Microbial diversity within the water column of a larval rearing system for the ornate rock lobster (Panulirus ornatus) Matthew S. Payne a,b, ⁎ , Mike R. Hall a , Raymond Bannister a,c , Lindsay Sly b , David G. Bourne a a Australian Institute of Marine Science, Tropical Aquaculture, PMB No 3, Townsville Mail Centre, QLD 4810, Australia b School of Molecular and Microbial Sciences, University of Queensland, St Lucia, QLD 4067, Australia c School of Marine Biology and Aquaculture, James Cook University, Townsville, QLD 4811, Australia Received 30 January 2006; received in revised form 27 March 2006; accepted 2 April 2006 Abstract The ornate tropical rock lobster, Panulirus ornatus has substantial potential as an aquaculture species though disease outbreaks during the animal's extended larval lifecycle are major constraints for success. In order to effectively address such disease-related issues, an improved understanding of the composition and dynamics of the microbial communities in the larval rearing tanks is required. This study used flow cytometry and molecular microbial techniques (clone libraries and denaturing gradient gel electrophoresis (DGGE)) to quantify and characterise the microbial community of the water column in the early stages (developmental stage I–II) of a P. ornatus larval rearing system. DGGE analysis of a 5000 L larval rearing trial demonstrated a dynamic microbial community with distinct changes in the community structure after initial stocking (day 1 to day 2) and from day 4 to day 5, after which the structure was relatively stable. Flow cytometry analysis of water samples taken over the duration of the trial demonstrated a major increase in bacterial load leading up to and peaking on the first day of the initial larval moult (day 7), before markedly decreasing prior to when N 50% of larvae moulted (day 9). A clone library of a day 10 water sample taken following a mass larval mortality event reflected high microbial diversity confirmed by statistical analysis indices. Sequences retrieved from both clone library and DGGE analyses were dominated by γ- and α-Proteobacteria affiliated organisms with additional sequences affiliated with β- and ε-Proteobacteria, Bacteroidetes, Cytophagales and Chlamydiales groups. Vibrio affiliated species were commonly retrieved in the clone library, though absent from DGGE analysis. Crown Copyright © 2006 Published by Elsevier B.V. All rights reserved. Keywords: Panulirus ornatus phyllosoma; Bacterial diversity; 16S rRNA; DGGE; Clone library; Flow cytometry 1. Introduction The global market demand for rock lobsters continues to exceed supply from the wild and as such there is an increasing interest in developing an aquaculture sector. Due to their value and importance in Australian wild fisheries, there has been particular emphasis on Jasus edwardsii ($177 million), J. verreauxi ($4.7 million) and Panulirus cygnus ($305 million) to become established as aquaculture species (ABARE, 2003). However, these species do not necessarily possess favourable attributes for culture. Although the wild fishery for the tropical ornate rock lobster (Panulirus ornatus), being 1 of 6 tropical species in Australia, is currently valued at only $5 million (ABARE, 2003), this species has particularly Aquaculture 258 (2006) 80 – 90 www.elsevier.com/locate/aqua-online ⁎ Corresponding author. Australian Institute of Marine Science, Tropical Aquaculture, PMB No 3, Townsville Mail Centre, QLD 4810, Australia. Tel.: +61 7 4753 4139; fax: +61 7 4772 5852. E-mail addresses: m.payne@aims.gov.au (M.S. Payne), d.bourne@aims.gov.au (D.G. Bourne). 0044-8486/$ - see front matter. Crown Copyright © 2006 Published by Elsevier B.V. All rights reserved. doi:10.1016/j.aquaculture.2006.04.001