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Sustained observations of microbial dynamics are rare, especially in southern hemisphere waters. The Australian Marine Microbial Biodiversity Initiative (AMMBI) provides methodologically standardized, continental scale, temporal phylogenetic amplicon sequencing data describing Bacteria, Archaea and microbial Eukarya assemblages. Sequence data is linked to extensive physical, biological and chemical oceanographic contextual information. Samples are collected monthly to seasonally from multiple depths at seven sites: Darwin Harbour (Northern Territory), Yongala (Queensland), North Stradbroke Island (Queensland), Port Hacking (New South Wales), Maria Island (Tasmania), Kangaroo Island (South Australia), Rottnest Island (Western Australia). These sites span ~30° of latitude and ~38° longitude, range from tropical to cold temperate zones, and are influenced by both local and globally significant oceanographic and climatic features. All sequence datasets are provided in both raw and processed fashion. Currently 952 samples are publically available for bacteria and archaea which include 88,951,761 bacterial (72,435 unique) and 70,463,079 archaeal (24,205 unique) 16 S rRNA v1-3 gene sequences, and 388 samples are available for eukaryotes which include 39,801,050 (78,463 unique) 18 S rRNA v4 gene sequences.

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The assemblage composition, biomass and dynamics of zooplankton and epibenthos were examined in a commercial shrimp (penaeid prawn) pond in subtropical Australia. Physicochemical characteristics of the pond water were measured concurrently. Numbers and biomass of zooplankton in the surface tows (140 mm mesh) varied from 111.7 ind. L À1 (324 mg L À1 ) to 8.3 ind. L À1 (44.2 mg L À1 ). Immediately after the ponds were stocked with shrimp postlarvae there was a rapid decline in zooplankton numbers, particularly the dominant larger copepods. We attributed this to predation by the shrimp postlarvae. Subsequent peaks in zooplankton numbers were principally due to barnacle nauplii. Changes in abundance and biomass of the zooplankton assemblage were not correlated with physicochemical characteristics. Epibenthic faunal abundance in the beam trawls (1 mm mesh) peaked at 14 ind. m À2 and the biomass at 0.8 g m À2 . Unlike zooplankton, the peaks in abundance of epibenthos did not correspond to the peaks in biomass. This was due to the large differences in the size of the dominant taxa across the season. Sergestids (Acetes sibogae) and amphipods were the most abundant taxa in beam trawl samples, with amphipods abundance increasing towards the end of the growout. Negative correlations were found between epibenthos abundance and pH and temperature. These relationships were strongly influenced by the high abundances of amphipods and may reflect an effect on the growth of macroalgae in the pond rather than a direct effect on the epibenthos. No correlations were found between epibenthic fauna biomass and physicochemical parameters. Abundances of epibenthic fauna were not related to zooplankton densities, indicating that this source of food was not likely to be a limiting factor. Neither the pond water exchange regime nor moon phase could explain changes in abundances of zooplankton or epibenthos assemblages. Zooplankton clearly contribute to the nutrition of shrimp postlarvae immediately after stocking. The establishment of an abundant assemblage of zooplankton before stocking shrimp postlarvae would appear to be beneficial, if not essential. Later in the season, zooplankton and epibenthos apparently contribute little to shrimp biomass. Owing to their relatively low biomass, the consumption of shrimp feeds by epibenthos is likely to be insignificant compared with that of the shrimp.