• Journal of Life Science
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• v.27 no.9
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• pp.1086-1095
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• 2017

There is growing interest in groundwater resources to overcome the loss of surface water resources due to climate change. An understanding of the microbial community of aquifers is essential for monitoring and evaluating groundwater contamination, as well as groundwater management. Most microorganisms that inhabit aquifer ecosystems are attached to sediment particles rather than planktonic, as is the case in groundwater. Since sampling aquifer sediment is not easy, groundwater, which contains planktonic microorganisms, is generally sampled in microbial community research. Although many studies have investigated microbial communities in contaminated aquifers, there are only a few reports of microbial communities in uncontaminated or pristine aquifers, resulting in limited information on aquifer microbial diversity. Such information is needed for groundwater quality improvement. This paper describes the ecology and community structure of groundwater bacteria in uncontaminated aquifers. The diversity and structures of microbial communities in these aquifers were affected by the concentration or distribution of substrates (e.g., minerals, organic matter, etc), in addition to groundwater characteristics and human activities. Most of the microbial communities in these uncontaminated aquifers were dominated by Proteobacteria. Studies of microbial communities in uncontaminated aquifers are important to better understand the biogeochemical processes associated with groundwater quality improvement. In addition, information on the microbial communities of aquifers can be used as a basis to monitor changes in community structure due to contamination.

• Journal of Microbiology and Biotechnology
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• v.32 no.10
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• pp.1275-1283
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• 2022

Understanding soil microbial community structure in the Arctic is essential for predicting the impact of climate change on interactions between organisms living in polar environments. The hypothesis of the present study was that soil microbial communities and soil chemical characteristics would vary depending on their associated plant species and local environments in Arctic mature soils. We analyzed soil bacterial communities and soil chemical characteristics from soil without vegetation (bare soil) and rhizosphere soil of three Arctic plants (Cassiope tetragona [L.] D. Don, Dryas octopetala L. and Silene acaulis [L.] Jacq.) in different local environments (coal-mined site and seashore-adjacent site). We did not observe any clear differences in microbial community structure in samples belonging to different plant rhizospheres; however, samples from different environmental sites had distinct microbial community structure. The samples from coal-mined site had a relatively higher abundance of Bacteroidetes and Firmicutes. On the other hand, Acidobacteria was more prevalent in seashore-adjacent samples. The relative abundance of Proteobacteria and Acidobacteria decreased toward higher soil pH, whereas that of Bacteroidetes and Firmicutes was positively correlated with soil pH. Our results suggest that soil bacterial community dissimilarity can be driven by spatial heterogeneity in deglaciated mature soil. Furthermore, these results indicate that soil microbial composition and relative abundance are more affected by soil pH, an abiotic factor, than plant species, a biotic factor.

• Korean Journal of Microbiology
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• v.35 no.1
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• pp.72-77
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• 1999

To investigate soil bacterial diversity according to vegelalioo types, utilizing ability of sole carbon sources and restriction enzyme patterns of 16s rDNA were analyzed. From the both results; five kinds of soil microbial communities were grouped as forest soil (Quercus mongolica and Pinus densi&ra vegetation), grass-agricultured soil and microbial communities of naked soil. But, both soil microbial communities of directily exlracted from ths soil and indirectly extracted from heterotrophic bacteria that cultured soil in LB medium showed very different similarity.

• Journal of Microbiology and Biotechnology
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• v.32 no.12
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• pp.1561-1572
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• 2022

Plastic pollution has been recognized as a serious environmental problem, and microbial degradation of plastics is a potential, environmentally friendly solution to this. Here, we analyzed and compared microbial communities on waste plastic films (WPFs) buried for long periods at four landfill sites with those in nearby soils to identify microbes with the potential to degrade plastics. Fourier-transform infrared spectroscopy spectra of these WPFs showed that most were polyethylene and had signs of oxidation, such as carbon-carbon double bonds, carbon-oxygen single bonds, or hydrogen-oxygen single bonds, but the presence of carbonyl groups was rare. The species richness and diversity of the bacterial and fungal communities on the films were generally lower than those in nearby soils. Principal coordinate analysis of the bacterial and fungal communities showed that their overall structures were determined by their geographical locations; however, the microbial communities on the films were generally different from those in the soils. For the pulled data from the four landfill sites, the relative abundances of Bradyrhizobiaceae, Pseudarthrobacter, Myxococcales, Sphingomonas, and Spartobacteria were higher on films than in soils at the bacterial genus level. At the species level, operational taxonomic units classified as Bradyrhizobiaceae and Pseudarthrobacter in bacteria and Mortierella in fungi were enriched on the films. PICRUSt analysis showed that the predicted functions related to amino acid and carbohydrate metabolism and xenobiotic degradation were more abundant on films than in soils. These results suggest that specific microbial groups were enriched on the WPFs and may be involved in plastic degradation.

• The Plant Pathology Journal
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• v.21 no.2
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• pp.93-98
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• 2005

Molecular ecological studies of microbial communities revealed that only tiny fraction of total microorganisms in nature have been identified and characterized, because the majority of them have not been cultivated. A concept, metagenome, represents the total microbial genome in natural ecosystem consisting of genomes from both culturable microorganisms and viable but non-culturable bacteria. The construction and screening of metagenomic libraries in culturable bacteria constitute a valuable resource for obtaining novel microbial genes and products. Several novel enzymes and antibiotics have been identified from the metagenomic approaches in many different microbial communities. Phenotypic analysis of the introduced unknown genes in culturable bacteria could be an important way for functional genomics of unculturable bacteria. However, estimation of the number of clones required to uncover the microbial diversity from various environments has been almost impossible due to the enormous microbial diversity and various microbial population structure. Massive construction of metagenomic libraries and development of high throughput screening technology should be necessary to obtain valuable microbial resources. This paper presents the recent progress in metagenomic studies including our results and potential of metagenomics in plant pathology and agriculture.

• Korean Journal of Soil Science and Fertilizer
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• v.47 no.6
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• pp.496-499
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• 2014

The present study investigated variations in soil microbial communities and the chemical properties of forest soils by differing amounts of penetrating sunlight. The soil temperature was significantly higher in higher light-penetrated soils. Higher light-penetrated soils (LP70) showed significantly more fungal communities than the lower light-penetrated soils (LP40 and LP50) (p < 0.05). The $NH_4$-N concentration in LP70 was significantly lower than those of LP40 and LP50, whereas the other chemical properties showed no significant difference among the soils. The cy19:0 to $18:1{\omega}7c$ ratio was significantly lower in LP70 than in LP 40 and LP50 showing the negative correlation of light level with microbial stresses (p < 0.05). The soil microbial communities and the chemical properties that showed positive eigenvector coefficients for PC1 were the fungi to bacteria, fungi, arbuscular mycorrhizal fungi, and Gram-positive bacteria, whereas negative eigenvector coefficients were found for $NH_4$-N, actinomycetes, Gram-negative bacteria, and bacteria. Consequently, the amount of penetrating light was responsible for microbial compositions in the forest soils in correlation with the concentration of $NH_4$-N and soil temperature.

• Korean Journal of Soil Science and Fertilizer
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• v.49 no.6
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• pp.783-788
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• 2016

Agricultural management of paddy soil depends on the effects of soil microbial activities. The present study evaluated the soil microbial community of 25 paddy soils in Gyeongnam Province by fatty acid methyl ester (FAME). The average of microbial communities in paddy soils were 32.2% of total bacteria, 16.7% of Gram-negative bacteria, 12.9% of Gram-positive bacteria, 2.0% of actinomycetes, 14.9% of fungi, and 1.3% of arbuscular mycorrhizal fungi. The communities of total bacteria (34.9%) and Gram-negative bacteria (19.4%) in soils with $30{\sim}35g\;kg^{-1}$ of organic matter were significantly larger than those in soils with other organic matter levels. However, soils with $20{\sim}30g\;kg^{-1}$ of organic matter had significantly low ratio of cy17:0 to $16:1{\omega}7c$ and cy19:0 to $18:1{\omega}7c$ as compared with soils with $30{\sim}35g\;kg^{-1}$ of organic matter, indicating microbial stress decreased (p < 0.05). In principal component analyses of soil microbial communities, Gram-negative bacteria should be considered as a potential responsible factor for the obvious microbial community differentiation that was observed between the two different organic matter levels in paddy fields. Thus, soils containing $20{\sim}30g\;kg^{-1}$ of organic matter were responsible for strong effect on microbial biomass and stress in paddy fields.

• Journal of Microbiology and Biotechnology
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• v.32 no.5
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• pp.564-574
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• 2022

Microbial diversity in the soil is responsive to changes in soil composition. However, the impact of soil amendments on the diversity and structure of rare and abundant sub-communities in agricultural systems is poorly understood. We investigated the effects of different Chinese herb residue (CHR) soil amendments and cropping systems on bacterial rare and abundant sub-communities. Our results showed that the bacterial diversity and structure of these sub-communities in soil had a specific distribution under the application of different soil amendments. The CHR soil amendments with high nitrogen and organic matter additives significantly increased the relative abundance and stability of rare taxa, which increased the structural and functional redundancy of soil bacterial communities. Rare and abundant sub-communities also showed different preferences in terms of bacterial community composition, as the former was enriched with Bacteroidetes while the latter had more Alphaproteobacteria and Betaproteobacteria. All applications of soil amendments significantly improved soil quality of newly created farmlands in whole maize cropping system. Rare sub-communitiy genera Niastella and Ohtaekwangia were enriched during the maize cropping process, and Nitrososphaera was enriched under the application of simple amendment group soil. Thus, Chinese medicine residue soil amendments with appropriate additives could affect soil rare and abundant sub-communities and enhance physicochemical properties. These findings suggest that applying soil composite amendments based on CHR in the field could improve soil microbial diversity, microbial redundancy, and soil fertility for sustainable agriculture on the Loess Plateau.

• Proceedings of the Microbiological Society of Korea Conference
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• 2008.05a
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• pp.19-19
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• 2008

• Asian-Australasian Journal of Animal Sciences
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• v.20 no.2
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• pp.283-294
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• 2007

Conventional culture-based methods of enumerating rumen microorganisms (bacteria, archaea, protozoa, and fungi) are being rapidly replaced by nucleic acid-based techniques which can be used to characterise complex microbial communities without incubation. The foundation of these techniques is 16S/18S rDNA sequence analysis which has provided a phylogenetically based classification scheme for enumeration and identification of microbial community members. While these analyses are very informative for determining the composition of the microbial community and monitoring changes in population size, they can only infer function based on these observations. The next step in functional analysis of the ecosystem is to measure how specific and, or, predominant members of the ecosystem are operating and interacting with other groups. It is also apparent that techniques which optimise the analysis of complex microbial communities rather than the detection of single organisms will need to address the issues of high throughput analysis using many primers/probes in a single sample. Nearly all the molecular ecological techniques are dependant upon the efficient extraction of high quality DNA/RNA representing the diversity of ruminal microbial communities. Recent reviews and technical manuals written on the subject of molecular microbial ecology of animals provide a broad perspective of the variety of techniques available and their potential application in the field of animal science which is beyond the scope of this treatise. This paper will focus on nucleic acid based molecular methods which have recently been developed for studying major functional groups (cellulolytic bacteria, protozoa, fungi and methanogens) of microorganisms that are important in nutritional studies, as well as, novel methods for studying microbial diversity and function from a genomics perspective.