ORCID Profile
0000-0002-5589-537X
Current Organisations
Seoul National University
,
University of Southern California
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Publisher: Springer Science and Business Media LLC
Date: 12-12-2013
Publisher: Cambridge University Press (CUP)
Date: 05-2010
DOI: 10.1666/09-105.1
Abstract: We provide the first detailed systematic taxonomy and paleoecological investigation of late Paleozoic brachiopod faunas from Korea. Specifically, we focus on the brachiopods from the Geumcheon-Jangseong Formation, the lower part of the Pyeongan Supergroup in the Taebaeksan Basin. The formation yields a variety of marine invertebrate fossils, including brachiopods, molluscs, echinoderms, corals, fusulinids, and conodonts. Diverse brachiopods are described from six siliciclastic horizons of the formation at three localities, including 23 species belonging to 20 genera with two new species: Rhipidomella parva n. sp. and Stenoscisma wooi n. sp. Three brachiopod assemblages of the late Moscovian (Pennsylvanian) age are recognized based on their species compositions and stratigraphic distributions, namely the Choristites, Rhipidomella , and Hustedia assemblages. The brachiopod faunal composition varies within each assemblage as well as between the Assemblages, most likely reflecting local paleoenvironmental and hence paleoecological differences. The Choristites Assemblage includes relatively large brachiopods represented by Derbyia, Choristites , and Stenoscisma and may have inhabited open marine to partly restricted marine environments, whereas the Rhipidomella and Hustedia Assemblages consist of a small number of small-sized brachiopods living in lagoonal environments. The Choristites Assemblage shows a close affinity with Moscovian brachiopod assemblages in the eastern Paleo-Tethys regions, especially the Brachythyrina lata-Choristites yanghukouensis-Echinoconchus elegans Assemblage of North China, whereas the Rhipidomella and Hustedia assemblages both exhibit strong endemism.
Publisher: Elsevier BV
Date: 2023
DOI: 10.1016/J.SCITOTENV.2022.159057
Abstract: Here we describe the potential for sediment microbial nitrogen-cycling gene (DNA) and activity (RNA) abundances to spatially resolve coastal areas impacted by seasonal variability in external nutrient inputs. Three sites were chosen within a nitrogen-limited embayment, Port Phillip Bay (PPB), Australia that reflect variability in both proximity to external nutrient inputs and the dominant form of available nitrogen. At three sediment depths (0-1 1-5 5-10 cm) across a 2 year study key genes involved in nitrification (archaeal amoA and bacterial β-amoA), nitrite reduction (clade I nirS and cluster I nirK, archaeal nirK-a), anaerobic oxidation of ammonium (anammox 16S rRNA phylogenetic marker) and nitrogen fixation (nifH) were quantified. Sediments impacted by a dominance of organic nitrogen inputs were characterised at all time-points and to sediment depths of 10 cm by the highest transcript abundances of archaeal amoA and archaeal nirk-a. Proximity to a dominance of external nitrate inputs was associated with the highest transcript abundances of nirS which temporally co-varied with seasonal changes in sediment nitrate. Sediments isolated from external inputs displayed the greatest depth-specific decrease in quantifiable transcript abundances. In these isolated sediments bacterial β-amoA transcripts were temporally associated with increased sediment ammonium levels. Across this nitrogen limited system variability in the abundance of bacterial β-amoA, archaeal amoA, archaeal nirk-a or nirS transcripts from the sediment surface (0-1 and 5 cm) demonstrated a capacity to improve our ability to monitor coastal zones impacted by anthropogenic nitrogen inputs. Specifically, the spatial detection sensitivity of bacterial β-amoA transcripts could be developed as a metric to determine spatiotemporal impacts of large external loading events. This temporal study demonstrates a capacity for microbial activity metrics to facilitate coastal management strategies through greater spatial resolution of areas impacted by external nutrient inputs.
Publisher: Springer Science and Business Media LLC
Date: 30-06-2011
Publisher: Hindawi Limited
Date: 2015
DOI: 10.1155/2015/875784
Abstract: Hypersaline systems near salt saturation levels represent an extreme environment, in which organisms grow and survive near the limits of life. One of the abundant members of the microbial communities in hypersaline systems is the square archaeon, Haloquadratum walsbyi . Utilizing a short-read metagenome from Lake Tyrrell, a hypersaline ecosystem in Victoria, Australia, we performed a comparative genomic analysis of H. walsbyi to better understand the extent of variation between strains/subspecies. Results revealed that previously isolated strains/subspecies do not fully describe the complete repertoire of the genomic landscape present in H. walsbyi . Rearrangements, insertions, and deletions were observed for the Lake Tyrrell derived Haloquadratum genomes and were supported by environmental de novo sequences, including shifts in the dominant genomic landscape of the two most abundant strains. Analysis pertaining to halomucins indicated that homologs for this large protein are not a feature common for all species of Haloquadratum . Further, we analyzed ATP-binding cassette transporters (ABC-type transporters) for evidence of niche partitioning between different strains/subspecies. We were able to identify unique and variable transporter subunits from all five genomes analyzed and the de novo environmental sequences, suggesting that differences in nutrient and carbon source acquisition may play a role in maintaining distinct strains/subspecies.
Publisher: Springer Science and Business Media LLC
Date: 28-04-2015
Publisher: Springer Science and Business Media LLC
Date: 03-06-2010
Abstract: Sponges form close relationships with bacteria, and a remarkable phylogenetic ersity of yet-uncultured bacteria has been identified from sponges using molecular methods. In this study, we use a comparative metagenomic analysis of the bacterial community in the model sponge Cymbastela concentrica and in the surrounding seawater to identify previously unrecognized genomic signatures and functions for sponge bacteria. We observed a surprisingly large number of transposable insertion elements, a feature also observed in other symbiotic bacteria, as well as a set of predicted mechanisms that may defend the sponge community against the introduction of foreign DNA and hence contribute to its genetic resilience. Moreover, several shared metabolic interactions between bacteria and host include vitamin production, nutrient transport and utilization, and redox sensing and response. Finally, an abundance of protein-protein interactions mediated through ankyrin and tetratricopeptide repeat proteins could represent a mechanism for the sponge to discriminate between food and resident bacteria. These data provide new insight into the evolution of symbiotic ersity, microbial metabolism and host-microbe interactions in sponges.
Publisher: Springer Science and Business Media LLC
Date: 06-2004
DOI: 10.1007/BF02910190
Publisher: Inter-Research Science Center
Date: 28-01-2021
DOI: 10.3354/AME01954
Abstract: Benthic microbial communities contribute to nitrogen (N) cycling in coastal ecosystems through taxon-specific processes such as anammox, nitrification and N-fixation and community attributed pathways such as denitrification. By measuring the total (DNA-based) and active (RNA-based) surface sediment microbial community composition and the abundance and activity profiles of key N-cycling genes in a semi-enclosed embayment—Port Phillip Bay (PPB), Australia—we show that although the total relative abundance of N-cycling taxa is comparatively lower close to estuary inputs (Hobsons Bay [HB]), the capacity for this community to perform erse Ncycling processes is comparatively higher than in sediments isolated from inputs (Central PPB [CPPB]). In HB, seasonal structuring of the sediment microbial community occurred between spring and summer, co-occurring with decreases in the activity profiles of anammox bacteria and organic carbon content. No changes were detected in the activity profiles of nitrifiers or the community-based pathway denitrification. Although no seasonal structuring of the sediment microbial community occurred in CPPB, the activity profiles of key N-cycling genes displayed comparatively higher within-site variability. These results show that despite N-cycling taxa representing a smaller fraction of the total community composition in estuary impacted sediments (HB) these microbial communities consistently engage in N-cycling processes and that seasonal instability in the composition of this community is not reflective of changes in its capacity to cycle N through coupled nitrification-denitrification but potentially via changes within the anammox community.
Publisher: Wiley
Date: 29-03-2023
Abstract: Spatial and temporal variability in benthic flux denitrification efficiency occurs across Port Phillip Bay, Australia. Here, we assess the capacity for untargeted metatranscriptomics to resolve spatiotemporal differences in the microbial contribution to benthic nitrogen cycling. The most abundant sediment transcripts assembled were associated with the archaeal nitrifier Nitrosopumilus . In sediments close to external inputs of organic nitrogen, the dominant transcripts were associated with Nitrosopumilus nitric oxide nitrite reduction ( nirK ). The environmental conditions close to organic nitrogen inputs that select for increased transcription in Nitrosopumilus ( amoCAB , nirK , nirS , nmo , hcp ) additionally selected for increased transcription of bacterial nitrite reduction ( nxrB ) and transcripts associated with anammox ( hzo ) but not denitrification (bacterial nirS / nirk ). In sediments that are more isolated from external inputs of organic nitrogen dominant transcripts were associated with nitrous oxide reduction ( nosZ ) and changes in nosZ transcript abundance were uncoupled from transcriptional profiles associated with archaeal nitrification. Coordinated transcription of coupled community‐level nitrification–denitrification was not well supported by metatranscriptomics. In comparison, the abundance of archaeal nirK transcripts were site‐ and season‐specific. This study indicates that the transcription of archaeal nirK in response to changing environmental conditions may be an important and overlooked feature of coastal sediment nitrogen cycling.
Publisher: Geological Society of London
Date: 2013
DOI: 10.1144/M38.19
Location: Australia
No related grants have been discovered for Duck Choi.