Jeffrey T. B. Kwik

Next-generation freshwater bioassessment: eDNA metabarcoding with a conserved metazoan primer reveals species-rich and reservoir-specific communities.

Freshwater habitats are of high conservation value and provide a wide range of ecosystem services. Effective management requires regular monitoring. However, conventional methods based on direct observation or specimen collection are so invasive, expensive and labour-intensive that frequent monitoring is uncommon. Here, we test whether the evaluation of environmental DNA (eDNA) from water based on a simple protocol can be used for assessing biodiversity. We use universal metazoan primers for characterizing water eDNA across horizontal and vertical spatial dimensions in two reservoirs with known species diversity for two key taxa. eDNA obtained directly from 42 samples × 15 ml water (total = 630 ml) per reservoir yielded DNA signatures for more than 500 metazoan species, of which 105 could be identified to species/genus based on DNA barcodes. We show that eDNA can be used to assign each water sample to its reservoir of origin, and that eDNA outperforms conventional survey methods in single-sample richness comparisons, while revealing evidence for hundreds of unknown species that are undetected by conventional bioassessment methods. eDNA also confirms the presence of a recently discovered invasive snail species and provides evidence for the continued survival of a rare native species of goby not sighted in that habitat since 2007. eDNA thus promises to be a useful addition to the bioassessment toolbox for freshwater systems.

Differences in fish assemblages in protected and non-protected freshwater streams in a tropical urbanized country

The importance of protected areas on native fish assemblage in freshwater streams is not well understood. We investigated differences in fish communities and environmental factors in 38 protected and non-protected streams in Singapore. Eight hundred and twenty-eight individuals from 33 species were documented (with one new record), with natives comprising 70.5% of all species. A canonical correspondence analysis found that protected streams were defined by lower pH, temperature, and conductivity, higher cross-sectional areas and water velocity and permit requirements, which was supported by a correspondence analysis that also found more native species in protected streams. Overall abundance of fish was higher in non-protected streams but consisted of higher proportions of non-native species. Conditional inference tree analysis of abiotic and biotic factors across sites found that pH and stream velocities predicted for higher native fish species richness. As such, protected streams with their limited accessibility to the public, low pH and faster flow regimes are more likely to maintain native fish assemblages. This reiterates the importance of maintaining protected areas that help conserve freshwater fish communities, especially in Singapore and other parts of Southeast Asia where there is high rate of habitat loss, modification and development.

An assessment of carbon dioxide gassing as a sampling technique for studies of the nekton of soft-sediment intertidal pools

The efficiency of carbon dioxide gassing in the collection of fish from soft-sediment pools was tested on 20 pools (average volume 12608 cm3) at Adams Beach, North Stradbroke Island, Queensland. Between 120 and 150 secs gassing at 15 l min−1 was required for collection of the entire community of each pool. Gassing in excess of 300 s resulted in mortalities of all nekton. It was found that temperature did not alter during gassing but pH dropped considerably from 8.00 to 5.10. Recovery of the pool pH took approximately four hours. Recovery by collected organisms and recovery of the pool environment indicate that CO2 gassing is a useful collection technique in studies of intertidal nekton.

Temporal Changes in Reef Community Structure at Bintan Island (Indonesia) Suggest Need for Integrated Management

Abstract: Reefs in Southeast Asia, such as those in Indonesias Riau archipelago, are among the most diverse habitats in the sea, but limited baseline data pose a severe challenge for their conservation. Here, we surveyed five reef sites along the northern coast of Bintan Island to determine the most recent condition of the benthic and fish communities. Fourteen years of resort development on the island have elapsed since the last survey in 1993. Using several diversity measures to compare the reefs then and in 2007, we found that abundances of hard corals and fish remained high (average of >50% coral cover and >0.7 fish/m3), but taxonomic richness was compromised. The most common taxa now account for greater proportions of fish counts at all sites and of coral cover at three of four comparable sites. These shifts in coral and fish assemblages may be explained by freshwater influences and development along the north coast of Bintan Island. Because the local community and tourism industry still rely heavily on the reefs, we advocate implementing a comprehensive, integrated coastal management plan that mitigates further reef declines and promotes sustainable use.