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Sea surface planktonic assemblages were sampled using environmental DNA at 1.5° latitudinal increments (from 39.5 to 11.5°S) following the 110°E meridian in the Eastern Indian Ocean to reveal factors structuring eukaryotic diversity. Metabarcoding the v4 region of the 18S rRNA gene revealed a eukaryotic assemblage over-dominated by amplicon sequence variants representing just four taxa that comprised 50% of reads, which were from copepods. Eukaryotes were predominantly heterotrophs and mixotrophs, with the presence of individual taxa responding to nutrient and temperature/oxygen gradients. Assemblage richness and diversity was greater at the northern end of the transect, but this diversity change occurred mostly around the sub-tropical front (∼35°S) with an unusually high degree of uniformity and non-monotonic progression in the alpha and beta diversity over the majority of the transect despite extending through distinct water masses, i.e., Indonesian Throughflow with tropical, low salinity waters, Subtropical Surface Water of high salinity waters and varying temperature, and Sub-Antarctic Mode Water with cooler and low salinity water. However, piecewise linear models of environmental and biotic data and fuzzy c-means clustering (with k = 2, 3 or 4) identified some discontinuities in the transect that were clumped at the southern end of the transect, although these cluster boundaries lacked consensus, being often poorly defined between the different data types. This eDNA data was largely concordant with morphological analyses, that also found the eukaryotic assemblage became largely stable northwards of the southernmost sampling points. These results contrast to other observations of diversity increasing monotonically toward the equator; i.e., eukaryotic communities were contrary to the “latitudinal diversity gradient hypothesis”. This accords with observations that extremely oligotrophic conditions can stabilise planktonic assemblages, despite significant latitudin

The recent dramatic decline in settlement in the population of the spiny lobster, Panulirus cygnus, may be due to changes in the oceanographic processes that operate offshore of Western Australia. It has been suggested that this decline could be related to poor nutritional condition of the post-larvae, especially lipid which is accumulated in large quantities during the preceding extensive pelagic larval stage. The current study focused on investigations into the lipid content and fatty acid (FA) profiles of lobster phyllosoma larvae from three mid to late stages of larval development (stages VI, VII, VIII) sampled from two cyclonic and two anticyclonic eddies of the Leeuwin Current off Western Australia. The results showed significant accumulation of lipid and energy storage FAs with larval development regardless of location of capture, however, larvae from cyclonic eddies had more lipid and FAs associated with energy storage than larvae from anticyclonic eddies. FA food chain markers from the larvae indicated significant differences in the food webs operating in the two types of eddy, with a higher level of FA markers for production from flagellates and a lower level from copepod grazing in cyclonic versus anticyclonic eddies. The results indicate that the microbial food web operating in cyclonic eddies provides better feeding conditions for lobster larvae despite anticyclonic eddies being generally more productive and containing greater abundances of zooplankton as potential prey for lobster larvae. Gelatinous zooplankton, such as siphonophores, may play an important role in cyclonic eddies by accumulating dispersed microbial nutrients and making them available as larger prey for phyllosoma. The markedly superior nutritional condition of lobster larvae feeding in the microbial food web found in cyclonic eddies, could greatly influence their subsequent settlement and recruitment to the coastal fishery.