DOCSLIB.ORG

Taxonomic and Environmental Annotation of Bacterial 16S Rrna Gene Sequences Via Shannon Entropy and Database Metadata Terms A

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Taxonomic and Environmental Annotation of Bacterial 16S Rrna Gene Sequences Via Shannon Entropy and Database Metadata Terms A Taxonomic and Environmental Annotation of Bacterial 16S rRNA gene sequences via Shannon Entropy and Database Metadata Terms by Ali Zeeshan Ijaz Hawkesbury Institute for the Environment Western Sydney University, Australia Thesis submitted: February 2017 A thesis submitted for fulfilment of the requirements of the degree of Doctor of Philosophy Dedication I would like to dedicate my thesis to my beloved grandfather, Iqbal Ahmad and my elder sister Sidrah Ijaz, who have taught me to work hard for the things that I aspire to achieve. Thank you for your support along the way. Acknowledgements I am greatly indebted to my PhD supervisor, Prof. Brajesh Singh and co-supervisor Dr. Christopher Quince for identifying and streamlining the research to be undertaken for the completion of my PhD at Hawkesbury Institute for the Environment, Western Sydney University. Their professional competence, supervision and continued support in all areas of personal and professional interest have been paramount towards completion of my studies with zeal and enthusiasm. All along I have had the opportunity to interact and enjoy the able guidance and support of other professional and competent people, with the foremost being Dr. Thomas Jeffries, to whom I extend my special thanks for his unending patience and time devotion to keep me on track and encouragement that made it possible to complete my studies. His competence and grasp of knowledge facilitated an environment that made it possible to perform my research in the right direction. I would also like to thank Jasmine Grinyer for her support in various aspects of paperwork. Lastly, I would like to thank my family for being extremely understanding and supportive all along the study period, including my brother Dr. Umer Zeeshan Ijaz, a Research fellow at University of Glasgow. Their support and encouragement gave me the resolve to complete my PhD while being under a serious ailment. Statement of Authentication The work presented in this thesis is, to the best of my knowledge and belief, original except as acknowledged in the text. It contains no material previously published or written by another person. I hereby declare that I have not submitted this material, either in full or in part, for a degree at this or any other institute. Signed Ali Zeeshan Ijaz 1st June 2018 Table of Contents Table of Contents ..................................................................................................................................... i List of Tables ........................................................................................................................................... iii List of Figures ........................................................................................................................................ vii List of Abbreviations ........................................................................................................................... xi Abstract..................................................................................................................................................... xii Chapter 1: General Introduction ................................................................................................... 1 1.1 Importance of Microbial Community Analysis ....................................................... 1 1.2 Taxonomic Annotation using Conserved Marker Genes .................................... 2 1.3 Environmental Annotation of Sequences ................................................................ 16 1.4 Knowledge Gaps................................................................................................................... 19 1.5 Aims and Objectives ........................................................................................................... 22 Chapter 2: Exploiting The Evolutionary Conservation of 16S rRNA Gene via Shannon Entropy ................................................................................................................................. 25 2.1 Introduction ........................................................................................................................... 25 2.2 Materials and Methods ..................................................................................................... 30 2.3 Results ...................................................................................................................................... 52 2.4 Discussion ............................................................................................................................... 60 2.5 Conclusion .............................................................................................................................. 64 Chapter 3: TaxaSE: Taxonomic Annotation via Shannon Entropy .............................. 66 3.1 Introduction ........................................................................................................................... 66 3.2 Materials and Methods ..................................................................................................... 72 3.3 Results ...................................................................................................................................... 82 3.4 Discussion ............................................................................................................................ 104 i 3.5 Conclusion ........................................................................................................................... 108 Chapter 4: Assigning Environmental Terms to Sequences using SEQenv ........... 110 4.1 Introduction ........................................................................................................................ 110 4.2 Materials and Methods .................................................................................................. 115 4.3 Results ................................................................................................................................... 127 4.4 Discussion ............................................................................................................................ 144 4.5 Conclusion ........................................................................................................................... 152 Chapter 5: Final Conclusion and Future Work .................................................................. 154 5.1 Conclusion ........................................................................................................................... 154 5.2 Future work ........................................................................................................................ 157 Appendix A. ......................................................................................................................................... 159 References ............................................................................................................................................ 189 ii List of Tables Table 2-1: Database as a m x n matrix where rows are sequences and columns represent alignment positions ............................................................................................ 32 Table 2-2: List of thresholds between 0 and 1 used for calculation of precision and recall ........................................................................................................................................ 42 Table 2-3: List of taxa removed at genus, family and class level from SILVA database.......................................................................................................................................... 45 Table 2-4: List of tools and scripts............................................................................................... 48 Table 2-5: Area under the curve for whole SILVA dataset based validation for both the percentage identity and Shannon entropy approach ............................ 53 Table 2-6: Area under the curve for removal of genera based validation for both percentage identity and Shannon entropy approach ............................................... 54 Table 2-7: Area under the curve for removal of families based validation for both percentage identity and Shannon entropy approach ............................................... 56 Table 2-8: Area under the curve for removal of class based validation for both percentage identity and Shannon entropy approach ............................................... 57 Table 3-1: Lists of tools and scripts developed for the TaxaSE pipeline. .................. 73 Table 3-2: Sample data used for real amplicon dataset analysis .................................. 75 Table 3-3: Thresholds selected for the TaxaSE system at different taxa levels ..... 79 Table 3-4: ADONIS results for OTU comparison at 97% similarity between TaxaSE and QIIME ..................................................................................................................... 89 Table 3-5: ANOSIM results for OTU comparison at 97% similarity between TaxaSE and QIIME ..................................................................................................................... 90 iii Table 3-6: ADONIS results for distinct taxonomic annotation comparison between TaxaSE, QIIME at 99% OTU similarity and QIIME at 97% OTU similarity ..................................................................................................................................... 102
Load more

Recommended publications
  • Managing Midas
    Managing MIDAs Managing MIDAs Harmonising the management of Multi-Internationally Designated Areas: Ramsar Sites, World Heritage sites, Biosphere Reserves and UNESCO Global Geoparks Thomas Schaaf and Diana Clamote Rodrigues INTERNATIONAL UNION FOR CONSERVATION OF NATURE WORLD HEADQUARTERS Rue Mauverney 28 1196 Gland, Switzerland Tel +41 22 999 0000 Fax +41 22 999 0002 www.iucn.org IUCN IUCN (International Union for Conservation of Nature) IUCN is a membership Union composed of both government and civil society organisations. It harnesses the experience, resources and reach of its more than 1,300 Member organisations and the input of more than 16,000 experts. IUCN is the global authority on the status of the natural world and the measures needed to safeguard it. www.iucn.org Ramsar Convention The Convention on Wetlands, called the Ramsar Convention, is an intergovernmental treaty that provides the framework for national action and international cooperation for the conservation and wise use of wetlands and their resources. Its mission is “the conservation and wise use of all wetlands through local and national actions and international cooperation, as a contribution towards achieving sustainable development throughout the world”. Under the “three pillars” of the Convention, the Contracting Parties commit to: work towards the wise use of all their wetlands; designate suitable wetlands for the list of Wetlands of International Importance (the “Ramsar List”) and ensure their effective management; and cooperate internationally on transboundary wetlands, shared wetland systems and shared species. www.ramsar.org NIO M O UN IM D R T IA A L • World Heritage Convention P • W L O A I R D L D N H O E M R I E TA IN G O The 1972 Convention concerning the Protection of the World Cultural and Natural Heritage recognises that certain E • PATRIM United Nations World Educational, Scientific and Heritage places on Earth are of “outstanding universal value” and should form part of the common heritage of humankind.
    [Show full text]
  • The Archaea Community Associated with Lava-Formed Gotjawal Forest Soil in Jeju, Korea
    Journal of Agricultural Chemistry and Environment, 2014, 3, 96-102 Published Online August 2014 in SciRes. http://www.scirp.org/journal/jacen http://dx.doi.org/10.4236/jacen.2014.33012 The Archaea Community Associated with Lava-Formed Gotjawal Forest Soil in Jeju, Korea Jong-Shik Kim1*, Man-Young Jung2, Keun Chul Lee3, Dae-Shin Kim4, Suk-Hyung Ko4, Jung-Sook Lee3, Sung-Keun Rhee2 1Gyeongbuk Institute for Marine Bioindustry, Uljin, Republic of Korea 2Department of Microbiology, Chungbuk National University, Cheongju, Republic of Korea 3Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea 4Research Institute for Hallasan, Jeju, Republic of Korea Email: *[email protected] Received 22 April 2014; revised 27 May 2014; accepted 23 June 2014 Copyright © 2014 by authors and Scientific Research Publishing Inc. This work is licensed under the Creative Commons Attribution International License (CC BY). http://creativecommons.org/licenses/by/4.0/ Abstract The abundance and diversity of archaeal assemblages were analyzed in soils collected from Gyo- rae Gotjawal forest, Jeju, Korea. Gotjawal soil refers to soil derived from a lava-formed forest, cha- racterized by high organic matter content, fertility, and poor rocky soil. Using domain-specific primers, archaeal 16S rRNA gene sequences were PCR amplified for clone library construction, and a total of 185 archaeal clones were examined. The archaeal clones were affiliated with the phyla Thaumarchaeota (96.2%) and Euryarchaeota (3.8%). The most abundant thaumarchaeal group (90.3% of the clones) was the group I.1b clade, which includes soil ammonia-oxidizing arc- haea. The unique characteristics of Gotjawal soil, including basalt morphology, vegetation, and groundwater aquifer penetration, may be reflected in the archaeal community composition.
    [Show full text]
  • Benefit What Is the JEJU MICE CARD? JEJU MICE CARD란?
    Benefit What is the JEJU MICE CARD? JEJU MICE CARD란? JEJU MICE CARD is a trans portation card that makes it easy to use bus (including re gular bus, limousine bus, City 12/18 Tour Bus, etc) on Jeju Island. You can comfortably recharge the card at all of theses con venience stores(GS25, Seven Eleven, CU). JEJU MICE CARD offers all card users up to 60% discount and other benefits related to all affiliated company such as various tourist attractions, hotels, restaurants, shopping stores, etc. JEJU MICE 카드는 제주도내 시내·외 버스 및 리무진, 시티투어버스 이용시 교통 카드로 사용가능하며, GS25, 세븐일레븐, CU 편의점에서 결제가능합니다. 또한, 제주도내 관광지, 체험프로그램, 맛집, 호텔 레스토랑 등 다양한 제휴 가맹점에서 최대 60%할인 혜택과 우대서비스를 제공합니다. * It’s charged 5,000 won at first. * 기본 5,000원이 충전되어 있습니다. Transportation card 교통카드 기능 You can use it when you use the transportation. 일반버스 및 리무진, 시티투어 버스 등 버스 이용시 교통카드로 사용 가능합니다. Easy recharging and payment at CVS 편의점에서 충전 및 결제가능 You can recharge it at CVS in Jeju easily. 제주도내 편의점에서 쉽게 충전하여 사용할 수 있습니다. How to Charge 충전방법 Cash recharging only 현금충전만 가능 편의점(CVS) * You can recharge JEJU MICE CARD at CVS(SEVEN ELEVEN, GS25, CU) 제주도내 편의점에서 충전가능합니다. How to use the JEJU MICE card 카드 사용방법 When you use the transportation 대중교통 이용 Touch Payment 단말기 접촉 * Must touch the card to the card reader when get on and get off * 승/하차시 반드시 태그해야 함 Affiliated JEJUPASS member stores DC 제휴 가맹점 할인 Present your card for Discount 제주마이스카드 제시 후 할인 You can get a 10% discount when you show JEJU MICE Card at the stores in ICC JEJU.
    [Show full text]
  • Motions Issued on 8 July 2012
    Congress Document WCC-2012-9.6* Motions Issued on 8 July 2012 World Conservation Congress, Jeju, Republic of Korea 6–15 September 2012 *This document is also submitted for agenda items 1.8, 2.1.6, 3.1.6, 4.1.6 and 6.1.6. Table of Contents Title Categories 001 Strengthening the motions process and enhancing implementation of IUCN Resolutions IUCN Governance 002 Improved opportunity for Member participation in IUCN IUCN Governance 003 Prioritizing IUCN membership awareness and support IUCN Governance 004 Establishment of the Ethics Mechanism IUCN Governance Strengthening of the IUCN National and Regional Committees and the optional use of the 005 three official languages in documents for internal and external communication by IUCN IUCN Governance and its Members Cooperation with regional government authorities in the implementation of the IUCN 006 IUCN Governance Programme 2013–2016 Establishing an Indigenous Peoples’ Organization (IPO) membership and voting category 007 IUCN Governance in IUCN Increasing youth engagement and intergenerational partnership across and through the 008 IUCN Governance Union 009 Encouraging cooperation with faith-based organizations and networks IUCN Governance 010 Establishment of a strengthened institutional presence of IUCN in North-East Asia IUCN Governance 011 Consolidating IUCN’s institutional presence in South America IUCN Governance 012 Strengthening IUCN in the insular Caribbean IUCN Governance 013 IUCN’s name IUCN Governance 014 Implementing Aichi Target 12 of the Strategic Plan for Biodiversity 2011–2020
    [Show full text]
  • Human Influence, Regeneration, and Conservation of the Gotjawal Forests
    Journal of Marine and Island Cultures (2013) 2, 85–92 Journal of Marine and Island Cultures www.sciencedirect.com Human influence, regeneration, and conservation of the Gotjawal forests in Jeju Island, Korea Hong-Gu Kang a,*, Chan-Soo Kim b, Eun-Shik Kim c,* a Department of Forest Resources, Graduate School, Kookmin University, Seoul 136-702, Republic of Korea b Warm-Temperate and Subtropical Forest Research Center, Korea Forest Research Institute, Jeju 697-050, Republic of Korea c Department of Forestry, Environment, and Systems, Kookmin University, Seoul 136-702, Republic of Korea Received 29 October 2013 Available online 5 December 2013 KEYWORDS Abstract Gotjawal, a uniquely formed forest vegetation on the lava terrain located at eastern and Conservation; western parts of Jeju Island, covers 6% of the island’s land surface. The Gotjawal forests play Ecosystem services; important roles in establishing the biological and cultural diversity while maintaining ecosystem ser- Gotjawal forests; vices. Recently, with the recognition of the diverse ecological and cultural values of the Gotjawal Human influence; forests, efforts to conserve the forests were conducted by adopting the resolutions of the Jeju World Jeju Island; Conservation Congress of the IUCN held in 2012. Despite its precious values, the Gotjawal forest is Regeneration being threatened by the developmental activities of large scale constructions projects. To under- stand the recent regeneration of the Gotjawal forests, ecological studies have been conducted at the Hankyeong-Andeok Gotjawal Terrain, which is located in the western part and occupies the largest area of the Gotjawal Terrain of Jeju Island. Major vegetation in the area includes the decid- uous broad-leaved forests (Acer palmatum–Styrax japonicus community), mixed deciduous and evergreen broad-leaved forests (Neolitsea aciculata–Styrax japonicus community), and evergreen broad-leaved forests (Quercus glauca community).
    [Show full text]
  • A Comparison of Computationally Predicted Functional Metagenomes and Microarray Analysis for Microbial P Cycle Genes in a Unique
    F1000Research 2018, 7:179 Last updated: 31 JUL 2021 BRIEF REPORT A comparison of computationally predicted functional metagenomes and microarray analysis for microbial P cycle genes in a unique basalt-soil forest [version 1; peer review: 2 approved] Erick S. LeBrun , Sanghoon Kang Center for Reservoir and Aquatic Systems Research, Department of Biology, Baylor University, Waco, TX, 76798-7388, USA v1 First published: 12 Feb 2018, 7:179 Open Peer Review https://doi.org/10.12688/f1000research.13841.1 Latest published: 12 Feb 2018, 7:179 https://doi.org/10.12688/f1000research.13841.1 Reviewer Status Invited Reviewers Abstract Here we compared microbial results for the same Phosphorus (P) 1 2 biogeochemical cycle genes from a GeoChip microarray and PICRUSt functional predictions from 16S rRNA data for 20 samples in the four version 1 spatially separated Gotjawal forests on Jeju Island in South Korea. The 12 Feb 2018 report report high homogeneity of microbial communities detected at each site allows sites to act as environmental replicates for comparing the two 1. Ye Deng, Chinese Academy of Sciences, different functional analysis methods. We found that while both methods capture the homogeneity of the system, both differed Beijing, China greatly in the total abundance of genes detected, as well as the 2. Joy D Van Nostrand , University of diversity of taxa detected. Additionally, we introduce a more comprehensive functional assay that again captures the homogeneity Oklahoma, Norman, USA of the system but also captures more extensive community gene and taxonomic information and depth. While both methods have their Any reports and responses or comments on the advantages and limitations, PICRUSt appears better suited to asking article can be found at the end of the article.
    [Show full text]
  • Jeju Batdam Agricultural System (Black Stone Fences)
    Jeju Batdam Agricultural System (Black stone fences) JUNE 2013 Jeju Special Self-Governing Province, Republic of Korea Contents □ SUMMARY INFORMATION □ DESCRIPTION OF THE AGRICULTURAL HERITAGE SYSTEM Ⅰ. Characteristics of Jeju Batdam Agricultural System / 3 1. Global (or national) importance 2. Jeju Batdam and securing food and livelihood 3. Biodiversity of Batdam and its ecological functions 4. Knowledge system and adapted technologies of the Jeju Batdam 5. Culture and value systems related to the Jeju Batdam 6. Remarkable landscapes of the Jeju Batdam Ⅱ. Socio-cultural characteristics related to the Jeju Batdam / 37 Ⅲ. History of the Jeju Batdam / 41 Ⅳ. Contemporary meanings of the Jeju Batdam / 44 Ⅴ. Threats and challenges Jeju Batdam faces / 46 Ⅵ. Efforts to preserve the Jeju Batdam / 47 Ⅶ. Action plans to preserve and utilize the Jeju Batdam / 52 Annex - List of Important Species / 55 □ Summery Information 1. Candidate's ･Jeju Batdam Agricultural system name 2. Applicant ･ Jeju Special Self-Governing Province ･ Ministry of Agriculture, Food & Rural Affairs, Republic of Korea 3. Supporting ･ Federation of Jeju Farmers Organization organization ･ Jeju Development Institute ･Dry-field farming areas in Jeju, around the core and buffer zones - 90km south from the Korean peninsula, connecting the continent (Russia, China) and the ocean (Japan, South Asia) - world-class resort and tourist destination with beautiful nature - 126°08´~126°58´E, 33°06´~34°00´N 4. Location ･ the southernmost administrative district in Korea, an island, accessible by boat or aircraft 5. Access - 1hr flight : Jeju ⇒ Seoul, Jeju ⇒ Shanghai, China - 2hr flight : Jeju ⇒ Tokyo, Japan 6. Area ･ 541.9 ㎢ ･ citrus orchards, dried-field farming crops(potato, carrot, garlic, white 7.
    [Show full text]
  • Sex Ratios and Spatial Structure of the Dioecious Tree Torreya Nucifera in Jeju Island, Korea
    Research Paper J. Ecol. Field Biol. 35(2): 111-122, 2012 Journal of Ecology and Field Biology Sex ratios and spatial structure of the dioecious tree Torreya nucifera in Jeju Island, Korea Hyesoon Kang1,* and Sookyung Shin1,2 1School of Biological Science and Chemistry, Sungshin Women’s University, Seoul 142-732, Korea 2Present address: Division of Forest Genetic Resources, Korea Forest Research Institute, Suwon 441-847, Korea Abstract The sex ratio and spatial structure of different sexes are major components that affect the reproductive success and pop- ulation persistence of dioecious plants. The differential reproductive costs between male and female plants are often believed to cause a biased sex ratio and spatial segregation of the sexes through slower growth and/or lower female sur- vivorship. In this study, we examined the sex ratio and spatial structure of one population of Torreya nucifera trees in Jeju Island, Korea. We also tested the effects of the current tending actions in relation to tree vitality. At the population level, the sex ratio of the 2,861 trees was significantly biased toward males; however, it also showed considerable variation among different diameter at breast height classes and across habitats according to terrain level (from upper to lower). In 1999, before tree management (tending) began, among the ecological traits examined, only climber coverage correlated with tree vitality. Intensive tending such as climber removal since 1999 clearly enhanced the vitality of the majority of trees, but its effects were more conspicuous in medium-sized trees than in small ones, in upper terrain trees than those in other terrains, and in females than in males.
    [Show full text]
  • Human Influence, Regeneration, and Conservation of the Gotjawal Forests in Jeju Island, Korea
    Journal of Marine and Island Cultures (2013) 2, 85–92 Journal of Marine and Island Cultures www.sciencedirect.com Human influence, regeneration, and conservation of the Gotjawal forests in Jeju Island, Korea Hong-Gu Kang a,*, Chan-Soo Kim b, Eun-Shik Kim c,* a Department of Forest Resources, Graduate School, Kookmin University, Seoul 136-702, Republic of Korea b Warm-Temperate and Subtropical Forest Research Center, Korea Forest Research Institute, Jeju 697-050, Republic of Korea c Department of Forestry, Environment, and Systems, Kookmin University, Seoul 136-702, Republic of Korea Received 29 October 2013 Available online 5 December 2013 KEYWORDS Abstract Gotjawal, a uniquely formed forest vegetation on the lava terrain located at eastern and Conservation; western parts of Jeju Island, covers 6% of the island’s land surface. The Gotjawal forests play Ecosystem services; important roles in establishing the biological and cultural diversity while maintaining ecosystem ser- Gotjawal forests; vices. Recently, with the recognition of the diverse ecological and cultural values of the Gotjawal Human influence; forests, efforts to conserve the forests were conducted by adopting the resolutions of the Jeju World Jeju Island; Conservation Congress of the IUCN held in 2012. Despite its precious values, the Gotjawal forest is Regeneration being threatened by the developmental activities of large scale constructions projects. To under- stand the recent regeneration of the Gotjawal forests, ecological studies have been conducted at the Hankyeong-Andeok Gotjawal Terrain, which is located in the western part and occupies the largest area of the Gotjawal Terrain of Jeju Island. Major vegetation in the area includes the decid- uous broad-leaved forests (Acer palmatum–Styrax japonicus community), mixed deciduous and evergreen broad-leaved forests (Neolitsea aciculata–Styrax japonicus community), and evergreen broad-leaved forests (Quercus glauca community).
    [Show full text]
  • Download From
    Information Sheet on Ramsar Wetlands (RIS) – 2009-2012 version Available for download from http://www.ramsar.org/ris/key_ris_index.htm. Categories approved by Recommendation 4.7 (1990), as amended by Resolution VIII.13 of the 8th Conference of the Contracting Parties (2002) and Resolutions IX.1 Annex B, IX.6, IX.21 and IX. 22 of the 9 th Conference of the Contracting Parties (2005). Notes for compilers: 1. The RIS should be completed in accordance with the attached Explanatory Notes and Guidelines for completing the Information Sheet on Ramsar Wetlands. Compilers are strongly advised to read this guidance before filling in the RIS. 2. Further information and guidance in support of Ramsar site designations are provided in the Strategic Framework and guidelines for the future development of the List of Wetlands of International Importance (Ramsar Wise Use Handbook 14, 3rd edition). A 4th edition of the Handbook is in preparation and will be available in 2009. 3. Once completed, the RIS (and accompanying map(s)) should be submitted to the Ramsar Secretariat. Compilers should provide an electronic (MS Word) copy of the RIS and, where possible, digital copies of all maps. 1. Name and address of the compiler of this form: FOR OFFICE USE ONLY . DD MM YY Mr. Jung Uisuk Deputy Director, Nature Policy Division, Nature Conservation Bureau, Ministry of Environment, Government Complex, Joongang-dong 1, Designation date Site Reference Number Gwacheon-si, Gyeonggi-do, Republic of Korea 2. Date this sheet was completed/updated: February 24, 2011 3. Country: Republic of Korea 4. Name of the Ramsar site: The precise name of the designated site in one of the three official languages (English, French or Spanish) of the Convention.
    [Show full text]
  • MINISTRY of ENVIRONMENT REPUBLIC of KOREA Government Complex Gwacheon, 88 Gwanmoonro, Gwacheon-Si, Gyeonggi-Do, 427-729, Republic of Korea Tel
    MINISTRY OF ENVIRONMENT REPUBLIC OF KOREA Government Complex Gwacheon, 88 Gwanmoonro, Gwacheon-si, Gyeonggi-do, 427-729, Republic of Korea Tel. 82-2-2110-6549 Fax. 82-2-504-9206 http://eng.me.go.kr ECOREA Environmental Review 2011, Korea MINISTRY OF ENVIRONMENT REPUBLIC OF KOREA Ecorea is a compound of the prefix“ Eco,”which suggests an ecologically sound and comfortable environment, and the name of the nation,“ Korea.” Contents The Minister’s Message 4 1. Overview of Korea 6 2. The Status and Trend of Environmental Quality 8 2-1. Nature 10 2-2. Air 18 2-3. Water 21 2-4. Soil 24 2-5. Waste 25 2-6. Chemicals 27 3. Environmental Issues and Measures 28 3-1. Nature Conservation and Biodiversity 30 3-2. Climate Change 39 3-3. Air Quality Management 44 3-4. Water Environment Management 49 3-5. Waste Resources Management 54 3-6. Environmental Health & Chemicals Management 59 3-7. Green Growth 66 3-8. International Environmental Cooperation 71 4. Leading Environmental Policies (2010) 84 4-1. Green Card 86 4-2. Four Major Rivers Restoration Project 91 4-3. Green City Pilot Project in Gangneung 98 4-4. Eco-friendly Food Culture 103 5. Subsidiary & Affiliated Organizations 108 5-1. National Institute of Environmental Research 110 5-2. National Institute of Environmental 113 Human Resources Development 5-3. Korea Environment Corporation 117 5-4. Korea National Park Service 120 5-5. SUDOKWON Landfill Site Management Corporation 124 5-6. Korea Environmental Industry & Technology Institute 127 6. Main Events in 2010 130 7.
    [Show full text]
  • Gotjawal Forest 1 Gotjawal Forest
    Gotjawal Forest 1 Gotjawal Forest Gotjawal Forest ] View of Gotjawal Forest. Forest in such a flat area is very rare in this densely populated South Korea] Korean name Hangul 곶자왈숲 Hanja n/a Revised Gotjawal sup Romanization McCune- Kotchawal sup Reischauer Gotjawal Forest covers the rocky area of aa lava on Jeju-do Island off South Korea’s southwestern coast. Traditionally, Jeju-do’s local residents called any forest "Gotjawal" when such a forest was found in rocky areas. Therefore, it is difficult to cultivate crops in the areas, so where could remain undisturbed by people. Etymology According to the Jeju Dialect Dictionary, "Gotjawal" refers to an unmanned and unapproachable forest mixed with trees and bushes.[1] However, Song Shi-tae suggested in his Ph.D. dissertation, to give a new meaning to the term "Gotjawal" [2] because as the Korean term "Gotjawal" shows specifically the feature of "AA Lava. Therefore, using the term "Gotjawal Lava" instead of "AA Lava" can be useful for the land management and groundwater management. In his another study in 2003,[3] , Song also asserted that protecting the Gotjawal area on Jeju is essential to protecting the island’s groundwater, as rain water penetrates directly into the groundwater aquifer in this Gotjawal area through cracks in this region’s rocky earth. Nevertheless, some people insist that the meaning of Gotjawal should not be restricted to geological features. They say the ecological, historical, and cultural context should also be considered [4] . But, it is still not clear how they define the meaning of Gotjawal. Gotjawal Forest 2 Features of Gotjawal Forest Three important features of Gotjawal forest are its formation in rocky areas, plants specific to this ecosystem, and rain water penetrating to the groundwater aquifer[5] .
    [Show full text]