Molecular Diet Analysis of Asian Clams for Supplementary Biodiversity Monitoring: A Case Study of Nakdong River Estuary

Environmental DNA (eDNA) extracted from the gut contents of filter feeders can be used to identify biodiversity in aquatic ecosystems. In this study, we used eDNA from the gut contents of the Asian clam Corbicula fluminea to examine biodiversity within estuarine ecosystem. Field sampling was conducted at three points in the Nakdong River Estuary, which is characterised by closed estuarine features resulting from the presence of an estuarine barrage. The collected C. fluminea samples were dissected to separate the gut contents, and the extracted eDNA was amplified using 18S V9 primer targeting all eukaryote-derived DNA. The amplified DNA was sequenced using a next-generation sequencing (NGS) technique, and a BLASTn search was performed based on the National Centre for Biotechnology Information (NCBI) database for taxa identification. We obtained 23 unique operational taxonomic units (OTUs), including fish (approximately 8.70%), copepods (approximately 17.39%), and green algae (approximately 21.74%), representing a wide range of habitats. Furthermore, 8 out of the 20 families were identified through comparisons with reference data from conventional field surveys, and the OTUs of elusive migratory fish were detected. The results support the application of C. fluminea as an eDNA sampler for supplementary biodiversity monitoring.

A molecular approach to identifying the relationship between resource use and availability in Eurasian otters (Lutra lutra)

In South Korea, the Eurasian otter (Lutra lutra (Linnaeus, 1758)), a semi-aquatic carnivore, is found mainly in lower order streams that tend to have a low abundance of preferred prey fish species. To investigate the relationship between resource use and availability, we used DNA barcoding to identify otter diet items in 24 otter spraints (faeces) from 16 sites along the Nakdong River basin from 4 to 6 June 2014. At these sites fish availability was assessed using scoop nets and casting nets. Fish formed the bulk of otter diet, which included also frogs, mammals, and reptiles. By DNA barcoding (success rate: 72.38%), we identified 79 prey items from 105 bone remains. The diet comprised mostly fish, but frogs, mammals, and reptiles were also identified. The fish fauna and otter diet composition differed significantly. Across the study sites, members of the Cyprinidae dominated in netted samples, but occurred less frequently in otter diet. Because most Cyprinidae are fast swimmers, otters also fed on benthic fishes and frogs, suggesting limited foraging flexibility in otters and specialization on more slowly moving prey.

Responses of fish assemblage structure to large-scale weir construction in riverine ecosystems

Worldwide, increasing amounts of dams and weirs have been established in rivers in recent decades, often with drastic effects on their ecosystems. Between late 2009 and 2011, 16 large-scale dams were built in the main channels of the four largest rivers in South Korea, eight of these along the main channel of Nakdong River (300 km, 520 km in total). We studied the effect of these constructions on the fish community in the riparian zone based on intensive fish field surveys conducted in the littoral zone during 2007-2017, analysis of fishermen's catch data and molecular analysis of the diet of the keystone species, largemouth bass (Micropterus salmoides). Our results, based on RDA and GLM analyses, showed that environmental characteristics and fish species composition changed significantly with dam construction. Total fish abundance and biomass decreased after the start of the weir construction and fish richness decreased with time. The abundance and biomass of exotic fish decreased during construction but recovered afterwards, leading to higher proportions of exotics. Dominance and Shannon indices did not change significantly from before to after construction, while the Evenness index showed a significant decreasing trend. A comparison of the diet composition of largemouth bass showed decreasing genetic variation after construction. The changes in Functional Feeding Group (FFG) of the benthic communities at the study sites did not coincide with FFG changes in the prey items of largemouth bass, indicating a transition in feeding mode from before to after construction. In conclusion, the endemic and native fish species were most sensitive and showed lower resilience to disturbance by the large-scale dam construction than the translocated and exotic species, and the lake-like ecosystems after construction markedly improved the competitive capacity of these exotic fish over the native and endemic species in the riparian zone of the river.

Complete mitochondrial genome of the freshwater bryozoan Pectinatella magnifica (Phylactolaemata: Plumatellida) assembled from next-generation sequencing data

The complete mitochondrial genome of the freshwater bryozoan Pectinatella magnifica was sequenced. The circular mitochondrial genome is 17,539 bp and consists of 13 protein-coding, two ribosomal RNA, and 22 transfer RNA genes (GenBank accession no. MG546680). The Bayesian comparative analysis of molecular evolution rates revealed no acceleration of the mitochondrial DNA (mtDNA) evolution of P. magnifica. Results of maximum likelihood analysis showed that this species clustered with other species of the phylum Bryozoa.

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

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.

Expression of MHC Class II, CD70, CD80, CD86 and pro-inflammatory cytokines is differentially regulated in oral epithelial cells following bacterial challenge

Oral epithelium may play a regulatory role in local immune responses when interacting with bacteria. The present study was undertaken to investigate the effects of selected bacterial pathogens found in periodontal and endodontic infections on oral epithelial cells. Expression of cell surface molecules (major histocompatibility complex (MHC) Class II, CD54, CD70, CD80 and CD86) and secretion of inflammatory cytokines (interleukin (IL)-1beta, IL-6, and tumor necrosis factor (TNF)-alpha) in response to selected bacterial challenge were examined on an immortalized oral epithelial cell line, HOK-18A and a skin epithelial cell line, HaCaT. Actinomyces viscosus, Actinomyces israelii, Fusobacterium nucleatum lipopolysaccharide (LPS) or primary human periradicular exudate from a granuloma were co-cultured with epithelial cells for 4 or 24 h. Subsequently, cell surface expression of MHC Class II, CD54, CD70, CD80 and CD86, along with pro-inflammatory cytokine levels were determined using flow cytometry, ELISA and RT-PCR. Results indicated that the selected oral bacteria have greater effects on oral versus skin epithelial cells. F. nucleatum increased MHC Class II and CD54 (ICAM-1) cell surface expression on HOK-18A and HaCaT cells. A. israelii also had enhancing effects on the expression of CD54 and MHC Class II. A. israelii and LPS induced a 2.8-fold (P < 0.001) and 4.4-fold (P < 0.005) TNF-alpha secretion, respectively, while F. nucleatum and LPS induced a 10-fold (P < 0.0004) and 6-fold (P < 0.01) IL-1beta secretion, respectively by HOK-18A. Interestingly, CD70, CD80, and CD86 were generally decreased upon bacteria and LPS challenge on HOK-18A. The effects of increased MHC Class II and decreased CD70 were also evident with challenge of human periradicular exudate on HOK-18A. The implications of the study are unique in that oral epithelial cells may play both activating and inhibitory roles in the host immune response towards infection by oral bacteria. We introduce a concept of 'dormancy' where the differential expression of key cell surface antigens on oral epithelial cells may keep the recruited immune effector cells in a state of unresponsiveness, thus contributing to the long term quiescent period observed in many periodontal and endodontic lesions.

Breast cancer, passive and active cigarette smoking and N-acetyltransferase 2 genotype

The relationship of breast cancer to cigarette smoking is inconsistent in the literature, possibly due in part to heterogeneity in carcinogen metabolism. N-acetyltransferase 2 (NAT2) enzyme activity is believed to play a role in the activation of tobacco smoke carcinogens. We examined the effect of NAT2 genetic polymorphisms on risk of breast cancer from active and passive smoking. Women were recruited from those who had suspicious breast masses detected clinically and/or mammographically. Questionnaire data were collected prior to biopsy diagnosis to blind subjects and interviewers. Histopathology showed 113 cases with mammary carcinoma (30 carcinoma in situ) and 278 controls with benign breast disease. NAT2 genotype was determined using allele-specific polymerase chain reaction amplification to detect slow acetylator mutations. Effects of passive and active tobacco smoke and of NAT2 genotype on breast cancer risk were examined with logistic regression controlling for known risk factors. Models first included all controls, and subsequently 107 with no or low risk (normal breast or no hyperplasia), and finally 148 with high risk (hyperplasia, atypical hyperplasia, complex fibroadenomas). Referents had no active or passive smoke exposure. We found no association between breast cancer risk and NAT2, smoking status (never, former, current), smoking duration, or cigarettes per day. There were no effects of passive exposure among never-smokers. Models were unchanged across control groups. There were no statistical interactions between tobacco smoke exposure and NAT2. The results were similar when restricting the analysis to invasive cancers. These findings do not support the hypothesis that NAT2 is a risk factor for breast cancer or that it alters susceptibility to tobacco smoke.

Breast cancer, heterocyclic aromatic amines from meat and N-acetyltransferase 2 genotype

Breast cancer risk has been hypothesized to increase with exposure to heterocyclic aromatic amines (HAAs) formed from cooking meat at high temperature. HAAs require enzymatic activation to bind to DNA and initiate carcinogenesis. N-acetyltransferase 2 (NAT2) enzyme activity may play a role, its rate determined by a polymorphic gene. We examined the effect of NAT2 genetic polymorphisms on breast cancer risk from exposure to meat by cooking method, doneness and estimated HAA [2-amino-1-methyl-6-phenylimidazole[4,5-b]pyridine (PhIP), 2-amino-3,8-dimethylimidazo[4,5-f]quinoxaline (MeIQx) and 2-amino-3,4,8-trimethylimidazo[4,5-f]quinoxaline (DiMeIQx)] intake. Women were recruited with suspicious breast masses and questionnaire data were collected prior to biopsy to blind subjects and interviewers to diagnoses. For 114 cases with breast cancer and 280 controls with benign breast disease, NAT2 genotype was determined using allele-specific PCR amplification to detect slow acetylator mutations. HAAs were estimated from interview data on meat type, cooking method and doneness, combined with a quantitative HAA database. Logistic regression models controlled for known risk factors, first including all controls, then 108 with no or low risk (normal breast or no hyperplasia) and finally 149 with high risk (hyperplasia, atypical hyperplasia, complex fibroadenomas). Meat effects were examined within NAT2 strata to assess interactions. We found no association between NAT2 and breast cancer. These Californian women ate more white than red meat (control median 46 versus 8 g/day). There were no significant associations of breast cancer with red meat for any doneness. White meat was significantly protective (>67 versus <26 g/day, OR 0.46, 95% CI 0.23-0.94, P for trend = 0.02), as was chicken, including well done, pan fried and barbecued chicken. MeIQx and DiMeIQx were not associated with breast cancer. A protective effect of PhIP was confounded after controlling for well done chicken. Results were unchanged using low or high risk controls or dropping 30 in situ cases. There was no interaction between NAT2 and HAAs. These findings do not support a role for HAAs from meat or NAT2 in the etiology of breast cancer. Further research is needed to explain the white meat association.