Trophic structures of artificial reef communities off the southern coast of the Korean peninsula as determined using stable isotope analyses.

The deployment of artificial reefs (ARs) has become a popular technique for creating new hard-bottom habitats, and for enhancing biodiversity and resource abundance for fisheries. We compared colonizing faunal assemblages and reef-associated food-web structures between ARs and nearby natural reefs (NRs) off the Korean coast using stable isotope techniques. Reef communities showed high compositional disparities in colonizing assemblages. Distinct δ13C and δ15N ranges of functional groups could be used to distinguish pelagic from benthic trophic pathways in the reef food web. The isotopic niches of entire faunal assemblages, as well as individual functional groups, overlapped between NRs and ARs, resulting in equivalency for the isotopic functional indices. Mixing model estimates for carnivorous invertebrates and fish suggested strong trophic links to reef-associated faunal prey at both reef types. Finally, these results highlight a convergence in trophic structure between ARs and NRs in accordance with functional diversity in the colonized faunal assemblages.

Shifting resource utilization of the lacustrine shrimp Palaemon paucidens in temperate coastal lagoons of Korea as revealed by stable isotopes.

The spatial and seasonal variations in resource use of the lacustrine shrimp Palaemon paucidens were investigated in three different Korean lagoon systems in June and October 2018 by measuring their carbon and nitrogen stable isotope ratios. P. paucidens had much higher δ13C values at the permanently open lagoon (PL) as compared to the intermittently open lagoons (ILs), revealing a disparity in resource utilization. Isotopic niches of the shrimp were relatively wider at the PL than at the ILs, suggesting a greater diversity of carbon pathways in the PL system. These results indicate that the degree of water exchange with the sea, associated with lagoon geomorphology, may be a major factor influencing resource availability for P. paucidens. Our findings suggest that the duration and degree of inlet opening may affect dietary variation at the population level, and may be one of the key components of sustainable management for coastal lagoon ecosystems.

Year-to-year variation in phytoplankton biomass in an anthropogenically polluted and complex estuary: A novel paradigm for river discharge influence.

We examined the effects of nutrient availability and turbidity on phytoplankton biomass over 9 years in Gwanyang Bay, Korea, which is an anthropogenically polluted and complex estuary. While dredging and reclamation shaped geochemical features, river discharge with low-turbidity water and sewage treatment plants contributed to nutrient loading. The replete levels of nutrients and short water-residence time suggest the inapplicability of the washout theory, whereas the presence of NH4+ suppressed the growth of phytoplankton. A reduction in the river discharge caused a concomitant decline in the loading and dilution of suspended particles. All these features led to an increase in SPM, light limitation, and NH4+ concentration. GLM estimates revealed negative effects of NH4+ and SPM on chlorophyll a over 9 years while SEM verified synergistic effects of NH4+ and SPM compared with positive effects of NO2 + NO3-. Our findings provide new insights into phytoplankton bloom dynamics in Gwangyang Bay.

Identifying patterns in the multitrophic community and food-web structure of a low-turbidity temperate estuarine bay.

Food web dynamics outline the ecosystem processes that regulate community structure. Challenges in the approaches used to capture topological descriptions of food webs arise due to the difficulties in collecting extensive empirical data with temporal and spatial variations in community structure and predator-prey interactions. Here, we use a Kohonen self-organizing map algorithm (as a measure of community pattern) and stable isotope-mixing models (as a measure of trophic interaction) to identify food web patterns across a low-turbidity water channel of a temperate estuarine-coastal continuum. We find a spatial difference in the patterns of community compositions between the estuarine and deep-bay channels and a seasonal difference in the plankton pattern but less in the macrobenthos and nekton communities. Dietary mixing models of co-occurring dominant taxa reveal site-specific but unchanging food web topologies and the prominent role of phytoplankton in the trophic base of pelagic and prevalent-detrital benthic pathways. Our approach provides realistic frameworks for linking key nodes from producers to predators in trophic networks.

Incorporation of Cochlodinium bloom-derived organic matter into a temperate subtidal macrobenthic food web as traced by stable isotopes.

Harmful algal blooms involving the dinoflagellate Cochlodinium polykrikoides occur every summer off the Korean peninsula's central southern coast. To determine whether Cochlodinium bloom-derived organic carbon is incorporated into the subtidal macrobenthic food web, we compared the δ13C and δ15N values of suspended particulate organic matter (SPOM) and sedimentary organic matter, and macrobenthic consumers between bloom and non-bloom seasons. Chemotaxonomic analysis revealed the presence of Cochlodinium blooms in summer and a predominance of diatoms in autumn. Both the δ13C and δ15N values of SPOM were higher in the bloom than in the non-bloom seasons. Such temporal shifts in the δ13C and δ15N values were also observed for most macrobenthic consumers collected in both seasons. Consistent temporal isotopic shifts in SPOM and macrobenthos revealed that the Cochlodinium bloom-derived carbon was incorporated into the coastal benthic food web, resulting from its increasing availability during blooms.

Seasonal Mixing-Driven System in Estuarine-Coastal Zone Triggers an Ecological Shift in Bacterial Assemblages Involved in Phytoplankton-Derived DMSP Degradation.

The coastal zone has distinguishable but tightly connected ecosystems from rivers to the ocean and globally contributes to nutrient cycling including phytoplankton-derived organic matter. Particularly, bacterial contributions to phytoplankton-derived dimethylsulfoniopropionate (DMSP) degradation have been recently evaluated by using advanced sequencing technologies to understand their role in the marine microbial food web. Here, we surveyed the bacterial diversity and community composition under seasonal water mixing in the bay of Gwangyang (GW), a semi-enclosed estuary at the southern tip of the Korea Peninsula. We detected phylogenetic dissimilarities among season-specific habitats in GW and their specific bacterial taxa. Additionally, bacterial contribution to degradation of phytoplankton-derived DMSP from estuarine to coastal waters at euphotic depths in GW was investigated as the presence or absence of DMSP demethylation gene, encoded by dmdA. Among the operational taxonomic units (OTUs) in GW bacterial communities, the most dominant and ubiquitous OTU1 was affiliated with the SAR11 clade (SAR11-OTU). The population dynamics of SAR11-OTU in dmdA-detected GW waters suggest that water mass mixing plays a major role in shaping bacterial communities involved in phytoplankton-derived DMSP demethylation.

Physiological responses of the abalone Haliotis discus hannai to daily and seasonal temperature variations.

Organisms inhabiting tidal mixing-front zones in shallow temperate seas are subjected to large semidiurnal temperature fluctuations in summer. The ability to optimize energy acquisition to this episodic thermal oscillation may determine the survival, growth and development of these ectotherms. We compared the physiological and molecular responses of Haliotis discus hannai cultivated in suspended cages to fluctuating or stable temperature conditions. Several physiological indicators (respiration, excretion rates and O:N) were measured in both conditions, and alterations in the proteome during thermal fluctuations were assessed. No summer mortality was observed in abalone cultivated in fluctuating temperatures compared with that at stable high temperatures. Metabolic rates increased sharply during stable warm summer conditions and fluctuated in accordance with short-term temperature fluctuations (20-26 °C). Ammonia excretion rates during acute responses were comparable in both conditions. When abalone were exposed to fluctuating temperatures, enzyme activities were downregulated and structure-related protein expression was upregulated compared with that at an acclimation temperature (26 °C), highlighting that exposure to low temperatures during fluctuations alters molecular processes. Our results reveal that modulation of physiological traits and protein expression during semidiurnal thermal fluctuations may buffer abalone from the lethal consequences of extreme temperatures in summer.

Comparative trophic structures of macrobenthic food web in two macrotidal wetlands with and without a dike on the temperate coast of Korea as revealed by stable isotopes.

This study characterized trophic structures of the macrobenthic food webs in two contrasting estuarine wetlands, with and without a dike, on the southern coast of Korea, based on the δ13C and δ15N values of dominant macrobenthic consumers. The pelagic algal biomasses were similar in the upper Phragmites australis-covered and lower bare intertidal habitats partitioned by the dike, but the microphytobenthos (MPB) biomasses were extremely low in the Phragmites bed. The consumer δ13C values were more negative and their isotopic niche width was much narrower in the upper than in the lower habitat at the diked site. These dissimilar spatial patterns between sites suggest a simplified food-web structure, which reflects the reduced availability of MPB in the upper habitat in the dike-impacted site. Overall, our findings suggest that restriction of the tides by dike construction induces local changes in basal resource availability and faunal composition, leading to macrobenthic community trophic reorganization.

A bloodstream infection by Ruminococcus gnavus in a patient with a gall bladder perforation.

Ruminococcus gnavus is frequently found among human gut microbiome. However, human bloodstream infections by R. gnavus have been reported only three times. Clinical details were lacking for one case; the other two cases with concurrent bacteremia in patients with diverticulitis. We report a case of R. gnavus bloodstream infection in a patient with a gall bladder perforation suggesting its association with damage to the gastrointestinal tract. R. gnavus was misidentified using biochemical test but 16S rRNA sequencing and Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry were useful for correct identification. With the advancement of identification method in clinical laboratory, more frequent identification of R. gnavus from clinical specimens is expected.

RNA expression analysis of efflux pump genes in clinical isolates of multidrug-resistant and extensively drug-resistant Mycobacterium tuberculosis in South Korea.

Tuberculosis (TB), caused by infection with Mycobacterium tuberculosis, is an important communicable disease. Various mechanisms of resistance to antituberculosis drugs have been reported; these are principally mutations in target genes. However, not all M. tuberculosis resistance can be explained by mutations in such genes. Other resistance mechanisms associated with drug transport, such as efflux pumps, have also been reported. In this study, we investigated the expression levels of three putative efflux pumps and mutations in target genes associated with injectable agents and fluoroquinolones with clinical MDR and XDR-TB isolates. Thirty clinical isolates of M. tuberculosis that had been phenotypically characterized were obtained from the Korean Institute of Tuberculosis. Of these, 14 were MDR-TB isolates resistant to at least one injectable aminoglycoside (amikacin; AMK, kanamycin; KAN, and/or capreomycin; CPM) and 16 were XDR-TB isolates. M. tuberculosis H37Rv (ATCC 27249) was used as a reference strain. Five putative genes (Rv1258c, Rv2686c, Rv2687c, Rv2688c and pstB) were selected for analysis in this study. Sequencing was performed to detect mutations in rrs and eis genes. qRT-PCR was performed to investigate expression levels of five efflux pump genes. Of the 30 isolates, 25 strains had mutations in rrs associated with resistance to KAN, CPM and AMK and two strains had eis mutations, as well as mutations in rrs. pstB (Rv0933) exhibited increased expression and Rv2687c and Rv2688c exhibited decreased expression compared to the reference strain. Increased expression of pstB in clinical drug-resistant tuberculosis isolates may contribute to drug resistance in M. tuberculosis. In our case, overexpression of Rv1258c may have been associated with resistance to kanamycin. No correlation was evident between Rv2686c, Rv2687c or Rv2688c expression and fluoroquinolone resistance. To explore the details of efflux pump drug-resistance mechanisms, further studies on efflux pump inhibitors, transcriptional regulators, such as whiB7, and additional efflux pump genes are needed.

ARAP, a Novel Adaptor Protein, Is Required for TCR Signaling and Integrin-Mediated Adhesion.

A novel adaptor protein was identified by analyzing phosphotyrosine proteomes from membrane rafts of activated T cells. This protein showed sequence similarity to a well-known T cell adaptor protein, adhesion and degranulation-promoting adaptor protein (ADAP); therefore, the novel protein was designated activation-dependent, raft-recruited ADAP-like phosphoprotein (ARAP). Suppression of ARAP impaired the major signaling pathways downstream of the TCR. ARAP associated with the Src homology 2 domain of Src homology 2-containing leukocyte protein of 76 kDa via the phosphorylation of two YDDV motifs in response to TCR stimulation. ARAP also mediated integrin activation but was not involved in actin polymerization. The results of this study indicate that a novel T cell adaptor protein, ARAP, plays a unique role in T cells as a part of both the proximal activation signaling and inside-out signaling pathways that result in integrin activation and T cell adhesion.

Combined Effects of Temperature and Seston Concentration on the Physiological Energetics of the Manila Clam Ruditapes philippinarum.

The suspension-feeding Manila clam Ruditapes philippinarum is a native species of the western Pacific that is now widely distributed around the globe because of its commercial importance. To determine the adaptive physiological responses to changing thermal and nutritional conditions, clearance, filtration, feces production, ammonium excretion, respiration rates, and scope for growth (SFG) were measured in adult clams. The clams were exposed to 24 treatments involving the combination of four water temperatures (8, 13, 18, and 23°C) and six concentrations of suspended particulate matter (SPM: 9.5 to 350.5 mg L(-1)). Physiological rates were standardized by using the mean (480 mg) of tissue dry weights of experimental clams using allometric equations between physiological variables and tissue dry weight. Higher clearance rates were recorded at higher temperatures and lower SPM concentrations, and these rates decreased with increasing SPM concentration at individual temperatures. Consumed energy increased with increasing temperature and SPM concentration, peaking at around 100-200 mg L(-1) at 18-23°C. Whereas fecal energy was largely determined by SPM concentration, ammonia excretion was mainly governed by temperature. Respiration rate studies revealed a predominant quadratic effect of temperature on the metabolism, indicating a lack of acclimatory adjustment of metabolic rate to rising temperature. SFG values were positive under almost all the treatment conditions and were much higher at higher SPM concentrations (> 45 mg L(-1)), with the highest level being recorded at 18°C and 100-200 mg L(-1) SPM. Increased filtration rate offset the increased metabolic cost at warm temperatures. Our holistic findings suggest that a high degree of physiological plasticity allows R. philippinarum to tolerate the wide range of temperatures and SPM concentrations that are found in tidal flats, accounting in part for the successful distribution of this species over a wide variety of geographical areas.

Phylogeographical particularity of the Mycobacterium tuberculosis Beijing family in South Korea based on international comparison with surrounding countries.

To understand the domestic population structure of Mycobacterium tuberculosis clinical isolates in the Republic of Korea, we genotypically analysed 80 isolates obtained from various geographical origins in the country. Of these, 64 (80.0 %) isolates were identified as Beijing family strains. It is particularly interesting that their phylogenetic classification, based on the ancient/modern separation and the presence/absence of the genomic region RD181, revealed a majority of the ancient (RD181+) subfamily in the population. The 15 loci of variable number of tandem repeat(s) of mycobacterial interspersed repetitive units (15-MIRU-VNTR) were also analysed. Combination with the previous VNTR data reported from surrounding countries revealed that the topology of the minimum spanning tree was linked tightly not to the geographical origins of the patients but to the phylogenetic characteristics of the isolates. These results show that the phylogeographical distribution of the M. tuberculosis Beijing family around far-eastern Asia could be estimated using international accumulation and comparison of VNTR genotyping data.

The role of chest CT scanning in TB outbreak investigation.

BACKGROUND: In TB outbreaks, detecting active cases is the key step in stopping transmission of the disease. The aim of this study was to evaluate the role of high-resolution CT (HRCT) scanning of the chest in the investigation of a TB outbreak that developed in a cohort of 92 soldiers in the South Korean army. METHODS: Outbreak investigation, including tuberculin skin test (TST), QuantiFERON TB Gold In-Tube (QFT) test, and simple chest radiograph (CXR), was performed. For participants with any abnormal findings in these tests, HRCT scanning was done. Active pulmonary TB was diagnosed based on sputum studies or HRCT scan findings. In addition, participants with positive results in both TST and QFT were treated as having a latent TB infection (LTBI). TST and QFT were repeated in participants with a positive result in one of these tests. CXR was repeated in all participants at 3 and 6 months of follow-up. RESULTS: Eighty-seven participants completed the study protocol. Among them, 18 active TB cases were diagnosed. Nine of these had normal CXR, but had lesions that were suggestive of active TB on HRCT scan. Twenty-two participants with normal HRCT scans and positive results with TST and QFT at initial investigation were treated as LTBI. Among 13 participants with normal CXR and positive results in either TST or QFT, nine completed a 3-month investigation. All but one of nine participants revealed positive results in both tests. CONCLUSION: Inclusion of HRCT scanning in the outbreak investigation of TB may be helpful in differentiating active TB from LTBI more reliably. TRIAL REGISTRATION: clinicaltrials.gov; Identifier: NCT00889759.