• Title, Summary, Keyword: Microbial ecology

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Microbial Community Analysis using RDP II (Ribosomal Database Project II):Methods, Tools and New Advances

  • Cardenas, Erick;Cole, James R.;Tiedje, James M.;Park, Joon-Hong
    • 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.

Next-generation approaches to the microbial ecology of food fermentations

  • Bokulich, Nicholas A.;Mills, David A.
    • BMB Reports
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    • v.45 no.7
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    • pp.377-389
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    • 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.

Application of Recent DNA/RNA-based Techniques in Rumen Ecology

  • McSweeney, C.S.;Denman, S.E.;Wright, A.-D.G.;Yu, Z.
    • 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.

Influence of Mucor mucedo immobilized to corncob in remediation of pyrene contaminated agricultural soil

  • Hou, Wei;Zhang, Le;Li, Xiaojun;Gong, Zongqiang;Yang, Yongwei;Li, Zhi
    • Environmental Engineering Research
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    • v.20 no.2
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    • pp.149-154
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    • 2015
  • In recent years, immobilization agents were introduced into organic contaminated soil remediation and more and more materials were screened and used as the immobilizing carrier. However, effect of the decomposition of the immobilizing carrier on the bioremediation was rarely concerned. Therefore, the decomposition experiment of immobilizing carrier -corncob was carried out in the lab with the efficient degradation fungi - Mucor mucedo (MU) existing, and polycyclic aromatic hydrocarbons (PAHs) residues E4/E6 of the dissolved organic matter and microbial diversity during the decomposition process were studied. The results showed that: a) during the decomposition, the degradation of pyrene (Pyr) was mainly in the first 28 d in which the content of extractable Pyr decreased rapidly and the highest decrease was in the treatment with only MU added. b) Anslysis of E4/E6 changes showed that rich microorganisms could promote aromatization and condensation of humus. c) From the diversity index analysis it can also be seen that there is no significant difference in effects of PAHs on the uniformity of microorganisms. These results will not only be useful to have a better understanding of the bioavailability of contaminants adsorbed to biodegradable carriers in PAHs contaminated soil remediation, but also be helpful to perfect the principle of immobilized microbial technique.

Application of Amplicon Pyrosequencing in Soil Microbial Ecology (토양미생물 생태 연구를 위한 증폭 파이로시퀀싱 기법의 응용)

  • Ahn, Jae-Hyung;Kim, Byung-Yong;Kim, Dae-Hoon;Song, Jaekyeong;Weon, Hang-Yeon
    • Korean Journal of Soil Science and Fertilizer
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    • v.45 no.6
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    • pp.1073-1085
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    • 2012
  • Soil microbial communities are immensely diverse and complex with respect to species richness and community size. These communities play essential roles in agricultural soil because they are responsible for most of the nutrient cycles in the soil and influence the plant diversity and productivity. However, the majority of these microbes remain uncharacterized because of poor culturability. Next-generation sequencing techniques have revolutionized many areas of biology by providing cheaper and faster alternatives to Sanger sequencing. Among them, amplicon pyrosequencing is a powerful tool developed by 454 Life Sciences for assessing the diversity of complex microbial communities by sequencing PCR products or amplicons. This review summarizes the current opinions in amplicon sequencing of soil microbial communities, and provides practical guidance and advice on sequence quality control, aligning, clustering, OTU- and taxon-based analysis. The last section of this article includes a few representative studies conducted using amplicon pyrosequencing.

Seasonal and Spatial Diversity of Picocyanobacteria Community in the Great Mazurian Lakes Derived from DGGE Analyses of 16S rDNA and cpcBA-IGS Markers

  • Jasser, Iwona;Krolicka, Adriana;Jakubiec, Katarzyna;Chrost, Ryszard J.
    • Journal of Microbiology and Biotechnology
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    • v.23 no.6
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    • pp.739-749
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    • 2013
  • The seasonal and spatial diversity of picocyanobacteria (Pcy) in lakes of the Great Mazurian Lakes (GLM) system was examined by DGGE analysis of molecular markers derived from the 16S-23S internal transcribed spacer (ITS) of the ribosomal operon and the phycocyanin operon (cpcBA-IGS). The study of nine lakes, ranging from mesotrophy to hypereutrophy, demonstrated seasonal variance of Pcy. The richness and Shannon diversity index calculated on the basis of both markers were higher in spring and lower in early and late summer. No statistically significant relationships were found between the markers and trophic status of the studied lakes or Pcy abundance. There were, however, statistically significant relationships between the diversity indices and sampling time. The analysis pointed to a different distribution of the two markers. The ITS marker exhibited more unique sequences in time and space, whereas a greater role for common and ubiquitous sequences was indicated by the cpcBA-IGS data. Examination of the Pcy community structure demonstrated that communities were grouped in highly similar clusters according to sampling season/time rather than to the trophic status of the lake. Our results suggest that time is more important than trophic status in shaping the diversity and structure of Pcy communities. The seasonal changes in picocyanobacteria and differences in diversity and community structures are discussed in the context of well-established ecological hypotheses: the PEG model, intermediate disturbance hypothesis (IDH), and horizontal gene transfer (HGT).

The Effect Estimation of Heavy Metals on the Microbial Activity during Leaf Litter Decomposition (낙엽분해동안 미생물 활성에 미치는 중금속의 영향 추정)

  • Shim, Jae-Kuk;Shin, Jin-Ho;Yang, Keum-Chul
    • Korean Journal of Environment and Ecology
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    • v.25 no.6
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    • pp.887-892
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    • 2011
  • This study was to find out influence of heavy metal concentration in plant on microbial activities during decomposition of Artenmisia princeps var. orientalis and Equisetum arvense collected from an abandoned mine and control site in Cheongyang-gun Chungcheongnam-do. Microbial respiration rate showed the highest value at the time of the first collection, and then tended to decline over time. The highest microbial respiration rate appeared in leaf litters with low heavy metal contents, and A. princeps var. orientalis and E. arvense collected and decomposed at the control site showed the fastest decomposition rate. For both A. princeps var. orientalis and E. arvense, litters with low heavy metal content appeared to have higher microbial biomass. There was apparent quantitative correlation between decomposition rate and cumulative respiration rate of leaf litters, and between decomposition rate and microbial biomass of leaf litters. Thus, the study result showed that leaf litter with higher heavy metal content had a negative impacts on the growth and activity of microbial decomposer during decomposition processes.