Genome Analysis of Two Bacterial Strains Isolated from Diseased
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CBD Fifth National Report
Fifth National Report of Japan to the Convention on Biological Diversity Government of Japan March 2014 Contents Executive Summary 1 Chapter 1 Biodiversity: the current situation, trends and threats 7 1.1 Importance of biodiversity 7 (1) Characteristics of biodiversity in Japan from the global perspective 7 (2) Biodiversity that supports life and livelihoods 9 (3) Japan causing impacts on global biodiversity 10 (4) The economic valuation of biodiversity 11 1.2 Major changes to the biodiversity situation and trends 12 (1) The current situation of ecosystems 12 (2) The current situation of threatened wildlife 17 (3) Impacts of the Great East Japan Earthquake on biodiversity 19 1.3 The structure of the biodiversity crisis 21 (1) The four crises of biodiversity 21 (2) Japan Biodiversity Outlook (JBO) 22 1.4 The impacts of changes in biodiversity on ecosystem services, socio-economy, and culture 24 (1) Changes in the distribution of medium and large mammals and the expansion of conflicts 24 (2) Alien species 24 (3) Impacts of changes in the global environment on biodiversity 26 1.5 Future scenarios for biodiversity 28 (1) Impacts of the global warming 28 (2) The impacts of ocean acidification on coral reefs 29 (3) The forecasted expansion in the distribution of sika deer (Cervus nippon ) 30 (4) Second crisis (caused by reduced human activities) 30 Chapter 2 Implementation of the National Biodiversity Strategy and Mainstreaming Biodiversity 32 2.1 Background to the formulation of the National Biodiversity Strategy of Japan and its development -
Rpon (Σ54) Is Required for Floc Formation but Not for Extracellular Polysaccharide Biosynthesis in a Floc-Forming Aquincola Tertiaricarbonis Strain
Lawrence Berkeley National Laboratory Recent Work Title RpoN (σ54) Is Required for Floc Formation but Not for Extracellular Polysaccharide Biosynthesis in a Floc-Forming Aquincola tertiaricarbonis Strain. Permalink https://escholarship.org/uc/item/9f26h2cp Journal Applied and environmental microbiology, 83(14) ISSN 0099-2240 Authors Yu, Dianzhen Xia, Ming Zhang, Liping et al. Publication Date 2017-07-01 DOI 10.1128/aem.00709-17 Peer reviewed eScholarship.org Powered by the California Digital Library University of California RpoN (σσ54) Is Required for Floc Formation but Not for Extracellular Polysaccharide Biosynthesis in a Floc-Forming Aquincola tertiaricarbonis Strain Dianzhen Yu,a,b Ming Xia,a,b Liping Zhang,a Yulong Song,a You Duan,a,b Tong Yuan,d,f Minjie Yao,c Liyou Wu,d Chunyuan Tian,e Zhenbin Wu,a Xiangzhen Li,c Jizhong Zhou,d Dongru Qiua Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Chinaa ; University of Chinese Academy of Sciences, Beijing, Chinab; Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Chinac ; Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USAd; School of Life Sciences and Technology, Hubei Engineering University, Xiaogan, Chinae; College of Life Science, Henan Agricultural University, Zhengzhou, Chinaf ABSTRACT Some bacteria are capable of forming flocs, in which bacterial cells become self-flocculated by secreted extracellular polysaccharides and other biopolymers. The floc-forming bacteria play a central role in activated sludge, which has been widely utilized for the treatment of municipal sewage and industrial wastewater. Here, we use a floc-forming bacterium, Aquincola tertiaricarbonis RN12, as a model to explore the biosynthesis of extracellular polysaccharides and the regulation of floc formation. -
A Simple Game-Theoretic Model for Upstream Fish Migration
Theory Biosci. DOI 10.1007/s12064-017-0244-3 ORIGINAL PAPER A simple game-theoretic model for upstream fish migration Hidekazu Yoshioka1 Received: 28 December 2016 / Accepted: 25 April 2017 Ó The Author(s) 2017. This article is an open access publication Abstract A simple game-theoretic model for upstream fish modulators of biochemical processes, and transport vectors migration, which is a key element in life history of (Winemiller and Jepsen 1998; Flecker et al. 2010). In diadromous fishes, is proposed. Foundation of the model is addition, many of them are economically and culturally a minimization problem on the cost of migration with the valuable fishery resources. Both their abundance and swimming speed and school size as the variables to be diversity have been highly affected by loss and degradation simultaneously optimized. Finding the optimizer ultimately of habitats and migration routes (Guse et al. 2015; Logez reduces to solving a self-consistency equation without et al. 2013; Radinger and Wolter 2015). Physical barriers, explicit solutions. Mathematical analytical results lead to such as dams and weirs, are the major factors that fragment the sufficient condition that the self-consistency equation habitats and migration routes of fish (Jager et al. 2015;Yu has a unique solution, which turns out to be identified with and Xu 2016). Analyzing fish migration has, therefore, the condition where the unique optimizer exists. Behavior been a key topic in current biological and ecological of the optimizer is analyzed both mathematically and research areas (Becker et al. 2015; Wang et al. 2012; White numerically to show its biophysical and ecological conse- et al. -
Javan Leopard PHVA Provisional Report May2020.Pdf
Conservation Planning Workshops for the Javan Leopard (Panthera pardus melasCon) Provisional Report Workshop organizers: IUCN Conservation Planning Specialist Group; Taman Safari Indonesia Institutional support provided by: Copenhagen Zoo, Indonesian Ministry of Forestry, Taman Safari Indonesia, Tierpark Berlin Cover photo: Javan leopard, Taman Nasional Baluran, courtesy of Copenhagen Zoo IUCN encourages meetings, workshops and other fora for the consideration and analysis of issues related to conservation, and believes that reports of these meetings are most useful when broadly disseminated. The opinions and views expressed by the authors may not necessarily reflect the formal policies of IUCN, its Commissions, its Secretariat or its members. The designation of geographical entities in this book, and the presentation of the material, do not imply the expression of any opinion whatsoever on the part of IUCN concerning the legal status of any country, territory, or area, or of its authorities, or concerning the delimitation of its frontiers or boundaries. © Copyright CPSG 2020 Traylor-Holzer, K., B. Holst, K. Leus and K. Ferraz (eds.). 2020. Conservation Planning Workshops for the Javan Leopard (Panthera pardus melas) Provisional Report. IUCN SSC Conservation Planning Specialist Group, Apple Valley, MN. A PDF of this document can be downloaded at: www.cpsg.org. Conservation Planning Workshops for the Javan Leopard (Panthera pardus melas) Jakarta, Indonesia Species Distribution Modeling and Population Viability Analysis Workshop 28 – 29 -
Cooperative Interaction of Janthinobacterium Sp. SLB01 and Flavobacterium Sp
International Journal of Molecular Sciences Article Cooperative Interaction of Janthinobacterium sp. SLB01 and Flavobacterium sp. SLB02 in the Diseased Sponge Lubomirskia baicalensis Ivan Petrushin 1,2,* , Sergei Belikov 1 and Lubov Chernogor 1 1 Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk 664033, Russia; [email protected] (S.B.); [email protected] (L.C.) 2 Faculty of Business Communication and Informatics, Irkutsk State University, Irkutsk 664033, Russia * Correspondence: [email protected] Received: 31 August 2020; Accepted: 25 October 2020; Published: 30 October 2020 Abstract: Endemic freshwater sponges (demosponges, Lubomirskiidae) dominate in Lake Baikal, Central Siberia, Russia. These sponges are multicellular filter-feeding animals that represent a complex consortium of many species of eukaryotes and prokaryotes. In recent years, mass disease and death of Lubomirskia baicalensis has been a significant problem in Lake Baikal. The etiology and ecology of these events remain unknown. Bacteria from the families Flavobacteriaceae and Oxalobacteraceae dominate the microbiomes of diseased sponges. Both species are opportunistic pathogens common in freshwater ecosystems. The aim of our study was to analyze the genomes of strains Janthinobacterium sp. SLB01 and Flavobacterium sp. SLB02, isolated from diseased sponges to identify the reasons for their joint dominance. Janthinobacterium sp. SLB01 attacks other cells using a type VI secretion system and suppresses gram-positive bacteria with violacein, and regulates its own activity via quorum sensing. It produces floc and strong biofilm by exopolysaccharide biosynthesis and PEP-CTERM/XrtA protein expression. Flavobacterium sp. SLB02 utilizes the fragments of cell walls produced by polysaccharides. These two strains have a marked difference in carbohydrate acquisition. -
Microbial Diversity of a Remote Aviation Fuel Contaminated
ntal & A me na n ly o t ir ic v a Udotong et al., J Environ Anal Toxicol 2015, 5:6 n l T E o Journal of f x o i l c DOI: 10.4172/2161-0525.1000320 o a n l o r g u y o J Environmental & Analytical Toxicology ISSN: 2161-0525 ResearchResearch Article Article OpenOpen Access Access Microbial Diversity of a Remote Aviation Fuel Contaminated Sediment of a Lentic Ecosystem in Ibeno, Nigeria Udotong IR1*, Uko MP1 and Udotong JIR2 1Department of Microbiology, University of Uyo, Uyo, Akwa Ibom State, Nigeria 2Department of Biochemistry, University of Uyo, Uyo, Akwa Ibom State, Nigeria Abstract Environmental pollution from Oil & Gas Exploration & Production (O&G E&P) activities remains one of the major problems in the oil-producing communities of Nigeria. This results from improper oily wastes disposal as well as incessant oil spills in the region. The operator’s lack of responsible business practices in wastes management and the over-dependence of the economy on oil and gas earnings, in the most part, exacerbate the problems of environmental pollution. Government's lack of political will power which treats issues on oil pollution with levity and long period of neglect of these polluted sites leave the environment ecologically destabilized. Studies to ascertain the ecological status of remote aviation fuel-contaminated sediment of a lentic ecosystem in Inua Eyet Ikot village, Ibeno, Nigeria, have been carried out using conventional microbiological culture-dependent methods. This methodology is known to reveal only <1% of the microbial diversity present. These results were therefore considered inaccurate and grossly misleading. -
Focus Group on Status and Trends and Red List Assessment Final Report
Focus Group on Status and Trends and Red List Assessment Final Report 1. Relevant Aichi Biodiversity targets Aichi Target 19 - Biodiversity Knowledge By 2020, knowledge, the science base and technologies relating to biodiversity, its values, functioning, status and trends, and the consequences of its loss, are improved, widely shared and transferred, and applied. Aichi Target 12 - Preventing Extinction By 2020, the extinction of known threatened species has been prevented and their conservation status, particularly of those most in decline, has been improved and sustained. Other relevant Aichi Targets are 1 (Awareness of Biodiversity Values), 2 (Integration of Biodiversity Values) , 5 (Loss of Habitats), 6 (Sustainable Fisheries), 7 (Areas under Sustainable Management), 8 (Pollution), 9 (Invasive Alien Species), 11 (Protected Areas), 14 (Essential Ecosystem Services) and 20 (Resource Mobilisation) 2. Leaders - Dr Michael Lau (WWF-HK) and Prof. Yvonne Sadovy (HKU) 3. Key experts/stakeholders involved in the discussions (a) Within the Steering Committee/Working Groups - Dr Gary Ades (KFBG), Prof Put Ang Jr. (CUHK), Mr Simon Chan (AFCD), Dr Andy Cornish (WWF-International), Prof. David Dudgeon (HKU), Dr Billy Hau (HKU), Dr Roger Kendrick, Mr Kevin Laurie (Hong Kong Coast Watch), Ms Samantha Lee (WWF-HK), Ms Louise Li (AFCD), Dr Ng Cho Nam (HKU), Dr Paul Shin (City U), Mr Samson So (Eco Institute), Prof. Nora Tam (City U), Mr Tam Po Yiu, Dr Jackie Yip (AFCD) (b) Outside the Steering Committee/Working Groups - Mr John Allcock (WWF-HK), Ms Aidia Chan (AFCD), Mr Christophe Barthelemy, Mr Geoff Carey (AEC), Dr John Fellowes (KFBG), Dr Stephan Gale (KFBG), Dr David Gallacher (AECOM), Dr Leszek Karczmarski (HKU), Dr Pankaj Kumar (KFBG), Mr Paul Leader (AEC), Ms Janet Lee (AFCD), Dr Michael Leven (AEC), Ms Angie Ng (CA), Dr Ng Sai-chit (AFCD), Mr Tony Nip (KFBG), Mr Stan Shea, Ms Shadow Sin (OPCF), Ms Ivy So (AFCD), Mr Ray So, Dr Sung Yik Hei (KFBG), Dr Alvin Tang (Muni Arborist Ltd), Dr Allen To (WWF-HK), Mr Yu Yat Tung (HKBWS) 4. -
The Seasonal Trophic Link Between Great Cormorant Phalacrocorax Carbo and Ayu Plecoglossus Altivelis Altivelis Reared for Mass Release
Ecol Res (2018) 33: 935–948 DOI 10.1007/s11284-018-1610-4 ORIGINAL ARTICLE Noriyuki Takai • Koh Kawabe • Kenta Togura Kentaro Kawasaki • Tomohiro Kuwae The seasonal trophic link between Great Cormorant Phalacrocorax carbo and ayu Plecoglossus altivelis altivelis reared for mass release Received: 10 August 2017 / Accepted: 9 March 2018 / Published online: 26 April 2018 Ó The Author(s) 2018 Abstract The feeding ecology of Great Cormorants Keywords Food chain Æ Foraging behavior Æ Stable (Phalacrocorax carbo) during the breeding season in the isotope Æ Stomach content Æ Fish fauna Kano River basin, central Japan, was examined to clarify the trophic relationship between the cormorants and ayu (Plecoglossus altivelis altivelis) reared for mass Introduction release in the river. The ayu was most frequently found in stomachs of cormorants culled during the breeding The Great Cormorant (Phalacrocorax carbo) is a pis- season, despite relatively poor catch in the year-round civorous bird inhabiting river basins and coastal seas in fish fauna research in the watershed. Carbon and Eurasia, Africa, Australia and the North America nitrogen stable isotope ratios of some ayu individuals (Simpson and Day 2004). The number of cormorants in extracted from the stomachs of the culled cormorants Japan had decreased in the mid 20th century, with a were similar to the isotopic values of ayu caught in the minimum population of £ 3000 individuals within the watershed, whereas the other stomach-content ayu country in 1971 (Fukuda et al. 2002). However, the showed peculiarly high nitrogen isotopic values, clearly population has recovered since the mid 1970s, and has distinct from the values of the ayu caught in the water- caused serious problems such as decimation of fresh- shed, and overlapped with the values of mass-release water fish stocks through feeding and forests through ayu. -
BMC Evolutionary Biology Biomed Central
BMC Evolutionary Biology BioMed Central Research article Open Access Mitogenomic evaluation of the historical biogeography of cichlids toward reliable dating of teleostean divergences Yoichiro Azuma1, Yoshinori Kumazawa*2,3, Masaki Miya4, Kohji Mabuchi1 and Mutsumi Nishida1 Address: 1Ocean Research Institute, The University of Tokyo, 1-15-1 Minamidai, Nakano-ku, Tokyo 164-8639, Japan, 2Division of Material Science and Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan, 3Department of Information and Biological Sciences, Graduate School of Natural Sciences, Nagoya City University, 1 Yamanohata, Mizuho-cho, Mizuho-ku, Nagoya 467-8501, Japan and 4Department of Zoology, Natural History Museum and Institute, Chiba, 955-2 Aoba-cho, Chuo-ku, Chiba 260-8682, Japan Email: Yoichiro Azuma - [email protected]; Yoshinori Kumazawa* - [email protected]; Masaki Miya - [email protected]; Kohji Mabuchi - [email protected]; Mutsumi Nishida - [email protected] * Corresponding author Published: 23 July 2008 Received: 18 March 2008 Accepted: 23 July 2008 BMC Evolutionary Biology 2008, 8:215 doi:10.1186/1471-2148-8-215 This article is available from: http://www.biomedcentral.com/1471-2148/8/215 © 2008 Azuma et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Recent advances in DNA sequencing and computation offer the opportunity for reliable estimates of divergence times between organisms based on molecular data. -
Anaerobic Mineralization of Quaternary Carbon Atoms: Isolation of Denitrifying Bacteria on Pivalic Acid (2,2-Dimethylpropionic Acid)
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Mar. 2003, p. 1866–1870 Vol. 69, No. 3 0099-2240/03/$08.00ϩ0 DOI: 10.1128/AEM.69.3.1866–1870.2003 Copyright © 2003, American Society for Microbiology. All Rights Reserved. Anaerobic Mineralization of Quaternary Carbon Atoms: Isolation of Denitrifying Bacteria on Pivalic Acid (2,2-Dimethylpropionic Acid) Christina Probian, Annika Wu¨lfing, and Jens Harder* Downloaded from Department of Microbiology, Max Planck Institute for Marine Microbiology, D-28359 Bremen, Germany Received 22 August 2002/Accepted 26 November 2002 The degradability of pivalic acid was established by the isolation of several facultative denitrifying strains belonging to Zoogloea resiniphila,toThauera and Herbaspirillum, and to Comamonadaceae, related to [Aquaspi- rillum] and Acidovorax, and of a nitrate-reducing bacterium affiliated with Moraxella osloensis. Pivalic acid was completely mineralized to carbon dioxide. The catabolic pathways may involve an oxidation to dimethyl- malonate or a carbon skeleton rearrangement, a putative 2,2-dimethylpropionyl coenzyme A mutase. http://aem.asm.org/ Quaternary carbon atoms bind with all four single bonds unable to respire oxygen (21). Our isolation strategy with pi- to carbon atoms. This structural motif is present in natural valic acid as sole electron donor and carbon source aimed at compounds as well as in xenobiotic substances. Resin acids, this physiology in order to obtain many strains quickly: enrich- tricyclic diterpenes, are present in cell walls and are discharged ment of an anaerobic nitrate-reducing population in liquid during the pulping process, yielding toxic wastewaters. Aerobic culture was followed by repeated aerobic growth on oxic plates growth of bacteria on defined resin acids has been studied to to obtain single colonies. -
10 Secrets of the White Cormorant the Cormorant Fishing (Ukai) of Miyoshi Cormorant fishing (Ukai) in Miyoshi Has a White Cormorant, a Rarity in Japan
Cultural Property of Miyoshi City 1 10 Secrets of the White Cormorant The Cormorant Fishing (Ukai) of Miyoshi Cormorant fishing (ukai) in Miyoshi has a white cormorant, a rarity in Japan. Do you have a name? How old are you? Where did you come from? My name is Shiroki (White I’m around 30 years old. 60 My hometown is Ya'an City in Sichuan Sparkle). My name was given years old if I were human. Province, China. Ya'an City is a sister city of in the hope that I would shine Perhaps I’m longer-living than Miyoshi City, and four birds were sent in 1992 Intangible Folk Cultural Property of Hiroshima Prefecture white and bright. you might have thought. and another four in 1994 as a gesture of Sino-Japanese friendship. Folk Skills Seen in the Cormorant Fishing of Miyoshi Beak It is very sharp, so it is filed down using a rasp. What is the difference with other cormorants? The black cormorant is a Japanese (Temminck's) cor- morant which lives in the ocean; I am a cormorant living Neck in the river. Japanese cormo- I am stouter and shorter than rant fishing uses the Japanese the Japanese cormorant cormorant from the sea, but in which dwells in coastal areas. China they use the Great Cor- morant, a bird of rivers. Feet Fine webbed feet as you can see. My webbed feet are also How large are you? white. Length 75 cm Wing span (when I spread my wings) is 90 cm; I am a little smaller than a Japanese cormorant The Cormorant Fishing of Miyoshi A Word from Shiroki Cormorant fishing (ukai) is a poetic tradition that symbolizes the summer nights of Miyoshi. -
(Plecoglossus Altivelis) in the Tien Yen River of Northern Vietnam
Downstream migration of newly-hatched ayu (Plecoglossus altivelis) in the Tien Yen River of northern Vietnam Author Hau Duc Tran, Midori Iida, Ken Maeda journal or Environmental Biology of Fishes publication title volume 100 number 10 page range 1329-1341 year 2017-08-03 Publisher Springer Netherlands Rights (C) 2017 Springer Science+Business Media B.V. This is a post-peer-review, pre-copyedit version of an article published in Environmental Biology of Fishes. The final authenticated version is available online at: https://doi.org/10.1007/s10641-017-0646-6 Author's flag author URL http://id.nii.ac.jp/1394/00000622/ doi: info:doi/10.1007/s10641-017-0646-6 Downstream migration of newly-hatched ayu (Plecoglossus altivelis) in the Tien Yen River of Northern Vietnam Hau Duc Tran ∙ Midori Iida ∙ Ken Maeda H. D. Tran () Hanoi National University of Education, 136 Xuan Thuy, Cau Giay, Hanoi, Vietnam e-mail: [email protected]; phone: 84-4-3834-6828; fax: 84-4-3754-9530 ORCID ID: orcid.org/0000-0002-2599-1045 M. Iida Sado Marine Biological Station, Faculty of Science, Niigata University, 87 Tassha, Sado, Niigata 952-2135, Japan ORCID ID: orcid.org/0000-0002-0294-1985 K. Maeda Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa 904-0495, Japan ORCID ID: orcid.org/0000-0003-3631-811X Abstract The ayu (Plecoglossus altivelis) is an annual, amphidromous, plecoglossid fish, distributed in Vietnam, China, Taiwan, Korea, and Japan. To date, ayu have been found only in two rivers in northern Vietnam, where little is known about their life history.