Samples of Phyllosoma were collected from trawls conducted on the Great Barrier Reef at depths of 1-100 m in May 2005. Phyllosoma were identified to genus (and to species level when possible) immediately upon collection using a dichotomous key.The total bacterial DNA associated with phyllosoma was extracted from two separately homogenized P. ornatus phyllosoma and one homogenized Panulirus penicillatus phyllosoma using the Qiagen DNeasy Tissue Kit (Qiagen, Hilden, Germany). Bacterial 16S rRNA gene was amplified from DNA extracted from phyllosoma using the primers 27f and 1492r.Partial and complete 16S rRNA gene sequences of bacterial clones were obtained using the primers 27f, 339f, 732f and 1492r; bacterial representatives were found from the following: a-Proteobacteria, Firmicutes, y-Proteobacteria, e-Proteobacteria, Bacteroidetes. Various indices and models were used to analyse the variation of microbial diversity within clone libraries. The genus affiliation of dominant bacterial sequences (Sulfitobacter, uncultured e-proteobacterium, Erythrobacter, Roseobacter, Exiguobacterium, Psychrobacter, Clostridium, Pseudomonas, Alteromonas, Paracoccus) retrieved from the clone libraries was recorded for wild Panulirus ornatus (PO1 and PO2) and Panulirus penicillatus (PP) phyllosoma samples.Phyllosoma samples were analysed by histology (examined using light microscopy to determine any internal lesions or disease); scanning electron microscopy (SEM) to determine bacterial colonization (external or internal); and fluorescence in situ hybridization (FISH) to examine bacteria in tissue sections (without detectable bacterial cells, with low bacterial density, occasional cell accumulations).The GenBank accession numbers assigned for nucleotide sequence data of all phyllosoma clones submitted are:DQ985883, DQ985884, DQ985885, DQ985886, DQ985887, DQ985888, DQ985889, DQ985890, DQ985891, DQ985892, DQ985893, DQ985894, DQ985895, DQ985896, DQ985897, DQ985898, DQ985899, DQ985900, DQ985901, DQ985902, DQ985903, DQ985904, DQ985905, DQ985906, DQ985907, DQ985908, DQ985909, DQ985910, DQ985911, DQ985912, DQ985913, DQ985914, DQ985915, DQ985916, DQ985917, DQ985918, DQ985919, DQ985920, DQ985921, DQ985922, DQ985923, DQ985924, DQ985925, DQ985926, DQ985927, DQ985928, DQ985929, DQ985930, DQ985931, DQ985932, DQ985933, DQ985934, DQ985935, DQ985936, DQ985937.

To determine the bacterial community associated with wild-caught, mid-stage larvae of spiny lobsters (Palinuridae) in their native oligotrophic marine environment, and to compare their diversity and composition with communities associated with aquaculture-reared larvae of the tropical rock lobster Panulirus ornatus, the current identified candidate for aquaculture in Australia.

The phylogenetic tree included closest relativeves (and accession numbers): Acidovorax sp. (AJ534865), Alteromonas sp. (AF427478), Citromicrobium bathoceanense (Y16267), Clostridium quinii (X76745), Cytophaga marinoflava (M58770), Erythrobacter citreus (AF118020), Exiguobacterium sp. (AY205564), hodothermus marinus (X77140), Pseudoalteromonas sp. (AF239705), Pseudoalteromonas sp. (AJ704790), Pseudoalteromonas sp. (AY258115), Pseudoalteromonas sp. (U80834), Pseudomonas saccharophila (AF368755), Psychrobacter arenosus (AJ609273), Psychrobacter marincola (AJ309941), Psychrobacter pacificensis (AB016054), Psychrobacter pacificensis (AB016055), Psychrobacter sp. (AJ551125), Roseobacter sp. (AJ536669), Staphylococcus saccharolyticus (L37602), uncultured a-Proteobacterium (AY033306), Uncultured e-Proteobacterium (AF367487), Vibrio alginolyticus (AF513447).