• Korean Journal of Environmental Agriculture
• /
• v.41 no.4
• /
• pp.335-343
• /
• 2022

BACKGROUND: Antibiotics used in animal husbandry for disease prevention and treatment have resulted in the rapid progression of antibiotic resistant bacteria which can be introduced into the environment through livestock feces/manure, disseminating antibiotic resistant genes (ARGs). In this study, fecal samples were collected from the livestock farms located in Jeju Island to investigate the relationship between microbial communities and ARGs. METHODS AND RESULTS: Illumina MiSeq sequencing was applied to characterize microbial communities within each fecal sample. Using quantitative PCR (qPCR), ten ARGs encoding tetracycline resistance (tetB, tetM), sulfonamide resistance (sul1, sul2), fluoroquinolone resistance (qnrD, qnrS), fluoroquinolone and aminoglycoside resistance (aac(6')-Ib), beta-lactam resistance (bla_TEM, bla_CTX-M), macrolide resistance (ermC), a class 1 integronsintegrase gene (intI1), and a class 2 integrons-integrase gene (intI2) were quantified. The results showed that Firmicutes and Bacteroidetes were dominant in human, cow, horse, and pig groups, while Firmicutes and Actinobacteria were dominant in chicken group. Among ARGs, tetM was detected with the highest number of copies, followed by sul1 and sul2. Most of the genera belonging to Firmicutes showed positive correlations with ARGs and integron genes. There were 97, 34, 31, 25, and 22 genera in chicken, cow, pig, human, and horse respectively which showed positive correlations with ARGs and integron genes. In network analysis, we identified diversity of microbial communities which correlated with ARGs and integron genes. CONCLUSION(S): In this study, antibiotic resistance patterns in human and livestock fecal samples were identified. The abundance of ARGs and integron genes detected in the samples were associated with the amount of antibiotics commonly used for human and livestocks. We found diverse microbial communities associated with antibiotics resistance genes in different hosts, suggesting that antibiotics resistance can disseminate across environments through various routes. Identifying the routes of ARG dissemination in the environment would be the first step to overcome the challenge of antibiotic resistance in the future.

• Journal of Microbiology and Biotechnology
• /
• v.29 no.4
• /
• pp.633-644
• /
• 2019

An advanced anaerobic expanded granular sludge bed (AnaEG) and an internal circulation (IC) reactor, which were adopted to treat starch processing wastewater (SPW) and ethanol processing wastewater (EPW), were comprehensively analyzed to determine the key factors that affected the granules and microbial communities in the bioreactors. The granule size of $900{\mu}m$ in the AnaEG reactor was smaller than that in the IC reactor, and the internal and external morphological structures of the granular sludge were also significantly different between the two types of reactors. The biodiversity, which was higher in the AnaEG reactor, was mainly affected by reactor type. However, the specific microbial community structure was determined by the type of wastewater. Furthermore, the dominant methanogens of EPW were mainly Methanosaeta and Methanobacterium, but only Methanosaeta was a major constituent in SPW. Compared with the IC reactor, characteristics common to the AnaEG reactor were smaller granules, higher biodiversity and larger proportion of unknown species. The comparison of characteristics between these two reactors not only aids in understanding the novel AnaEG reactor type, but also elucidates the effects of reactor type and wastewater type on the microbial community and sludge structure. This information would be helpful in the application of the novel AnaEG reactor.

• Research in Plant Disease
• /
• v.26 no.4
• /
• pp.202-209
• /
• 2020

Organic farming is necessary to sustainable agriculture, preserve biodiversity and continued growth the sector in agriculture. In organic farming, reduced usage of chemical agents that adversely affect human health and environment, employing amino acids and oil cake fertilizer, plant extracts, and microbial agents are used to provide safe agricultural products to consumers. To investigation microbiome structure, we proceeded on the pepper plant with difference fertilizers and treatments in organic agriculture for three years. The microbial communities were analyzed by the next generation sequencing approach. Difference soil microbiota communities were discovered base on organic fertilizer agents. Occurrences of virus and anthracnose diseases had a low incidence in conventional farming, whereas bacteria wilt disease had a low incidence in microbial agents treated plots. Microbe agents, which applied in soil, were detected in the microbial community and the funding suggested the applied microbes successfully colonized in the organic farming environment.

• Korean Journal of Soil Science and Fertilizer
• /
• v.44 no.1
• /
• pp.118-126
• /
• 2011

Ester-linked fatty acid methyl ester (EL-FAME) profiles were used to describe differences in soil microbial communities influenced by conventional farming system (CFS), and organic farming system (OFS) in controlled horticultural land. Soil physicochemical properties and soil microbial communities were determined in the experimental fields. Higher organic matter content in OFS reduced soil bulk density which in turn increased the soil porosity. Generally, soil chemical properties in OFS were higher than those of CFS, but EC value in OFS was significantly lower than that of CFS. With the exception of Fe content, other macronutrient contents and pH in both farming system decreased with the soil depth. Soil microbial biomass of OFS was approximately 1.3 times in topsoil and 1.8 times in subsoil higher than those of CFS. Lower ratios of cy17:0 to $16:1{\omega}7c$ and cy19:0 to $18:1{\omega}7c$ were found in the CFS soils than the OFS soils, indicating that microbial stress decreased. The ratio of MUFA to SFA was higher in OFS due to organic input to the soil. In principal components analysis (PCA), the first variable accounted for 54.3%, while the second for 27.3%, respectively. The PC1 of the PCA separated the samples from CFS and OFS, while the PC2 of the PCA separated the samples from topsoil and subsoil. EL-FAMEs with the positive eigenvector coefficients for PC1 were cy17: 0 to $16:1{\omega}7c$ ratio, cy19:0 to $18:1{\omega}7c$ ratio, soil pH, soil organic matter, and soil $NO_3$-N content. Our findings suggest that the shifting cy19:0 to $18:1{\omega}7c$ ratio should be considered as potential factors responsible for the clear microbial community differentiation observed between different cultivation systems and soil depth in controlled horticultural land.

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

• The Plant Pathology Journal
• /
• v.37 no.4
• /
• pp.396-403
• /
• 2021

Fire blight disease, caused by Erwinia amylovora, could damage rosaceous plants such as apples, pears, and raspberries. In this study, we designed to understand how E. amylovora affected other bacterial communities on apple rhizosphere; twig and fruit endosphere; and leaf, and fruit episphere. Limited studies on the understanding of the microbial community of apples and changes the community structure by occurrence of the fire blight disease were conducted. As result of these experiments, the infected trees had low species richness and operational taxonomic unit diversity when compared to healthy trees. Rhizospheric bacterial communities were stable regardless of infection. But the communities in endosphere and episphere were significanlty affected by E. amylovora infection. We also found that several metabolic pathways differ significantly between infected and healthy trees. In particular, we observed differences in sugar metabolites. The finding provides that sucrose metabolites are important for colonization of E. amylovora in host tissue. Our results provide fundamental information on the microbial community structures between E. amylovora infected and uninfected trees, which will contribute to developing novel control strategies for the fire blight disease.

• Korean Journal of Environmental Biology
• /
• v.17 no.3
• /
• pp.279-284
• /
• 1999

To investigate soil bacterial diversity according to vegetation types, directly extracted DNA from 5 different soils were cross-hybridized with each other as a probe and target. Pinus densiflora soil was shown the highest value then agricultured soil＞naked soil＞grass soil＞Quercus mongolicas soil in the order of diversity. Cluster analysis by similarity showed that soil microbial communities were categorized into three groups.

• The Plant Pathology Journal
• /
• v.39 no.4
• /
• pp.397-408
• /
• 2023

Fire blight disease, caused by Erwinia amylovora, is a devastating affliction in apple cultivation worldwide. Chemical pesticides have exhibited limited effectiveness in controlling the disease, and biological control options for treating fruit trees are limited. Therefore, a relatively large-scale survey is necessary to develop microbial agents for apple trees. Here we collected healthy apple trees from across the country to identify common and core bacterial taxa. We analyzed the endophytic bacterial communities in leaves and twigs and discovered that the twig bacterial communities were more conserved than those in the leaves, regardless of the origin of the sample. This finding indicates that specific endophytic taxa are consistently present in healthy apple trees and may be involved in vital functions such as disease prevention and growth. Furthermore, we compared the community metabolite pathway expression rates of these endophyte communities with those of E. amylovora infected apple trees and discovered that the endophyte communities in healthy apple trees not only had similar community structures but also similar metabolite pathway expression rates. Additionally, Pseudomonas and Methylobacterium-Methylorobrum were the dominant taxa in all healthy apple trees. Our findings provide valuable insights into the potential roles of endophytes in healthy apple trees and inform the development of strategies for enhancing apple growth and resilience. Moreover, the similarity in cluster structure and pathway analysis between healthy orchards was mutually reinforcing, demonstrating the power of microbiome analysis as a tool for identifying factors that contribute to plant health.

• Journal of Microbiology and Biotechnology
• /
• v.26 no.4
• /
• pp.757-762
• /
• 2016

The group of Fe(III) oxide-reducing bacteria includes exoelectrogenic bacteria, and they possess similar properties of transferring electrons to extracellular insoluble-electron acceptors. The exoelectrogenic bacteria can use the anode in microbial fuel cells (MFCs) as the terminal electron acceptor in anaerobic acetate oxidation. In the present study, the anodic community was compared with the community using Fe(III) oxide (ferrihydrite) as the electron acceptor coupled with acetate oxidation. To precisely analyze the structures, the community was established by enrichment cultures using the same inoculum used for the MFCs. High-throughput sequencing of the 16S rRNA gene revealed considerable differences between the structure of the anodic communities and that of the Fe(III) oxide-reducing community. Geobacter species were predominantly detected (>46%) in the anodic communities. In contrast, Pseudomonas (70%) and Desulfosporosinus (16%) were predominant in the Fe(III) oxide-reducing community. These results demonstrated that Geobacter species are the most specialized among Fe(III)-reducing bacteria for electron transfer to the anode in MFCs. In addition, the present study indicates the presence of a novel lineage of bacteria in the genus Pseudomonas that highly prefers ferrihydrite as the terminal electron acceptor in acetate oxidation.

• BMB Reports
• /
• v.45 no.7
• /
• pp.377-389
• /
• 2012

Food fermentations have enhanced human health since the dawn of time and remain a prevalent means of food processing and preservation. Due to their cultural and nutritional importance, many of these foods have been studied in detail using molecular tools, leading to enhancements in quality and safety. Furthermore, recent advances in high-throughput sequencing technology are revolutionizing the study of food microbial ecology, deepening insight into complex fermentation systems. This review provides insight into novel applications of select molecular techniques, particularly next-generation sequencing technology, for analysis of microbial communities in fermented foods. We present a guideline for integrated molecular analysis of food microbial ecology and a starting point for implementing next-generation analysis of food systems.