• Journal of Environmental Impact Assessment
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• v.20 no.6
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• pp.845-856
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• 2011

In order to establish fundamental data for stream restoration and environmental flow, we investigated inhabitation and species diversity of fish to substrate size in the typical streams of Geum River Basin. Field monitoring including fish sampling was conducted from October 2007 to October 2009. Substrate size was determined according to six different : silt (Si), sand (Sa), fine gravel (Fg), coarse gravel (Cg), cobbles (Co) and boulders (Bo). A total number of fish caught in the 18 sites was 7,649 representing 10 families 50 species, and Si, Sa, Fg, Cg, Co and Bo stations occupied 30, 29, 38, 30, 27 and 17 species, respectively. The most frequently found species in number was pale chum (Zacco platypus, 29.7%, n=2,275) followed by Z. koreanus (22.5%, n=1,720) in total stations. Biological diversity with increase of substrate size from the dominance of part species showed higher values as dominance index, lower and diversity, richness and evenness index. Index of biological integrity (IBI) and qualitative habitat evaluation index (QHEI) scores decreased with increase of substrate size. Therefore, it is necessary to make an effort on stream rehabilitation with evaluation of physical habitat condition by indicator species in order to maintain biodiversity and perform ecological restoration.

• Mycobiology
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• v.50 no.5
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• pp.326-344
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• 2022

The fungal-like family Saprolegniaceae (Oomycota), also called "water mold," includes mostly aquatic saprophytes as well as notorious aquatic animal pathogens. Most studies on Saprolegniaceae have been biased toward pathogenic species that are important to aquaculture rather than saprotrophic species, despite the latter's crucial roles in carbon cycling of freshwater ecosystems. Few attempts have been made to study the diversity and ecology of Saprolegniaceae; thus, their ecological role is not well-known. During a survey of oomycetes between 2016 and 2021, we investigated the diversity and distribution of culturable Saprolegniaceae species in freshwater ecosystems of Korea. In the present study, members of Saprolegniaceae were isolated and identified at species level based on their cultural, morphological, and molecular phylogenetic analyses. Furthermore, substrate preference and seasonal dynamics for each were examined. Most of the species were previously reported as animal pathogens; however, in the present study, they were often isolated from other freshwater substrates, such as plant debris, algae, water, and soil sediment. The relative abundance of Saprolegniaceae was higher in the cold to cool season than that in the warm to hot season of Korea. This study enhances our understanding of the diversity and ecological attributes of Saprolegniaceae in freshwater ecosystems.

• Animal cells and systems
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• v.16 no.1
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• pp.69-76
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• 2012

This study was conducted to examine how a low-head dam removal (partial removal) could affect benthic macroinvertebrate communities in a stream. Benthic macroinvertebrates and substrates were seasonally sampled before and after dam removal (March 2006-April 2007). Benthic macroinvertebrates and substrates were quantitatively sampled from immediately upstream (upper: pool) and downstream (lower: riffle) sites, the location of the dam itself (middle), and immediately above the impoundment (control: riffle). After the removal, species richness and density of benthic macroinvertebrates as well as the EPT group (Ephemeroptera, Plecoptera and Trichoptera) increased to higher levels than those before the removal, while functional feeding groups and habitat orientation groups changed more heterogeneously at the upper site. At the lower site, species richness and density decreased somewhat immediately after dam removal, which was associated with an increase of silt and sand, but recovered after monsoon floods which helped to enhance substrate diversity at the upper site. Decreased dominance index and increased diversity index in both the upper and lower sites are evidence of positive effects from the dam removal. In conclusion, we suggest that even a partial removal of a dam, resulting in increased substrate diversity in the upper site, could sufficiently help rehabilitate lost ecological integrity of streams without major habitat changes.

• Journal of Korean Society on Water Environment
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• v.35 no.6
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• pp.539-549
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• 2019

In 2016, Benthic Macroinvertebrates Streambed Index (BMSI) was proposed as an index to evaluate streams as benthic macroinvertebrate depending on the substrate type of streambed. However, orignal BMSI were selected without consideration of water quality. Analyzes without water quality do not constitute biological indices based solely on the substrate type of streambed. Therefore, in this study, the indicator value was improvement in consideration of water quality, and the distribution characteristics of benthic macroinvertebrates according to the substrate type of streambed were analyzed under relatively equal water quality conditions. We surveyed 20,155 sampling units in Korea from 2008 to 2018, and we re-estimated each lithophility of 191 taxa. As a result of estimating the streambed of each newly lithophilic value classification group considering the water quality, it was different from the original lithophilic value. Representative integer lithophilic values were newly calculated from 126 taxa among the 191 index taxa used in the analysis. The correlation between new constructed BMSI and community structure was compared and analyzed. It showed extreamely significance (p<0.001) in the dominance index, diversity index, abundance index, and evenness index of the community structure. Diversity index, abundance index, and evenness index showed positive correlation, and dominance index showed negative correlation. The correlation coefficient (r) was the highest in the richness index of about 0.664.

• Journal of Korean Society on Water Environment
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• v.33 no.6
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• pp.728-735
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• 2017

Many restoration projects are underway to revive disturbed streams. In order to achieve successful stream restoration, a variety of microhabitats should be created to promote biological diversity. Research on biological classification of microhabitats is essential for biological diversity. However, research on classification using only physical environmental factors has been carried out. The purpose of this study is to classify and quantify the microhabitat of the stream by using macroinvertebrates systematically. In this study, eight wadeable streams and four non-wadeable streams were surveyed to identify the benthic macroinvertebrates in these various microhabitats. Among the physical environmental factors (current velocity, water depth, substrate), the particle size of the substrate was the most influential factor in the emergence of the Habitat Orientaion Groups. Among the HOGs, clinger and burrower were highly correlated with physical environment factors and showed the opposite tendency. The distribution of clinger and burrower according to the physical environmental factors showed two tendencies based on the current velocity (0.3 m/s) and water depth (0.4 m). In addition, the particle size of the substrate showed three trends (${\leq}-5.0$, -5.0 < mean diameter ${\leq}-2.0$, > -2.0). Based on the abundance tendency of these two HOGs, the microhabitats were classified into nine types, from a eupotamic microhabitat to a lentic microhabitat. Classification of the microhabitats using HOGs can be employed for creating microhabitats to promote biological diversity in future stream restoration plans.

• Journal of Microbiology and Biotechnology
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• v.28 no.8
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• pp.1339-1345
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• 2018

2-Keto-3-deoxy-6-phosphogluconate (KDPG) aldolase, which catalyzes aldol cleavage and condensation reactions, has two distinct substrate-binding sites. The substrate-binding mode at the catalytic site and Schiff-base formation have been well studied. However, structural information on the phosphate-binding loop (P-loop) is limited. Zymomonas mobilis KDPG aldolase is one of the aldolases with a wide substrate spectrum. Its structure in complex with the substrate-mimicking 3-phosphoglycerate (3PG) shows that the phosphate moiety of 3PG interacts with the P-loop and a nearby conserved serine residue. 3PG-binding to the P-loop replaces water molecules aligned from the P-loop to the catalytic site, as observed in the apostructure. The extra electron density near the P-loop and comparison with other aldolases suggest the diversity and flexibility of the serine-containing loop among KDPG aldolases. These structural data may help to understand the substrate-binding mode and the broad substrate specificity of the Zymomonas KDPG aldolase.

• Asian-Australasian Journal of Animal Sciences
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• v.28 no.6
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• pp.888-895
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• 2015

Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and subsequent sub-cloning and sequencing were used in this study to analyze the molecular phylogenetic diversity and spatial distribution of bacterial communities in different spatial locations during the cooling stage of composted swine manure. Total microbial DNA was extracted, and bacterial near full-length 16S rRNA genes were subsequently amplified, cloned, RFLP-screened, and sequenced. A total of 420 positive clones were classified by RFLP and near-full-length 16S rDNA sequences. Approximately 48 operational taxonomic units (OTUs) were found among 139 positive clones from the superstratum sample; 26 among 149 were from the middle-level sample and 35 among 132 were from the substrate sample. Thermobifida fusca was common in the superstratum layer of the pile. Some Bacillus spp. were remarkable in the middle-level layer, and Clostridium sp. was dominant in the substrate layer. Among 109 OTUs, 99 displayed homology with those in the GenBank database. Ten OTUs were not closely related to any known species. The superstratum sample had the highest microbial diversity, and different and distinct bacterial communities were detected in the three different layers. This study demonstrated the spatial characteristics of the microbial community distribution in the cooling stage of swine manure compost.

• Proceedings of the Microbiological Society of Korea Conference
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• 2008.05a
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• pp.118-118
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• 2008

The phylogenetic diversity of microbial communities in calcareous mats from Spearfish Creek, a freshwater stream located in the Black Hills of South Dakota, was examined using PCR-based 16S rDNA sequence analysis. In this study, two types of calcareous mats were compared: mature mats formed on the natural substrate of rock surfaces and developing mats on an artificial substrate of glass slides. Among 63 unique isolates from a clone library of 16S rRNA genes from mature mat samples, there were 8 phyla of Bacteria represented. The predominant phylum was Proteobacteria (48%), with the $\beta$ subclass being the largest group. Denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA genes from slide samples collected at intervals for four months showed considerable diversity of the microbial community from the earliest stages of community development. Amplicons isolated from DGGE gels and sequenced indicated that community succession has occurred without increasing microbial diversity. However, light microscopic analysis revealed a significant increase in microbial cell density throughout the community development. Scanning electron microscopy of mat samples provides evidence that diatoms are also important members of calcareous mat communities.

• Korean Journal of Soil Science and Fertilizer
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• v.49 no.2
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• pp.144-156
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• 2016

Soil is a dynamic biological system, in which it is difficult to determine the composition of microbial communities. Knowledge of microbial diversity and function in soils are limited because of the taxonomic and methodological limitations associated with studying the organisms. In this review, approaches to measure microbial diversity in soil were discussed. Research on soil microbes can be categorized as structural diversity, functional diversity and genetic diversity studies, and these include cultivation based and cultivation independent methods. Cultivation independent technique to evaluate soil structural diversity include different techniques such as Phospholipid Fatty Acids (PLFA) and Fatty Acid Methyl Ester (FAME) analysis. Carbon source utilization pattern of soil microorganisms by Community Level Physiological Profiling (CLPP), catabolic responses by Substrate Induced Respiration technique (SIR) and soil microbial enzyme activities are discussed. Genetic diversity of soil microorganisms using molecular techniques such as 16S rDNA analysis Denaturing Gradient Gel Electrophoresis (DGGE) / Temperature Gradient Gel Electrophoresis (TGGE), Terminal Restriction Fragment Length Polymorphism (T-RFLP), Single Strand Conformation Polymorphism (SSCP), Restriction Fragment Length Polymorphism (RFLP) / Amplified Ribosomal DNA Restriction Analysis (ARDRA) and Ribosomal Intergenic Spacer Analysis (RISA) are also discussed. The chapter ends with a final conclusion on the advantages and disadvantages of different techniques and advances in molecular techniques to study the soil microbial diversity.

• Journal of Environmental Science International
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• v.5 no.1
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• pp.61-69
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• 1996

The combined wastewater of municipal landfill leachate and municipal sewage was treated using several sets of bench-scale aerated circulating system including porous media. Investigated items in this experiment were the dominant protozoa and metazoa in this system, the variation of microfauna relationship between operating condition and dominant genera. Also considered the factors determining dominant genera and their role. The outcome of this research is as follows; 1. Aspidisca, Vorticella, Truhellophyllum, Lecane, Philodina, Cyclops were mainly appeared prior to combinding leachate, while Trachelocerca, Bodo, Glaucoma were the dominant genera after combinding leachate. 2. As to metazoa, Nematode and Philodina were not influenced by 5oA leachate mixing ratio, meanwhile Crustacea has high sensitivity for increased leachate mixing ratio and it was not appeared in 5% leachate mixing ratio. 3. The appropriate treatability could'nt be expected at the above 10% leachate mixing ratio. Especially, in the condition of 20% leachate mixing ratio, all of the microfauna were affected damage seriously on their existence. Meanwhile hydraulic retention time, substrate loading rate and slut자e production rate didn't give notable influence on increasing the number of microfauna. 4. As to protozoa, saprozoic and holozoic species were appeared commonly and polysaprobic species were dominent. 5. Filamentous organsms were nearly not affected by leachate mixing. It seems that they could live without any trouble at the 10% leachate mixing ratio, if the substrate is sufficient. 6. Diversity of microfauna had a reducing trernd as the sewage was mixed with leachate.