• Environmental Engineering Research
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• v.14 no.1
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• pp.3-9
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• 2009

Microorganisms play an important role in the geochemical cycles, industry, environmental cleanup, and biotechnology among other fields. Given the high microbial diversity, identification of the microorganism is essential in understanding and managing the processes. One of the most popular and powerful method for microbial identification is comparative 16S rRNA gene analysis. Due to the highly conserved nature of this essential gene, sequencing and later comparison of it against known rRNA databases can provide assignment of the bacteria into the taxonomy, and the identity of its closest relatives. Isolation and sequencing of 16S rRNA genes directly from natural environments (either from DNA or RNA) can also be used to study the structure of the whole microbial community. Nowadays, novel sequencing technologies with massive outputs are giving researchers worldwide the chance to study the microbial world with a depth that was previously too expensive to achieve. In this article we describe commonly used research approaches for the study of individual microorganisms and microbial communities using the tools provided by Ribosomal Database Project website.

• Environmental Engineering Research
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• v.23 no.1
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• pp.62-69
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• 2018

In the present study, long-term heavy metals (HMs) contaminated soil samples from a well-known Pb/Zn smelting area in the southwest of China were collected, and physicochemical and biological characteristics of these samples were evaluated. Soil samples contained different concentrations of HMs, namely Pb, Zn, Cu, and Cd. Enzyme activity analyses combined with microcalorimetric analysis were used for soil microbial activity evaluation. Results showed that two soil samples, containing almost the highest concentrations of HMs, also shared the greatest microbial activities. Based on correlation coefficient analysis, high microbial activity in heavily HMs contaminated soil might be due to the high contents of soil organic matter and available phosphorus in these samples. High-throughput sequencing technique was used for microbial community structure analysis. High abundance of genera Sphingomonas and Thiobacillus were also observed in these two heavily contaminated soils, suggesting that bacteria belonging to these two genera might be further isolated from these contaminated soils and applied for future studies of HMs remediation. Results of present study would contribute to the evaluation of microbial communities and isolation of microbial resources to remediate HMs pollution.

• Journal of dental hygiene science
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• v.19 no.2
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• pp.86-95
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• 2019

The modern era of microbial genome analysis began in earnest in the 2000s with the generalization of metagenomics and gene sequencing techniques. Studying complex microbial community such as oral cavity and colon by a pure culture is considerably ineffective in terms of cost and time. Therefore, various techniques for genomic analysis have been developed to overcome the limitation of the culture method and to explore microbial communities existing in the natural environment at the gene level. Among these, DNA fingerprinting analysis and microarray chip have been used extensively; however, the most recent method of analysis is metagenomics. The study summarily examined the overview of metagenomics analysis techniques, as well as domestic and foreign studies on disease genomics and cluster analysis related to oral metagenome. The composition of oral bacteria also varies across different individuals, and it would become possible to analyze what change occurs in the human body depending on the activity of bacteria living in the oral cavity and what causality it has with diseases. Identification, isolation, metabolism, and presence of functional genes of microorganisms are being identified for correlation analysis based on oral microbial genome sequencing. For precise diagnosis and treatment of diseases based on microbiome, greater effort is needed for finding not only the causative microorganisms, but also indicators at gene level. Up to now, oral microbial studies have mostly involved metagenomics, but if metatranscriptomic, metaproteomic, and metabolomic approaches can be taken together for assessment of microbial genes and proteins that are expressed under specific conditions, then doing so can be more helpful for gaining comprehensive understanding.

• Journal of Life Science
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• v.34 no.7
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• pp.453-464
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• 2024

The fermentation of ganjang is known to be greatly influenced by the microbial communities derived from its primary ingredients, meju and sea salt. This study investigated the effects of changes in meju size on the distribution and correlation of microbial communities in ganjang fermentation, to enhance its fermentation process. Ganjang was prepared using whole meju and meju divided into thirds, and samples were collected at 7-day intervals over a period of 28 days for microbial community analysis based on 16S rRNA gene sequencing. At the genus level, during fermentation, ganjang made with whole meju exhibited a dominance of Chromohalobacter (day 7), Pediococcus (day 14), Bacillus (day 21), and Pediococcus (day 28), whereas ganjang made with meju divided into thirds consistently showed a Pediococcus predominance over the 28 days. Beta-diversity analysis of microbial communities in ganjang with different meju sizes revealed significant separation of microbial communities at fermentation days 7 and 14 but not at days 21 and 28 across all experimental groups. The linear discriminant analysis effect size (LEfSe) was determined to identify biomarkers contributing to microbial community differences at days 7 and 14, showing that on day 7, potentially halophilic microbes such as Gammaproteobacteria, Firmicutes, Oceanospirillales, Halomonadaceae, Bacilli, and Chromohalobacter were prominent, whereas on day 14, lactic acid bacteria such as Pediococcus acidilactici, Lactobacillaceae, Pediococcus, Bacilli, Leuconostocaceae, and Weissella were predominant. Furthermore, correlation analysis of microbial communities at the genus and species levels revealed differences in correlation patterns between meju sizes, suggesting that meju size may influence microbial interactions within ganjang.

• Korean Journal of Soil Science and Fertilizer
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• v.44 no.1
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• pp.127-145
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• 2011

Various environmental ecosystems are valuable sources for microbial ecology studies, and their analyses using recently developed molecular ecological approaches have drawn significant attention within the scientific community. Changes in the microbial community structures due to various anthropogenic activities can be evaluated by various culture-independent methods e.g. ARISA, DGGE, SSCP, T-RFLP, clone library, pyrosequencing, etc. Direct amplification of total community DNA and amplification of most conserved region (16S rRNA) are common initial steps, followed by either fingerprinting or sequencing analysis. Fingerprinting methods are relatively quicker than sequencing analysis in evaluating the changes in the microbial community. Being an efficient, sensitive and time- and cost effective method, T-RFLP is regularly used by many researchers to access the microbial diversity. Among various fingerprinting methods T-RFLP became an important tool in studying the microbial community structure because of its sensitivity and reproducibility. In this present review, we will discuss the important developments in T-RFLP methodology to distinguish the total microbial diversity and community composition in the various ecosystems.

• Proceedings of the PSK Conference
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• 2002.04a
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• pp.94-95
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• 2002

• 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.

• Korean Journal of Environmental Agriculture
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• v.38 no.3
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• pp.185-196
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• 2019

BACKGROUND: This study investigated the effects of rice genetically modified to be resistant against rice blast and rice bacterial blight on the soil microbial community. A comparative analysis of the effects of rice genetically modified rice choline kinase (OsCK1) gene for disease resistance (GM rice) and the Nakdong parental cultivar (non-GM rice) on the soil microbial community at each stage was conducted using rhizosphere soil of the OsCK1 and Nakdong rice. METHODS AND RESULTS: The soil chemistry at each growth stage and the bacterial and fungal population densities were analyzed. Soil DNA was extracted from the samples, and the microbial community structures of the two soils were analyzed by pyrosequencing. No significant differences were observed in the soil chemistry and microbial population density between the two soils. The taxonomic analysis showed that Chloroflexi, Proteobacteria, Firmicutes, Actinobacteria, and Acidobacteria were present in all soils as the major phyla. Although the source tracking analysis per phylogenetic rank revealed that there were differences in the bacteria between the GM and non-GM soil as well as among the cultivation stages, the GM and non-GM soil were grouped according to the growth stages in the UPGMA dendrogram analysis. CONCLUSION: The difference in bacterial distributions between Nakdong and OsCK1 rice soils at each phylogenetic level detected in microbial community analysis by pyrosequencing may be due to the genetic modification done on GM rice or due to heterogeneity of the soil environment. In order to clarify this, it is necessary to analyze changes in root exudates along with the expression of transgene. A more detailed study involving additional multilateral soil analyses is required.

• Environmental Engineering Research
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• v.12 no.5
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• pp.231-237
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• 2007

The microbial eco-physiology has been the vital key of microbial ecological research. Unfortunately, available methods for direct identity of microorganisms and for the investigation of their activity in complicated community dynamics are limited. In this study, metagenomics was considered as a promising functional genomics tool for improving our understanding of microbial eco-physiology. Its potential applications and challenges were also reviewed. Because of tremendous diversity in microbial populations in environment, sequence analysis for whole metagenomic libraries from environmental samples seems to be unrealistic to most of environmental engineering researchers. When a target function is of interest, however, sequence analysis for whole metagenomic libraries would not be necessary. For this case, nucleic acids of active populations of interest can be selectively gained using another cutting-edge functional genomic tool, SIP (stable isotope probing) technique. If functional genomes isolated by SIP can be transferred into metagenomic library, sequence analysis for such selected functional genomes would be feasible because the reduced size of clone library may become adequate for sequencing analysis. Herein, integration of metagenomics with SIP was suggested as a novel functional genomics approach to study microbial eco-physiology in environment.

• Korean Journal of Soil Science and Fertilizer
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• v.46 no.6
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• pp.474-481
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• 2013

Understanding the microbial community structure of agricultural soils is important for better soil management in order to improve soil quality. Phospholipid fatty acid analysis has been popularly used in determining the microbial community structure in different ecosystems. The microbial community structure of paddy soil under long-term fertilizer treatments was investigated after 45 years using PLFA analysis. Treatments were control (no fertilization, Con), compost (COM), NPK, NPK+compost (NPKC), PK, NK, and NP. Soil chemical properties were mainly affected by the addition of compost and inorganic P fertilizer. Total nitrogen and organic matter contents were significantly higher in treatments with compost while available $P_2O_5$ and exchangeable calcium were significantly higher in treatments with added inorganic P fertilizer. It was found that microbial communities were responsive to the different fertilizer treatments. PLFA results showed that the soils were dominated by gram-negative bacteria, followed by the actinomycetes, then gram-positive bacteria, and fungi. Principal component analysis of the soil chemical properties and PLFA composition proved to be a more reliable tool because it was more responsive to the changes in soil chemical properties.