Developing the next generation of Sediment profile imaging camera system

The Sediment profiling imaging (SPI) camera can be a convenient tool to assess marine benthic environments. It is possible to study the sediment-animal-water relationship according to chemical, biological and physical properties on a small scale of the seafloor. Further, the SPI is and has been used to inform stakeholders in academia and industry about benthic health, however, potentially associated artefacts with inserting the camera into the sediment have not been studied yet. Therefore, it is important to assess the potential artefacts and if necessary, develop a new generation of SPI cameras or a correction factor for SPI camera use. This thesis covers two main components, the first part evaluated the impact of particle displacement of the Sediment profiling imaging (SPI) camera, and other SPI-like devices when inserted into the sediment and potentially associated artefacts. The second part focuses on overcoming the particle displacement artefacts by developing new optical sensors that are able to distinguish oxic from anoxic sediment. Previous research has shown that inserting SPI-like devices into the sediment can have an impact on particle displacement by pushing oxygenated surface sediments to deeper sediment depths, so-called smearing, and subsequently making anthropogenically-disturbed sediment appear healthier than it may actually be. The potential particle displacement has been first investigated with two SPI-like devices in Chapters 2 and 3. First, a laboratory-based testing device, termed the SPI purpose-built sediment chamber (SPI-PUSH) and second an intertidal field-based device termed the Dummy SPI. In chapter 4, a real SPI was used to perform in-situ experiments to assess the potential artefact associated with the SPI system. The SPI-PUSH differed structurally the most from the real SPI system as a flat plate was lowered in an enclosed space within a laboratory environment. Whereas the intertidal Dummy SPI was structurally and dimensionally similar to the real SPI and can be easily deployed in intertidal flats and gather valuable data. The structural differences between the three systems were taken into account when comparing the results. Inert-dyed sediment particles, so-called luminophores were used to demonstrate the extent of particle displacement caused by the SPI and SPI-like devices being pushed into the sediment. Pictures of potential particle smearing were taken and analysed for all three devices. Three different approaches have been used to analyse the particle smearing on the pictures taken: the point measurement, the grid measurement, and the luminophore coverage (%) per depth row. Using three different methods to analyse the particle smearing helped to explore how the analysing method has an impact on the results. In chapters 2 and 3, the analysing methods used did not differ from each other whereas in chapter 4 the results differed, therefore, the luminophore coverage per depth row method was established. Analysing the luminophore coverage for each row parallel to the sediment surface was the most robust method trialled. The point and the grid measurement are potentially less accurate. For example, the point measurement does not account for most of the imaged area, whereas in the grid method any amount of luminophores in each 0.7 x 0.7 cm grid counted, might overestimate the particle smearing. The mean particle smearing measured with the SPI-PUSH directly behind the inserted plate was 2.9 ± 1.5 cm (mean ± SD, n = 5) for mud sediments with sand-like luminophores, 4.3 ± 2.5 cm (mean ± SD, n = 5) for fine sand sediments with sand-like luminophores and 1.9 ± 1.1 cm (mean ± SD, n = 5) for medium sand sediments with mud-like luminophores. The mean particle smearing during the Dummy SPI experiments was 5.5± 2.2 cm (mean ± SD, n = 12) and 3.7 ± 2.3 cm (mean ± SD, n = 4) for the real SPI system using sand-like luminophores in sandy sediments. The data in this thesis shows that future studies using the SPI camera, or any other periscope-like device, need to acknowledge that smearing may be significant. Particle displacement of surface sediment could lead to overestimating the apparent redox potential discontinuity (aRPD) layer. The aRPD is used in environmental indices like the Benthic Habitat Quality (BHQ) index and could therefore overestimate the health of the marine environment. In this thesis, the intertidal Dummy SPI was not only used as a proxy for the real SPI system. The intertidal SPI was successfully tested to be used as a stand-alone system to assess intertidal soft sediment environments. The second part of the thesis focused on developing the next generation of the SPI camera system (Chapter 5). Chapter 5, therefore explores if a miniaturised optical sensor can detect oxic and anoxic sediment based on the sediment colour. If an optical sensor would be able to assess the aRPD reliably the size of the probe would simultaneously reduce the smearing artefacts. Three different devices were trialled: the chip, the Tiny SPI and the coupler end. The chip was used with two optical fibres, one to send light into the sediment and one to detect the reflected light. The Tiny SPI is simpler built using only one fibre and a coupler to send light into the sediment and detect the light reflected. The coupler end is an even simpler professionally manufactured version sending light the sediment with one fibre and a coupler as well as detecting the reflected signal. The development of an optical sensor that could reliably measure the sediment colour was more difficult than anticipated. During the development of the sensor, the original prototype of a chip-based device was simplified to the Tiny SPI and eventually to the coupler end, to aim for repeatable and reliable data output. Unfortunately, it was not possible to gain consistent and reliable results. Although the approach was conceptually valid, the development was not straightforward and would have required a greater investment of time which lies beyond the scope of this thesis. The data of Chapters 2, 3 and 4, successfully showed that particle subduction from the surface can be significant, with a smearing of up to 3.7 ± 1.2 cm (n = 5) for all SPI-like devices in varying soft sediments. The results in chapter 4 indicate that the particle smearing might differ with the sediment grain size. However, the relationship between sediment grain size and smearing depth needs further investigation. This could be investigated by utilising the intertidal Dummy SPI (Chapter 3). In chapter 5, the attempt to miniaturise the SPI camera for the next generation has proven to not be as straightforward as expected, however, it provided valuable information on potential suitable starting points for future research. All three SPI-like devices, the laboratory-based SPI-PUSH, the intertidal Dummy SPI and the real SPI camera were representative of the actual smearing that takes place when using real SPI system. Therefore, improving the current existing systems might be more beneficial than developing a new generation of SPI. Future research should account for particle smearing when using SPI and SPI-like devices this would additionally improve the data quality. Data gathered with any SPI system, if uncorrected for smearing, may lead to incorrect assumptions regarding benthic health, which could ultimately lead to inappropriate management decisions

Sediment profile imaging: laboratory study into the sediment smearing effect of a penetrating plate

Sediment profiling imaging (SPI) is a versatile and widely used method to visually assess the quality of seafloor habitats (e.g., around fish farms and oil and gas rigs) and has been developed and used by both academics and consultancy companies over the last 50 years. Previous research has shown that inserting the flat viewport of an SPI camera into the sediment can have an impact on particle displacement pushing oxygenated surface sediments to deeper sediment depths and making anthropogenically-disturbed sediment appear healthier than they may actually be. To investigate the particle displacement that occurs when a flat plate is inserted into seafloor sediments, a testing device, termed the SPI purpose-built sediment chamber (SPI-PUSH) was designed and used in a series of experiments to quantify smearing where luminophores were used to demonstrate the extent of particle displacement caused by a flat plate being pushed into the sediment. Here, we show that the plate of the SPI-PUSH caused significant smearing, which varied with sediment type and the luminophore grain size. The mean particle smearing measured directly behind the inserted plate was 2.9 ± 1.5 cm for mud sediments with sand-like luminophores, 4.3 ± 2.5 cm for fine sand sediments with sand-like luminophores and 1.9 ± 1.1 cm for medium sand sediments with mud-like luminophores. When the mean depth of particle smearing was averaged over a larger sediment volume (11 cm3) next to the inserted plate, substantial differences were seen between the plate-insertion experiments and controls highlighting the potential extent of smearing artefacts that may be produced when a SPI camera penetrates the seafloor. This experimental data shows that future studies using the SPI camera, or any other periscope-like device (e.g., planar optodes) need to acknowledge that smearing may be significant. Furthermore, it highlights that a correction factor may need to be applied to these data (e.g., the depth of apparent redox potential discontinuity layer) to correctly interpret SPI camera images and better determine the effect of anthropogenic impacts on seafloor habitats

Hemimetabolous genomes reveal molecular basis of termite eusociality

Around 150 million years ago, eusocial termites evolved from within the cockroaches, 50 million years before eusocial Hymenoptera, such as bees and ants, appeared. Here, we report the 2-Gb genome of the German cockroach, Blattella germanica, and the 1.3-Gb genome of the drywood termite Cryptotermes secundus. We show evolutionary signatures of termite eusociality by comparing the genomes and transcriptomes of three termites and the cockroach against the background of 16 other eusocial and non-eusocial insects. Dramatic adaptive changes in genes underlying the production and perception of pheromones confirm the importance of chemical communication in the termites. These are accompanied by major changes in gene regulation and the molecular evolution of caste determination. Many of these results parallel molecular mechanisms of eusocial evolution in Hymenoptera. However, the specific solutions are remarkably different, thus revealing a striking case of convergence in one of the major evolutionary transitions in biological complexity

Zootermopsis nevadensis manual gene annotations

Manual gene annotation in gff3 format for the termite Zootermopsis nevadensis. Part of the manuscript "Hemimetabolous genomes reveal molecular basis of termite eusociality.

Macrotermes natalensis manual gene annotations

Manual gene annotation in gff3 format for the termite Macrotermes natalensis. Part of the manuscript "Hemimetabolous genomes reveal molecular basis of termite eusociality.