Can We Use Functional Genetics to Predict the Fate of Nitrogen in Estuaries?

Increasing nitrogen (N) loads present a threat to estuaries, which are among the most heavily populated and perturbed parts of the world. N removal is largely mediated by the sediment microbial process of denitrification, in direct competition to dissimilatory nitrate reduction to ammonium (DNRA), which recycles nitrate to ammonium. Molecular proxies for N pathways are increasingly measured and analyzed, a major question in microbial ecology, however, is whether these proxies can add predictive power around the fate of N. We analyzed the diversity and community composition of sediment nirS and nrfA genes in 11 temperate estuaries, covering four types of land use in Australia, and analyzed how these might be used to predict N removal. Our data suggest that sediment microbiomes play a central role in controlling the magnitude of the individual N removal rates in the 11 estuaries. Inclusion, however, of relative gene abundances of 16S, nirS, nrfA, including their ratios did not improve physicochemical measurement-based regression models to predict rates of denitrification or DNRA. Co-occurrence network analyses of nirS showed a greater modularity and a lower number of keystone OTUs in pristine sites compared to urban estuaries, suggesting a higher degree of niche partitioning in pristine estuaries. The distinctive differences between the urban and pristine network structures suggest that the nirS gene could be a likely gene candidate to understand the mechanisms by which these denitrifying communities form and respond to anthropogenic pressures.

DNA barcoding reveals overlooked marine fishes.

With more than 15 000 described marine species, fishes are a conspicuous, diverse and increasingly threatened component of marine life. It is generally accepted that most large-bodied fishes have been described, but this conclusion presumes that current taxonomic systems are robust. DNA barcoding, the analysis of a standardized region of the cytochrome c oxidase 1 gene (COI), was used to examine patterns of sequence divergence between populations of 35 fish species from opposite sides of the Indian Ocean, chosen to represent differing lifestyles from inshore to offshore. A substantial proportion of inshore species showed deep divergences between populations from South African and Australian waters (mean = 5.10%), a pattern which also emerged in a few inshore/offshore species (mean = 0.84%), but not within strictly offshore species (mean = 0.26%). Such deep divergences, detected within certain inshore and inshore/offshore taxa, are typical of divergences between congeneric species rather than between populations of a single species, suggesting that current taxonomic systems substantially underestimate species diversity. We estimate that about one third of the 1000 fish species thought to bridge South African and Australian waters actually represent two taxa.

DNA barcoding discriminates echinoderm species.

DNA barcode sequences (a 657-bp segment of the mtDNA cytochrome oxidase I gene, COI) were collected from 191 species (503 specimens) of Echinodermata. All five classes were represented: Ophiuroidea, Asteroidea, Echinoidea, Holothuroidea and Crinoidea. About 30% of sequences were collected specifically for this study, the remainder came from GenBank. Fifty-one species were represented by multiple samples, with a mean intraspecific divergence of 0.62%. Several possible instances of cryptic speciation were noted. Thirty-two genera were represented by multiple species, with a mean congeneric divergence of 15.33%. One hundred and eighty-seven of the 191 species (97.9%) could be distinguished by their COI barcodes. Those that could not were from the echinoid genus Amblypneustes. Neighbour-joining trees of COI sequences generally showed low bootstrap support for anything other than shallow splits, although with very rare exceptions, members of the same class clustered together. Two ophiuran species, in both nucleotide and amino acid neighbour-joining trees, grouped loosely as sister taxa to Crinoidea rather than Ophiuroidea; sequences of these two species appear to have evolved very quickly. Results suggest that DNA barcoding is likely to be an effective, accurate and useful method of species diagnosis for all five classes of Echinodermata.