Fine-scale variability in phytoplankton community structure and inherent optical properties measured from an autonomous underwater vehicle Alex Cunningham a, * , David McKee a , Susanne Craig a , Glen Tarran b , Claire Widdicombe b a Department of Physics and Applied Physics, University of Strathclyde, 107 Rottenrow, Glasgow, G4 ONG, Scotland, UK b Plymouth Marine Laboratory, Prospect Place, Plymouth, PL1 3DH, UK Received 6 December 2002; accepted 26 May 2003 Abstract The relationship between inherent optical properties (IOPs), phytoplankton community structure and the abundance of suspended particles in the size range 3 – 500 Am was studied near the Isles of Scilly (UK) in May 2000. Autosub, an autonomous submersible vehicle specifically designed for science missions, was used as an instrument-positioning platform. It carried a CTD system, an ac-9+ dual tube spectrophotometer, a prototype submersible flow cytometer and an Aqua-monitor water sampler. The vehicle made a 10-km transect at constant depth across a boundary between water masses with contrasting remote sensing reflectance, which was located using SeaWiFs ocean colour imagery. This boundary corresponded to a sharp (1 km) transition between one phytoplankton community consisting of coccolithophores, flagellates and dinoflagellates, and a second community dominated by diatoms and flagellates. Inherent optical properties measured along the autonomous underwater vehicle (AUV) track showed marked changes in magnitudes, ratios, spectral shapes and fine-scale spatial variability. These changes were well correlated with variations in the composition of the suspended particle assemblage measured by microscopy and in situ flow cytometry. D 2003 Elsevier B.V. All rights reserved. Keywords: AUV; Flow cytometry; Optical water types; Optical classification; Scattering coefficient; Phytoplankton optics; UK; English channel; Isles of Scilly 1. Introduction The inherent optical properties (IOPs) of seawater are influenced by the size and shape of phytoplankton cells as well as by their numerical abundance (Morel, 1991, 1994), and it is possible to calculate the optical properties of model phytoplankton assemblages with reasonable accuracy (Ciotti et al., 1999; Stramski et al., 2001). On the other hand, inverse methods for deriving information on phytoplankton communities from optical measurements are still at an early stage of development (Kirkpatrick et al., 2000). One practical problem hindering the validation of these methods is 0924-7963/$ - see front matter D 2003 Elsevier B.V. All rights reserved. doi:10.1016/S0924-7963(03)00088-5 * Corresponding author. Tel.: +44-141-548-3474; fax: +44-141- 552-2891. E-mail address: a.cunningham@strath.ac.uk (A. Cunningham). www.elsevier.com/locate/jmarsys Journal of Marine Systems 43 (2003) 51 – 59