"Universal" DNA primers LCO 1490 and HCO 2198 were originally designed from three coding and six anticoding strands by comparing highly conserved regions of mitochondrial cytochrome c oxidase subunit I (COI) genes across 15 taxa. These primers have been successful in amplifying a 710-bp fragment of highly conserved regions of the COI gene for more than 80 invertebrate species from 11 phyla. In the present study, 130,843 variations were reviewed in the primer region of mitochondrial molecular markers by comparing 725 COI sequences from the kingdom Animalia. It was found that, for 177 invertebrate species, the forward primer (LCO 1490) showed only four conserved regions, compared to 12 in the original study. For ascidians, fungi and vertebrates, it showed approximately 50 % conserved regions, dropping to one conserved region for echinoderms. However, the reverse primer (HCO 2198) was highly conserved across 725 COI primer sequences. A similar pattern was observed in amino acid distributions. There was a significant difference in the means of base pair differences from the level of family, genus and species for LCO 1490 [analysis of variance (ANOVA), F 6,188 = 8.193, P < 0.001] and at the level of genus and species for HCO 2198 (ANOVA, F 6,77 = 2.538, P < 0.027). We conclude that, at different taxonomic levels, it is possible to design forward primers from reference sequences belonging to the level of order (maximum 5 bp differences), family (maximum 6 bp differences) or genus (maximum 1 bp difference). Reverse primers can be designed from the level of family (maximum 5 bp differences) or genus (maximum 2 bp differences).

Taxonomy of the genus Ceriodaphnia Dana, 1853 (Cladocera: Daphniidae) has been uncertain for a long time, the species richness was often underestimated due to (1) a morphological similarity among the species and (2) their great morphological inter-and intra-populational variability. Support for this conclusion comes from the first analysis of three molecular markers for Australian representatives of this genus, two mitochondrial (COI and 16s) and one nuclear (28s) genes. Sequence analysis indicates the existence of three sibling Australian species belonging to the complex. Further work is required to establish species boundaries and investigate potential morphological diagnoses. Comparison of COI sequences with all other published sequences from the genus Ceriodaphnia revealed no common clades among continents pointing to the regional endemism within this group, which could suggest its Mesozoic differentiation.

Cyanobacteria and other microbes are important moderators of biogeochemical processes in semi-arid floodplain wetlands with varying inundation regimes. Inundation is a key environmental driver for floodplain biological communities. Little is known about the effect of historical inundation frequency on the spatial abundance of floodplain–wetland Cyanobacteria and other microbes. In this study, soil samples were collected at two locations with a gradient of low-to-high inundation frequency in the Macquarie Marshes, south-east Australia. We used high-throughput sequencing to estimate the proportional abundance of the soil Cyanobacteria and other dominant microbes, targeting the bacterial 16S rRNA gene. Of the microbes recovered, Cyanobacteria constituted proportionally a minor component, relative to other dominant phyla like Proteobacteria and Actinobacteria. Linear regression (generalised least-squares) models accounting for spatial autocorrelation showed that historical inundation frequency had no significant effect on the proportional abundance of Cyanobacteria at both wetlands studied. However, inundation frequency had a significant positive effect on the proportional abundance of Proteobacteria and a significant negative effect on the proportional abundance of Actinobacteria. Cyanobacteria seem to occupy a different hydrological niche from Proteobacteria and Actinobacteria in semi-arid floodplain wetlands, suggesting taxon-dependent response of floodplain microbial communities to varying inundation regimes and associated soil conditions in those environments.

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Valid identification of species of freshwater zooplankton is the first step to understand population structures, abundance, and diversity in the pelagic environment. While some Australian taxa can be easily identified morphologically, e.g., Calamoecia ampulla (Searle, 1911), most other species of freshwater micrometazoans are difficult to identify without specialised training, resulting in limited and even incorrect identification of the various taxa. The use of DNA barcodes, for species identification and discrimination, has added a new dimension to the traditional phenotypic approach and allows researchers to understand the patterns of genetic variability and to overcome taxonomic difficulties in the identification of the species from different life history stages. We used mitochondrial gene cytochrome c oxidase I (COI) to examine the species status of common planktonic microcrustaceans in two South Australian reservoirs. COI analyses indicated that the zooplankton specimens examined from the order Diplostraca and the class Maxillopoda, which were assigned binomial names a priori from the genera Bosmina, Boeckella, Chydorus, Calamoecia and Daphnia, possessed distinct COI sequences and nested cohesively within the genealogy, except for individuals of Ceriodaphnia cf. cornuta and a Ceriodaphnia species complex that formed 4 clusters. These clusters were not explicitly identified morphologically. The present study does improve and contribute to the understanding of the status of taxonomy and biogeography of micro-crustaceans in South Australia. This information is crucial for the application of these species in studies of local and regional environmental change over varying time scales. We recommend the integration of traditional morphology with DNA barcoding-based examination, to facilitate species identification, especially for applied research.