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URI [dataset] University of Southampton Faculty of Natural and Environmental Sciences School of Ocean and Earth Science Advances in the state-of-the-art in the quantitative ecology of the marine megabenthos Volume 1 of 1 by Noëlie Marie Aline Benoist ORCID iD 0000-0003-1978-3538 Thesis for the degree of Doctor of Philosophy September 2020 UNIVERSITY OF SOUTHAMPTON ABSTRACT FACULTY OF NATURAL AND ENVIRONMENTAL SCIENCES School of Ocean and Earth Science Thesis for the degree of Doctor of Philosophy ADVANCES IN THE STATE-OF-THE-ART IN THE QUANTITATIVE ECOLOGY OF THE MARINE MEGABENTHOS by Noëlie Marie Aline Benoist This study attempts to advance the quantitative ecology of the megabenthos by (i) adopting and developing the use of mass seabed photography, and by (ii) extending body-size-based ecosystem assessment to this group. The metabolic theory of ecology (MTE) builds from simple bio-energetic assumptions of individual metabolism to make predictions about ecological processes from individual structure and functioning, to community and ecosystem dynamics. Under the ‘energetic equivalence rule’, or Damuth’s rule, the population density of living organisms is related to a -3/4 power of body mass, indicating equal resource acquisition across body-size classes. In the marine environment, meio- to macrobenthic assemblages have be usefully modelled as a notional single trophic level, suggesting energetic equivalence throughout the two fractions. That concept is tested here by extension to the megabenthos. The body-size structure of benthic assemblages was examined in four contrasting settings: two shelf-sea sites in the Celtic Sea (Greater Haig Fras marine conservation zone; Shelf-Sea Biogeochemistry area), and two deep- sea sites (Porcupine Abyssal Plain sustained observatory, PAP-SO, northeast Atlantic; Clarion-Clipperton Zone, CCZ, northeast Pacific). Imagery data were collected using autonomous underwater vehicles, allowing consistent assessment of the megabenthos in the form of individual-based body-size spectral analyses, over landscape-scale areas encompassing multiple habitat types. For the well-known Celtic Shelf and PAP-SO assemblages, species- specific length-weight relationships were used to derive individual biomass data. However, that was not possible for the poorly studied CCZ fauna, prompting the development of a generalised volumetric method for individual body-mass estimation. The MTE framework was used to investigate the effects of seafloor temperature and resource supply on the stocks and flows of mass and energy at these sites. The results of this study demonstrate the practical advantage of mass seabed photography in the quantitative ecological assessment of the megabenthos. The volumetric methodology developed overcomes the taxonomic, temporal, and spatial, dependencies known to impact length-weight relationships. The megabenthos body-size distributions produced were broadly consistent across sites, and generally conformed to the MTE expectations, i.e. controlled by both seafloor temperature and resource supply. These results suggest a much greater ecological significance of the megabenthos than has generally been assumed, i.e. at the PAP-SO site they account for 93% of the total metabolically active standing stock carbon biomass, and 27% of total benthic carbon respiration. Individual-based body-size spectral analyses, coupled with the MTE framework, provide a robust baseline for assessing ecological patterns, and for monitoring change. List of contents List of contents vii List of tables xi List of figures xiii List of equations xvii Declaration of Authorship xix Acknowledgements xxi Nomenclature xxiii Chapter 1 Introduction 1 1.1 General introduction ................................................................... 1 1.2 Metabolic theory of ecology ......................................................... 4 1.3 Benthic size spectra ................................................................... 8 1.4 Ecological energetics of the benthos ........................................... 12 1.5 Ph.D. thesis aims ..................................................................... 13 Chapter 2 Study sites and environmental settings 17 2.1 Introduction ............................................................................ 17 2.2 Shelf-sea study sites in the Celtic Sea ........................................ 19 2.3 Deep-sea study sites ................................................................ 22 2.3.1 Porcupine Abyssal Plain, NE Atlantic ................................... 22 2.3.2 Clarion-Clipperton Zone, NE Pacific .................................... 24 Chapter 3 Materials and methods 27 3.1 Introduction ............................................................................ 27 3.2 Data collection for epifaunal megabenthos assemblages ............... 28 3.2.1 AUV photographic field survey ........................................... 28 3.2.2 Image processing ............................................................ 34 3.2.3 Image analysis ................................................................ 34 3.3 Data collection for infaunal macrobenthos assemblages ................ 36 3.3.1 Multi-corer field survey ..................................................... 36 3.3.2 Faunal sediment sample processing ................................... 38 3.3.3 Macrobenthos sample analysis........................................... 38 3.4 Individual biomass estimation ................................................... 39 3.5 Construction of body-size spectra .............................................. 40 vii List of contents 3.6 Analytical methods ................................................................... 42 3.7 Estimation of seafloor carbon stocks and flows ............................ 43 3.8 Sampling effort and limitations .................................................. 43 Chapter 4 A generalised volumetric method to estimate the biomass of photographically surveyed benthic megafauna 47 4.1 Abstract .................................................................................. 49 4.2 Introduction ............................................................................ 50 4.2.1 Biomass as an essential variable ........................................ 50 4.2.2 Existing benthic megafauna biomass data ........................... 51 4.2.3 Photographic estimation of individual biomass ..................... 52 4.2.4 The need for a generalised method .................................... 54 4.3 Materials and Methods .............................................................. 56 4.3.1 Evaluation of current methods ........................................... 56 4.3.2 A generalised volumetric method (GVM) ............................. 56 4.3.3 Method validation with physical specimens .......................... 59 4.3.4 Method trial in a photographic case study ........................... 61 4.4 Results and Discussion ............................................................. 63 4.4.1 Evaluation of current methods ........................................... 63 4.4.2 Validation with physical specimens ..................................... 67 4.4.3 Celtic Sea case study trial ................................................. 71 4.4.4 Generalised volumetric method ......................................... 73 4.5 Conclusions ............................................................................. 75 Chapter 5 Shelf-sea sites 77 Part 5.A Monitoring mosaic biotopes in a marine conservation zone by autonomous underwater vehicle .............................. 79 5.A.1 Abstract ............................................................................... 80 5.A.2 Introduction ......................................................................... 81 5.A.3 Methods ............................................................................... 84 5.A.3.1 Field survey ................................................................. 84 5.A.3.2 Image data generation .................................................. 84 5.A.3.3 Faunal community analysis ............................................ 86 5.A.4 Results ................................................................................ 87 5.A.4.1 Standing stocks ............................................................ 87 5.A.4.2 Faunal diversity ............................................................ 88 5.A.4.3 Faunal composition ....................................................... 90 5.A.5 Discussion ...........................................................................