previous studies that used other materials such as fly ash and blast furnace slag. Whilst this material cannot then be recycled to land it gave the student good experience in techniques for analyzing the phosphorous adsorption capabilities in the form of adsorption isotherms, spectrometry, training in laboratory methods, and SEM analysis. The isotherm results were unusual (probably as a result of the cement interactions and high pH), which resulted in the student learning how to use PHREEQC to undergo surface complexation modeling and find that the phosphorous sorption capabilities of iron ochre had a high dependence on pH. Samples were run using ICP-AES to assess whether interferences in the molybdate-blue measurements, were partly responsible for the peculiar shaped isotherms. Time spent on the SEM gave the student detailed high-resolution images of the pellet samples produced. This gave the student an introductory experience into high resolution microscopy techniques and demonstrated the porosity of the pellets.

Extreme events in montain soils

Based: Lancaster University

Project objectives:
To determine the effects of extreme climate events on the cycling of soil c in mointain soils. The placement aimed at training field and lab ecological methods, and the running of a short-term experiment under controlled conditions with a focus on gas exchange.

Project outcomes:
The student experienced working in the mountains of Scotland, field sampling and sampling design.

They constructed a controlled mesocosm study setup, and developed understanding on how to instrument and monitor such an installation.

They gained skills in gas exchange and flux calculations

They also developed data handling skills.

Resilience of UK agricultural soils to extreme flooding events and the impacts on greenhouse gas fluxes

Based: Centre for Ecology & Hydrology, Lancaster

Project objectives:
This project looks at the impacts of flooding (duration and seasonal variation) on plant productivity, microbial community assemblages and greenhouse gas exchange after extreme flooding on grassland and arable crop systems.

Project outcomes:
Training was provided in numerous field and laboratory techniques allowing analysis of greenhouse gas samples, plant biomass and soil sampling. The main outcome produced a complex R script to allow rapid calculation and quality control of greenhouse gas flux data from experimental samples analysed through gas chromatographs. This output was led and completed by the student to a very high standard, and provides the framework to save the group considerable time when calculating flux rates from GC samples, ready for statistical analysis. The student was able to learn in a state of the art laboratory setting how basic ecological data is collected, and then use his mathematics background to develop an R code to reduce time and errors in producing flux data.

The idea is for this code to be worked up into a user-friendly package that can be submitted to the EIDC data center.

Inter-specific and environmental variability in woody functional traits of tropical trees

Based: Centre for Ecology & Hydrology, Edinburgh

Project objectives:
The core aim of the project is to examine variability in branch wood traits of tropical trees, across soil environments and across species. The project will make use of existing data and unprocessed samples from 10 field sites across northern Borneo. Data are already available for the soil and climatic conditions of the sites, foliar traits and branch wood density. The focal, practical element of the project will be to analyse the anatomy of wood samples. As such, the project objectives are:

  1. Research and design the study of wood anatomy (for example, methods to quantify vessel area, diameter and density, measures which are theoretically related to sapflow and resistance to cavitation under drought stress)
  2. Prepare samples for analysis, using a microtome to thinly slice wood samples and microscope to photograph samples
  3. Analyse photographs using freely available image analysis software
  4. Collate the newly acquired wood trait data with other existing data (environment, species, other traits)
  5. Design research questions and conduct relevant statistical analysis on the dataset (most likely using multivariate data analysis techniques)
  6. Write a report to detail project findings. The study is highly novel because relatively little is known about variability of woody traits, when compared with foliar traits and simple measures such as wood density. It could reveal important insight into how the forest communities of Borneo are structured.

Project outcomes:
The study is highly novel, generating new knowledge about the relationships between tree woody traits, the environment and the community composition of Borneo’s forests. As such I envisage an opportunity for the student to be involved in continued collaboration to publish a peer-reviewed research paper on the topic; this would give the student insight into the process of peer-reviewed publication which is a core activity of research scientists. The student will also have opportunities to present the research undertaken at CEH, RBGE and/or Edinburgh University if they wish. This will enable them to gain experience of presenting their work orally and an opportunity to hear insight from other academics and professionals.

The project will give the student opportunity to experience two different research environments (CEH and RBGE). The project was also be co-supervised by a PhD candidate at the University of Edinburgh, giving the student the opportunity to learn about an academic research department, outside their field (Geosciences) and to learn from all supervisors and institutions about possible career paths. The practical component of the work gave a good flavour for laboratory methods and how these sit alongside field methods to generate complete datasets. The use of photography and software for image and data analysis will add to the breadth of skills used and developed.

The student had the opportunity to develop directions for the research and their quantitative skills were particularly important for learning and applying statistical analyses to a relatively complex dataset.

Sticky dead microbes: Stabilization of microbial necromass carbon in grassland soil

Based: Lancaster University

Project objectives:
To provide the student with experience in current ecological research, experimental design, grassland field sampling, and soil, microbial and sable isotope methods in the laboratory, More specifically, this project developed an experiment that tested a novel concept in ecology: that dead soil microorganisms are “sticky” and bind to each other. The outcome of this experiment as the potential to shift our understanding of soil carbon stabilization mechanisms. Part of the project objectives were thus to instill this excitement for the current research in the student.

Project outcomes:
The student spent the first two weeks learning about the research field and contributing to the design of the experiment. He spent six weeks practicing soil ecology methods in field sampling, lab handling and environmental microbiology in preparation for the project incubation. He set up and carried out this on week incubation experiment, then in his final week begand the process of greenhouse gas and soil analysis. these collected experiences provided an exciting research experience and furthered the student’s interest in a research career.

The student has Contributed an oral presentation to the Plant-Soil community at Lancaster and CEH Lancaster, explaining the rationale of the project, and the experimental design. Analysis is ongoing, and I anticipate that the main research output will be a manuscript. The student has expressed interest in being a part of the publication process.