Hyunbin Jo

Application of DNA barcoding for identification of freshwater carnivorous fish diets: Is number of prey items dependent on size class for Micropterus salmoides?

Understanding predator–prey interactions is a major challenge in ecological studies. In particular, the accurate identification of prey is a fundamental requirement in elucidating food-web structure. This study took a molecular approach in determining the species identity of consumed prey items of a freshwater carnivorous fish (largemouth bass, Micropterus salmoides), according to their size class. Thirty randomly selected gut samples were categorized into three size classes, based on the total length of the bass. Using the universal primer for the mtDNA cytochrome oxidase I (COI) region, polymerase chain reaction (PCR) amplification was performed on unidentified gut contents and then sequenced after cloning. Two gut samples were completely empty, and DNA materials from 27 of 28 gut samples were successfully amplified by PCR (success rate: 96.4%). Sequence database navigation yielded a total of 308 clones, containing DNA from 26 prey items. They comprised four phyla, including seven classes, 12 orders, and 12 families based on BLAST and BOLD database searches. The results indicate that largemouth bass show selective preferences in prey item consumption as they mature. These results corroborate a hypothesis, presence of ontogenetic diet shift, derived through other methodological approaches. Despite the practical limitations inherent in DNA barcoding analysis, high-resolution (i.e., species level) identification was possible, and the predation patterns of predators of different sizes were identifiable. The utilization of this method is strongly recommended for determining specific predator–prey relationships in complex freshwater ecosystems.

Investigation of bioaccumulation and biotransformation of polybrominated diphenyl ethers, hydroxylated and methoxylated derivatives in varying trophic level freshwater fishes

The concentrations and distributions of polybrominated diphenyl ethers (PBDEs) and their hydroxylated and methoxylated derivatives (OH- and MeO-BDEs) were determined in seven representative fish species from a river in the Republic of Korea. The PBDEs and their derivatives were found to be accumulated in the internal organs of the fish to different extents. PBDEs were preferentially accumulated in the internal organs rather than muscle tissue, and especially, showed increasing accumulation tendencies with increasing bromination level in liver. The OH-BDEs and MeO-BDEs were preferentially accumulated in the liver and gastrointestinal tract, respectively. MeO-BDE concentrations were found to increase according to relative trophic level, suggesting that the PBDE derivatives can be biomagnified to a greater extent than the parent PBDEs in freshwater food webs. In a comparison with the dissolved analyte concentrations in the water that were measured by using semi-permeable membrane devices, the greater uptake of non-ortho substituted MeO-BDEs by fish was observed.

Discovering hidden biodiversity: The use of complementary monitoring of fish diet based on DNA barcoding in freshwater ecosystems

Abstract Ecological monitoring contributes to the understanding of complex ecosystem functions. The diets of fish reflect the surrounding environment and habitats and may, therefore, act as useful integrating indicators of environmental status. It is, however, often difficult to visually identify items in gut contents to species level due to digestion of soft‐bodied prey beyond visual recognition, but new tools rendering this possible are now becoming available. We used a molecular approach to determine the species identities of consumed diet items of an introduced generalist feeder, brown trout (Salmo trutta), in 10 Tasmanian lakes and compared the results with those obtained from visual quantification of stomach contents. We obtained 44 unique taxa (OTUs) belonging to five phyla, including seven classes, using the barcode of life approach from cytochrome oxidase I (COI). Compared with visual quantification, DNA analysis showed greater accuracy, yielding a 1.4‐fold higher number of OTUs. Rarefaction curve analysis showed saturation of visually inspected taxa, while the curves from the DNA barcode did not saturate. The OTUs with the highest proportions of haplotypes were the families of terrestrial insects Formicidae, Chrysomelidae, and Torbidae and the freshwater Chironomidae. Haplotype occurrence per lake was negatively correlated with lake depth and transparency. Nearly all haplotypes were only found in one fish gut from a single lake. Our results indicate that DNA barcoding of fish diets is a useful and complementary method for discovering hidden biodiversity.

Search of optimal locations for species- or group-specific primer design in DNA sequences: Non-dominated Sorting Genetic Algorithm II (NSGA-II)

Abstract In this study, we applied Non-dominated Sorting Genetic Algorithm II (NSGA-II) to the problem of identifying appropriate locations in cytochrome oxidase I (COI) gene for species- or group-specific primer design. As concerns about ecological management grow, quantification of predator-prey interaction has become a central issue in ecology. Recently, improved techniques have allowed for the extensive use of genomic DNA barcoding for qualitative analysis. However, quantification of DNA barcoding results is important and still needs to be resolved. Even though species- or group-specific primers that can be used for samples containing multiple species are difficult to design, species- or group-specific primers are a practical solution for quantification in the current era. To resolve this issue, we present here an efficient method for discovering the regions of a DNA sequence that have the highest inter-species variability by applying the NSGA-II algorithm. DNA sequence information for the COI gene region was obtained for 24 species from Jo et al. (2014). These sequences were transformed into binary data, either 0 (not different) or 1 (different), to reflect sequence conservation at each base for all combinations of two species. These data were analyzed by two objective functions, the average and standard deviation of the difference, which were used in the NSGA-II algorithm to search for appropriate DNA locations for species-specific primer design. The NSGA-II program identified four solutions (possible primer binding sites); consequently NSGA-II is believed to be a suitable algorithm for species-specific primer design, and is expected to make this difficult and time-consuming process more efficient.

Long-term changes in fish community and the impact of exotic fish, between the Nakdong River and Upo Wetlands

To evaluate fish community changes and the impact of exotic fish between the Nakdong River (lotic) and Upo Wetlands (lentic) using long-term ecological monitoring results, we conducted seasonal surveys of the fish community from 2005 to 2010. A fixed shore net (mesh 15 × 15 mm), cast net (7 × 7 mm), and scoop-net (5 × 5 mm) were used to collect fish specimens. Changes in the fish community were not significantly different in the Nakdong River and Upo Wetlands, respectively (R s > 0.322, N = 44, P < 0.05). Changes in the fish community between the Nakdong River and Upo Wet lands were identified as significant according to the results of cluster analysis. The relative abundance of exotic species increased steadily during the study period, and reached 34.2% and 89.7% in the Nakdong River and Upo Wetlands, respectively, in 2010. The bluegill (Lepomis macrochirus) was used to evaluate the level of health according to prevalence around all study sites. The length-weight relationship for bluegill in the Upo Wetlands was shown to have the highest values, via the formula (W = aL b ), with an average of 3.26 for the ‘b’ variable. According to the results of this study, lentic and lotic systems differed significantly; exotic species had an impact on both the lentic and lotic systems, but the impact of exotic species in lentic systems was greater than in the lotic systems. Additionally, the exotic species tested herein (bluegill) adapted well in the lentic system.

Spatial-temporal distribution of carabid beetles in wetlands

In this study, we investigated carabid beetles residing in the wetlands to understand their ecological adaptation and strategy selection associated with restricted resources and habitat limitation. The species richness, abundance, seasonal activity, and spatial distribution of the carabid beetles between the Mujechi Wetlands (wetland sites) and Mt. Jeongjok (mountain sites) have been compared. A total of 1,733 individual beetles from 30 species were collected and classified at the studied sites. The wetland sites were identified as having lower species richness and abundance for carabid beetles when compared with the adjacent mountain sites, whereas these beetles were observed to be dominant in the wetland sites than in the adjacent mountain sites. Calosoma inquisitor cyanescens, Carabus sternbergi sternbergi, and Carabus jankowskii jankowskii species were dominant in both the wetland and mountain sites. These species showed significant ly different seasonal activity patterns in the wetland sites relative to the mountain sites. Although the three listed carabid species were observed to be widely distributed throughout the wetland sites, they still showed preference for drier sites, which clearly shows a distinction in their habitats. The results of the spatial-temporal distribution of carabid beetles in the wetland sites reflect their special strategies regarding space and time partitioning for maintaining their population. The distribution patterns of carabid beetles in the wetland sites also showed the desiccation gradient and environmental changes prevalent in wetlands. Ecological surveys, which use carabid beetles in the wetlands, can then be performed when restoring wetlands and for establishing management practices for improving the habitat quality.

Wetland Conservation Action Plan of Local Government: Gyeongsangnam Province, South Korea

We systematically analyzed the Wetland Conservation Action Plan of Gyeongsangnam Province to evaluate conservation status in local government level. Project topics were categorized into 1) wetland infrastructure, 2) wetland conservation and wise use, 3) education and awareness, and 4) conservation framework. From 2010 to 2013, 42 projects (145 cases, 88,899 million won) were implemented by 14 affiliated organizations under Gyeongsangnam Provincial Government. The number of projects and budget size has been decreased over 4 years, besides most of main projects were continued. The budgets were largely used for wetland project of cities and counties. Development and implementation of various conservation projects may have considerable potential values in wetland conservation, while it is still difficult to assess their overall effectiveness in the society. Diverse wetland management practices in Gyeongsangnam Provincial Government have accumulated fundamental practices and knowledge for an effective local conservation. These administrative experiences will further benefit other local government to establish wetland management framework. To accelerate policy diffusion to other local governments, Gyeongsangnam Province needs to promote and share leading experiences and information of wetland conservation. Enhanced local government framework by the legislation at central government will further support country-level management plans and practices.