Jung-Ho Hyun

Quantification of Ammonia-Oxidizing Bacteria and Factors Controlling Nitrification in Salt Marsh Sediments

ABSTRACT To elucidate the geomicrobiological factors controlling nitrification in salt marsh sediments, a comprehensive approach involving sediment geochemistry, process rate measurements, and quantification of the genetic potential for nitrification was applied to three contrasting salt marsh habitats: areas colonized by the tall (TS) or short (SS) form of Spartina alterniflora and unvegetated creek banks (CBs). Nitrification and denitrification potential rates were strongly correlated with one another and with macrofaunal burrow abundance, indicating that coupled nitrification-denitrification was enhanced by macrofaunal burrowing activity. Ammonia monooxygenase (amoA) gene copy numbers were used to estimate the ammonia-oxidizing bacterial population size (5.6 × 104 to 1.3 × 106 g of wet sediment−1), which correlated with nitrification potentials and was 1 order of magnitude higher for TS and CB than for SS. TS and CB sediments also had higher Fe(III) content, higher Fe(III)-to-total reduced sulfur ratios, higher Fe(III) reduction rates, and lower dissolved sulfides than SS sediments. Iron(III) content and reduction rates were positively correlated with nitrification and denitrification potential and amoA gene copy number. Laboratory slurry incubations supported field data, confirming that increased amounts of Fe(III) relieved sulfide inhibition of nitrification. We propose that macrofaunal burrowing and high concentrations of Fe(III) stimulate nitrifying bacterial populations, and thus may increase nitrogen removal through coupled nitrification-denitrification in salt marsh sediments.

Variations and Controls of Sulfate Reduction in the Continental Slope and Rise of the Ulleung Basin off the Southeast Korean Upwelling System in the East Sea

Despite its importance in carbon mineralization pathways, relatively little is known about sulfate reduction along a continental slope and rise. We investigated the temporal and spatial variations and controls of sulfate reduction rates (SRRs) in the continental margin sediment of the Ulleung basin (UB), off the southeast Korean upwelling system in the East Sea. SRRs ranged from 1.22 to 8.07 mmol m−2 d−1 at the slope sites and from 0.69 to 3.18 mmol m−2 d−1 at the basin sites. These values were exceptionally higher than those observed within other marginal seas and were comparable to SRR values at the same depth range in the Peruvian and Chilean upwelling systems. The high sulfate reduction in the UB was attributable to enhanced primary production in the water column associated with coastal upwelling and a high export flux of large organic particles into the basin via the Ulleung warm eddy. The depth integrated SRR was approximately 4 times higher in the highly productive spring (4.91 ± 2.55 mmol m−2 d−1) than during the summer, which exhibited a stratified water column (1.28 ± 0.48 mmol m−2 d−1). In the meantime, despite the high organic carbon content (> 2.5% dry wt.) in the UB, the SRR was consistently suppressed in the Mn oxide-enriched (174 μ mol cm−3) surface sediments of the continental rise. Overall, these results indicate that the production of organic carbon in the water column and its subsequent deposition on the seafloor is the primary source controlling the temporal variability of sulfate reduction, whereas the Mn oxides that were enriched in the basin are responsible for the spatial variability of the SRR in the UB. Carbon oxidation in the UB accounted for approximately 30% of primary production and approximately 60% of the export flux, indicating that the continental slope and rise of the UB is a region of rapid organic carbon turnover and nutrient regeneration.

A global proteome study of Mycobacterium gilvum PYR-GCK grown on pyrene and glucose reveals the activation of glyoxylate, shikimate and gluconeogenetic pathways through the central carbon metabolism highway

Various hydrocarbons have been released into the environment as a result of industrialization. An effective way of removing these materials without further environmental contamination is microbial bioremediation. Mycobacterium gilvum PYR-GCK, a bacteria isolated from a PAH polluted estuary, was studied using comparative shotgun proteomics to gain insight on its molecular activity while using pyrene and glucose as sole carbon and energy sources. Based on annotated genomic information, a confirmation analysis was first performed to confirm its pyrene degradation activity, using gas chromatography–mass spectrometry technology. One dimensional gel electrophoresis and liquid chromatography–mass spectrometry technologies employed in the proteomics analysis revealed the expression of pyrene degrading gene products along with upregulated expression of proteins functioning in the glyoxylate and shikimate pathways, in the pyrene-induced cells. The study also revealed the pathway of pyrene degraded intermediates, via partial gluconeogenesis, into the pentose phosphate pathway to produce precursors for nucleotides and amino acids biosynthesis.

Impacts of long-line aquaculture of Pacific oysters (Crassostrea gigas) on sulfate reduction and diffusive nutrient flux in the coastal sediments of Jinhae–Tongyeong, Korea

We investigated the environmental impacts of long-line aquaculture of Pacific oysters (Crassostrea gigas) on sediment geochemistry and carbon oxidation by sulfate reduction and diffusive benthic nutrient flux in a coastal ecosystem in Korea. Inventories of the NH4(+) and HPO4(2-) at the farm site were 7.7-11.5 and 1.8-8.0 times higher, respectively, than those at a reference site. Sulfate reduction rates (SRRs) at the oyster farm were 2.4-5.2 times higher than SRRs at the reference site. The SRRs at the farm site were responsible for 48-99% (average 70%) of the total C oxidation in the sediment. The diffusive benthic fluxes of NH4(+) and HPO4(2-) at the oyster farm were comparable to 30-164% and 19-58%, respectively, of the N and P demands for primary production, and were responsible for the enhanced benthic microalgal biomass on the surface sediment.

Rates of Sulfate Reduction and Iron Reduction in the Sediment Associated with Abalone Aquaculture in the Southern Coastal Waters of Korea

We investigated geochemical properties, and microbial sulfate- and iron(Ⅲ) reduction in sediment influenced by the aquaculture of abalone in the Nohwa-do, southern coastal sea in Korea. Concentrations of ammonium, phosphate, and sulfide in the pore-water were higher at farm sites than at control sites. The differences between the 2 types of sites were most apparent in terms of the weights of abalone and the temperature increase during September. Accordingly, the rates of sulfate reduction at the farm sites during September (61 m㏖ S m?²d?¹) were 3-fold higher than the sulfate reduction during May (20 m㏖ S m?²d?¹1). In contrast, Fe(Ⅲ) reduction rates were highest at the control sites in May, but its significance was relatively decreased at farm sites during September when sulfate reduction rates were highest. During September, benthic ammonium flux was 3-fold greater at the farm sites (35 m㏖ N m?²d?¹) than at the control sites (12 m㏖ N m?²d?¹), and phosphate flux was 8-fold higher at the farm sites (0.018 m㏖ P m?²d?¹) than at control sites (0.003 m㏖ P m?²d?¹). Overall results indicated that the inappropriate operation of a large-scale aquaculture farm may result in excess input of biodeposits and high nutrient fluxes from the sediment, thereby decreasing diversity of the benthic ecosystem and deepening eutrophication in coastal waters.

Macrozoobenthic Communities of the Deep Sea Sediments in the Northeastern Pacific Ocean

Macrobenthos were collected at 7 stations located from to with 1o interval along the longitude of using a box corer with sampling area of in July, 1999. In order to see the vertical distribution of macrobenthos in sediments, each subcore sample was divided into 5 layers with 1 cm interval up to 6 cm depth. Each subcore sample was sieved through 0.3 mm mesh screen and fixed with 10% Rose Bengal added formalin. A total of 22 faunal groups in 11 phyla were sampled and the average density was . Foraminiferans comprised 34.8% of total specimens were the most abundant fauna, and followed by nematodes (27.5%), polychaete worms (15.7%), and benthic harpactoid copepods (10.4%). A latitudinal trend was shown in the distribution of macrobenthos; the maximum density of appeared at station N06 and the most poverished community occurred at station N09 with the density of . The density of typical macrofaunal taxa except foraminiferans and nematods was . In the vertical distribution of macrobenthos, more than 70% of macrobenthos occurred in the upper 2 cm layer, and upper 4 cm layer contained about 90% of macrofauna. Polychaete worms consisted of 22 families, and cirratulid and paraonid worms were dominant polychaete species. The prominant feeding guilds of polychaete worms were SDT (surface, descretely motile, tenaculate feeding) and SMX (surface, motile, non-jawed); they comprised more than 50% of polychaete abundance. These feeding guilds of polychaete worms suggests that the deep sea benthos should be well adapted the newly settled deposits from water column, but this should be clarified by the further studies.

Potential environmental impact of deep seabed manganese nodule mining on the synechococcus (cyanobacteria) in the northeast equatorial pacific: Effect of bottom water‐sediment slurry

Synechococcus (photoautotrophic cyanobacteria) are among the major primary producers in the oligotrophic open ocean. Potential environmental impacts of bottom water and sediment intrusion on the Synechococcus population in the surface water column of the northeast equatorial Pacific were investigated during the KODOS (Korea Deep Ocean Study) 95–2 cruise. The growth of Synechococcus was limited primarily by Fe deficit and secondarily by nitrogenous nutrients. Since bottom water and sediment are abundant in both inorganic nutrients and trace metab, the addition of bottom water‐sediment slurry to surface water samples stimulated the growth of Synechococcus. Our results together with other experimental estimation suggest that certain impacts could occur on the photoautotrophic plankton biomass in the water column by the surface discharge of bottom water and sediment during large‐scale and long‐term commercial mining of Mn nodules. More quantitative estimation for those environmental aspects in the water colum...

Comparison of Sulfate Reduction Rates Associated with Geochemical Characteristics at the Continental Slope and Basin Sediments in the Ulleung Basin, East Sea

In conjunction with geochemical characteristics, rate of sulfate reduction was investigated at two sediment sites in the continental slope and rise (basin) of the Ulleung Basin in the East Sea. Geochemical sediment analysis revealed that the surface sediments of the basin site (D2) were enriched with manganese oxides (348 μ㏖ ㎝?³) and iron oxides (133 μ㏖ ㎝?³), whereas total reduced sulfur (TRS) in the solid phase was nearly depleted. Sulfate reduction rates (SRRs) ranged from 20.96 to 92.87 n㏖ ㎝?³ d?¹ at the slope site (M1) and from 0.65 to 22.32 n㏖ ㎝?³ d?¹ at the basin site (D2). Depth integrated SRR within the top 10 ㎝ depth of the slope site (M1; 5.25 m㏖ m?² d?¹) was approximately 6 times higher than that at the basin site (D2; 0.94 m㏖ m?² d?¹) despite high organic content (＞2.0% dry wt.) in the sediment of both sites. The results indicate that the spatial variations of sulfate reduction are affected by the distribution of manganese oxide and iron oxide-enriched surface sediment of the Ulleung Basin.

Microbial Community Structure Associated with Biogeochemical Processes in the Sulfate–Methane Transition Zone (SMTZ) of Gas-hydrate-bearing Sediment of the Ulleung Basin, East Sea

ABSTRACT We investigated the biogeochemical constituents, microbial communities and functional genes (mcr and dsr) associated with anaerobic methane oxidation and sulfate reduction, and metabolic activities by sulfate reduction in the sulfate–methane transition zone (SMTZ) of gas-hydrate-bearing sediment of the Ulleung Basin in the East Sea. Maxima in the sulfate reduction rate (12.6 nmol cm−3 d−1), CO concentration (83 μM), and gene abundances of dsrA (9.1 × 106 copies cm−3) and mcrA (11.6 × 106 copies cm−3) occurred in the SMTZ. The peaks of CO consistently found in the SMTZ suggested that CO is an intermediate metabolic product related to methane oxidation. Candidate division JS1, the predominant bacterial group that comprised 59.0–63.7% of the 16S rRNA gene sequences, was recognized as an important organic carbon oxidizer. Both Marine Benthic Group D (MBGD) and Marine Benthic Group B (MBGB), which constituted 40.8–52.9 and 10.3–43.9% of the 16S rRNA gene sequences, respectively, were the dominant archaeal groups. Analysis of functional gene diversity revealed that anaerobic methanotroph-1-related phylotypes appeared to be the major CH4 oxidizer, whereas Firmicutes-like group was a predominant sulfate reducer in the 0.8 mbsf in SMTZ with low SO42− concentration. Overall results indicated that JS1 and two archaeal groups (MBGB and MBGD) seem to play a significant role in carbon and elements cycles in the gas-hydrate-bearing subsurface sediment of the Ulleung Basin.

Fine-scale Microbial Communities Associated with Manganese Nodules in Deep-sea Sediment of the Korea Deep Ocean Study Area in the Northeast Equatorial Pacific

Despite its potential significance for industrial utilization, any activities associated with the mining of manganese (Mn) nodules might have substantial impacts on benthic ecosystems. Because microorganisms respond quickly to changing environmental conditions, a study of microbial communities provides a relevant proxy to assess possible changes in benthic ecosystems associated with mining activities. We investigated fine-scale microbial community composition and diversity inside and on the surface of Mn nodules and in nearby deep-sea sediments in the Korea Deep Ocean Study (KODOS) area located in the Clarion-Clipperton Fracture Zone (CCFZ) of the northeast equatorial Pacific. Although microbial cell density was lower within nodules (3.21 × 106 cells g-1) than in sediment (2.14 × 108 cells g-1), nodules provided a unique habitat for microorganisms. Manganese-oxidizing bacteria including Hyphomicrobium and Aurantimonas in Alphaproteobacteria and Marinobacter in Gammaproteobacteria were abundant in nodules, which implied that these bacteria play a significant role in nodule formation. In contrast, Idiomarina in Gammaproteobacteria and Erythrobacter and Sulfitobacter in Alphaproteobacteria were abundant in sediments. Meanwhile, Thaumarchaeota, a phylum that consists of ammonia-oxidizing chemolithoautotrophs, were the predominant archaeal group both in nodules and sediment. Overall, microbial communities in Mn nodules were unique compared to those observed in sediments. Furthermore, the phylogenetic composition of microorganisms in the KODOS area was distinguishable from that in the nodule provinces claimed by China and Germany in the CCFZ and nodule fields in the central South Pacific Gyre, respectively.