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Estudo Da Diversidade E Atividade Bacteriana Em Solos De Floresta E Sob Cultivo De Cana-De-Açúcar
UNIVERSIDADE ESTADUAL PAULISTA - UNESP CÂMPUS DE JABOTICABAL ESTUDO DA DIVERSIDADE E ATIVIDADE BACTERIANA EM SOLOS DE FLORESTA E SOB CULTIVO DE CANA-DE-AÇÚCAR Wellington Marcelo Queixas Moreira Biólogo 2013 UNIVERSIDADE ESTADUAL PAULISTA - UNESP CÂMPUS DE JABOTICABAL ESTUDO DA DIVERSIDADE E ATIVIDADE BACTERIANA EM SOLOS DE FLORESTA E SOB CULTIVO DE CANA-DE-AÇÚCAR Wellington Marcelo Queixas Moreira Orientadora: Prof. Dra.Lúcia Maria Carareto Alves Tese apresentada à Faculdade de Ciências Agrárias e Veterinárias – UNESP, Câmpus de Jaboticabal, como parte das exigências para a obtenção do título de Doutor em Microbiologia Agropecuária. 2013 Moreira, Wellington Marcelo Queixas M838e Estudo da diversidade e atividade bacteriana em solos de floresta e sob cultivo de cana-de-açúcar / Wellington Marcelo Queixas Moreira. – – Jaboticabal, 2013 xiii, 103 p.: il.; 28 cm Tese (doutorado) - Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, 2013 Orientadora:Lúcia Maria Carareto Alves Banca examinadora: Antonio Carlos Monteiro, Haroldo Alves Pereira Júnior, Luciano Takeshi Kishi, Mariana Carina Frigieri Salaro Bibliografia 1. Ciclos biogeoquímicos. 2. gene 16S rRNA. 3. Saccharum spp. 4. Hipervariáveis V I. Título. II. Jaboticabal-Faculdade de Ciências Agrárias e Veterinárias. CDU 579.22:633.61 Ficha catalográfica elaborada pela Seção Técnica de Aquisição e Tratamento da Informação – Serviço Técnico de Biblioteca e Documentação - UNESP, Câmpus de Jaboticabal. DADOS CURRICULARES DO AUTOR Wellington Marcelo Queixas Moreira – nascido em Bebedouro (SP), em 24 de fevereiro de 1983, graduou-se em Ciências Biológicas pelo Centro Universitário UNIFAFIBE em Bebedouro (SP), no ano de 2004. Ingressou no Curso de Especialização, em 2006, recebendo o título de Especialista em Biologia Molecular e Biotecnologia, pela Universidade de Franca (UNIFRAN) em junho de 2007. -
SPC Beche-De-Mer Information Bulletin #39 – March 2019
ISSN 1025-4943 Issue 39 – March 2019 BECHE-DE-MER information bulletin v Inside this issue Editorial Towards producing a standard grade identification guide for bêche-de-mer in This issue of the Beche-de-mer Information Bulletin is well supplied with Solomon Islands 15 articles that address various aspects of the biology, fisheries and S. Lee et al. p. 3 aquaculture of sea cucumbers from three major oceans. An assessment of commercial sea cu- cumber populations in French Polynesia Lee and colleagues propose a procedure for writing guidelines for just after the 2012 moratorium the standard identification of beche-de-mer in Solomon Islands. S. Andréfouët et al. p. 8 Andréfouët and colleagues assess commercial sea cucumber Size at sexual maturity of the flower populations in French Polynesia and discuss several recommendations teatfish Holothuria (Microthele) sp. in the specific to the different archipelagos and islands, in the view of new Seychelles management decisions. Cahuzac and others studied the reproductive S. Cahuzac et al. p. 19 biology of Holothuria species on the Mahé and Amirantes plateaux Contribution to the knowledge of holo- in the Seychelles during the 2018 northwest monsoon season. thurian biodiversity at Reunion Island: Two previously unrecorded dendrochi- Bourjon and Quod provide a new contribution to the knowledge of rotid sea cucumbers species (Echinoder- holothurian biodiversity on La Réunion, with observations on two mata: Holothuroidea). species that are previously undescribed. Eeckhaut and colleagues P. Bourjon and J.-P. Quod p. 27 show that skin ulcerations of sea cucumbers in Madagascar are one Skin ulcerations in Holothuria scabra can symptom of different diseases induced by various abiotic or biotic be induced by various types of food agents. -
Yellow Coloured Mats from Lava Tubes of La Palma (Canary Islands, Spain
www.nature.com/scientificreports OPEN Yellow coloured mats from lava tubes of La Palma (Canary Islands, Spain) are dominated by Received: 27 July 2017 Accepted: 16 January 2018 metabolically active Actinobacteria Published: xx xx xxxx Jose L. Gonzalez-Pimentel1, Ana Z. Miller 1, Valme Jurado1, Leonila Laiz1, Manuel F. C. Pereira2 & Cesareo Saiz-Jimenez1 Microbial diversity in lava tubes from Canary Islands (Spain) has never been explored thus far ofering a unique opportunity to study subsurface microbiology. Abundant yellow coloured mats developing on coralloid speleothems in a lava tube from La Palma Islands were studied by next-generation sequencing and DNA/RNA clone library analyses for investigating both total and metabolically active bacteria. In addition, morphological and mineralogical characterization was performed by feld emission scanning electron microscopy (FESEM), micro-computed tomography, X-ray difraction and infrared spectroscopy to contextualize sequence data. This approach showed that the coralloid speleothems consist of banded siliceous stalactites composed of opal-A and hydrated halloysite. Analytical pyrolysis was also conducted to infer the possible origin of cave wall pigmentation, revealing that lignin degradation compounds can contribute to speleothem colour. Our RNA-based study showed for the frst time that members of the phylum Actinobacteria, with 55% of the clones belonging to Euzebyales order, were metabolically active components of yellow mats. In contrast, the DNA clone library revealed that around 45% of clones were afliated to Proteobacteria. Composition of microbial phyla obtained by NGS reinforced the DNA clone library data at the phylum level, in which Proteobacteria was the most abundant phylum followed by Actinobacteria. Microbial mats frequently coat extensive areas of walls and ceilings of karstic caves and lava tubes, usually devel- oping yellow, tan, orange, grey, pink and white-coloured bioflms1–6. -
Complete Genome Sequence of Acidimicrobium Ferrooxidans Type Strain (ICPT)
Lawrence Berkeley National Laboratory Lawrence Berkeley National Laboratory Title Complete genome sequence of Acidimicrobium ferrooxidans type strain (ICPT) Permalink https://escholarship.org/uc/item/4cd3q8tr Author Clum, Alicia Publication Date 2009-07-20 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Standards in Genomic Sciences (2009) 1: 38-45 DOI:10.4056/sigs.1463 Complete genome sequence of Acidimicrobium ferrooxidans type strain (ICPT) Alicia Clum1, Matt Nolan1, Elke Lang2, Tijana Glavina Del Rio1, Hope Tice1, Alex Copeland1, Jan-Fang Cheng1, Susan Lucas1, Feng Chen1, David Bruce3, Lynne Goodwin3, Sam Pitluck1, Natalia Ivanova1, Konstantinos Mavromatis1 , Natalia Mikhailova1, Amrita Pati1, Amy Chen4, Krishna Palaniappan4, Markus Göker2, Stefan Spring2, Miriam Land5, Loren Hauser5, Yun- Juan Chang5, Cynthia C. Jeffries5, Patrick Chain1,6, Jim Bristow1, Jonathan A. Eisen1,7, Victor Markowitz4, Philip Hugenholtz1, Nikos C. Kyrpides1, Hans-Peter Klenk2, and Alla Lapidus1* 1 DOE Joint Genome Institute, Walnut Creek, California, USA 2 DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany 3 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico USA 4 Biological Data Management and Technology Center, Lawrence Berkeley National Labora- tory, Berkeley, California, USA 5 Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA 6 Lawrence Livermore National Laboratory, Livermore, California, USA 7 University of California Davis Genome Center, Davis, California, USA *Corresponding author: Alla Lapidus Keywords: Moderate thermophile, ferrous-iron-oxidizing, acidophile, Acidomicrobiales. Acidimicrobium ferrooxidans (Clark and Norris 1996) is the sole and type species of the ge- nus, which until recently was the only genus within the actinobacterial family Acidimicrobia- ceae and in the order Acidomicrobiales. -
Marine Cyanolichens from Different Littoral Zones Are
bioRxiv preprint doi: https://doi.org/10.1101/209320; this version posted February 6, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Marine cyanolichens from different littoral 2 zones are associated with distinct bacterial 3 communities 4 Nyree J. West*1, Delphine Parrot2†, Claire Fayet1, Martin Grube3, Sophie Tomasi2 5 and Marcelino T. Suzuki4 6 1 Sorbonne Universités, UPMC Univ Paris 06, CNRS, Observatoire Océanologique de Banyuls (OOB), 7 F-66650, Banyuls sur mer, France 8 2 UMR CNRS 6226, Institut des Sciences chimiques de Rennes, Equipe CORINT « Chimie Organique 9 et Interfaces », UFR Sciences Pharmaceutiques et Biologiques, Univ. Rennes 1, Université Bretagne 10 Loire, F-35043, Rennes, France 11 3 Institute of Plant Sciences, University of Graz, A-8010 Graz, Austria 12 4 Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Laboratoire de Biodiversité et Biotechnologies 13 Microbiennes (LBBM), Observatoire Océanologique, F-66650, Banyuls sur mer, France 14 †Current address: GEOMAR Helmholtz Centre for Ocean Research Kiel, Research Unit Marine 15 Natural Products Chemistry, GEOMAR Centre for Marine Biotechnology, 24106 Kiel, Germany 16 *Corresponding author: 17 Observatoire Océanologique de Banyuls sur mer, F-66650 Banyuls sur mer, France 18 19 Tel: +33 (0)4 30 19 24 29, Fax: +33 (0)4 68 88 73 98 20 Email: [email protected] 21 1 bioRxiv preprint doi: https://doi.org/10.1101/209320; this version posted February 6, 2018. -
Diversity and Distribution of Actinobacteria Associated with Reef Coral Porites Lutea
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Frontiers - Publisher Connector ORIGINAL RESEARCH published: 21 October 2015 doi: 10.3389/fmicb.2015.01094 Diversity and distribution of Actinobacteria associated with reef coral Porites lutea Weiqi Kuang 1, 2 †, Jie Li 1 †, Si Zhang 1 and Lijuan Long 1* 1 CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China, 2 College of Earth Science, University of Chinese Academy of Sciences, Beijing, China Actinobacteria is a ubiquitous major group in coral holobiont. The diversity and spatial Edited by: and temporal distribution of actinobacteria have been rarely documented. In this Sheng Qin, study, diversity of actinobacteria associated with mucus, tissue and skeleton of Porites Jiangsu Normal University, China lutea and in the surrounding seawater were examined every 3 months for 1 year on Reviewed by: Syed Gulam Dastager, Luhuitou fringing reef. The population structures of the P.lutea-associated actinobacteria National Collection of Industrial were analyzed using phylogenetic analysis of 16S rRNA gene clone libraries, which Microorganisms Resource Center, demonstrated highly diverse actinobacteria profiles in P. lutea. A total of 25 described India Wei Sun, families and 10 unnamed families were determined in the populations, and 12 genera Shanghai Jiao Tong University, China were firstly detected in corals. The Actinobacteria diversity was significantly different P. Nithyanand, SASTRA University, India between the P. lutea and the surrounding seawater. Only 10 OTUs were shared by *Correspondence: the seawater and coral samples. -
Geological and Geo-Morphological Influences on Some Sea-Cumber
Geological and geo-morphological influences on some Sea-cucumber species in Northwest coast of Sri Lanka S.U.P. Jinadasa and D.C.T. Dissanayake National Aquatic Resources Research and Development Agency (NARA), Crow Island, Colombo 15, Sri Lanka Email: [email protected] or [email protected] Abstract Objectives Abundance and Mean The Continental shelf of Sri Lanka is having highly productive Major Objectives ecosystems mainly sea grass beds, marshy lands and coral reefs. The overall objectives of the research is development of a These ecosystems are valuable resource for the coastal communities relationship between bottom sediment distribution and the marine scientists. Also coastal ecosystems have been geomorphology and sea-cucumber abundance in northwest utilized as a food source and income generator to each coastal coast of Sri Lanka. nations. The current study is focused on bottom geology and relative Minor Objectives abundance of sea cucumber species Holoturia atra and Holothuria edulis which are commercially exploited in north western coast of (a) Collection of high relief hard bottom data and Digital Sri Lanka. This was the first effort in Sri Lanka to study abundance (a) (b) (c) Elevation Model (DEM) of the area of sea cucumbers with bottom sedimentological status. However, the Fig. 3(a), 3(b), 3(c) illustrate the gravel, sand and silt/ mud (b) Identification of gravel, sand, silt beds and comparison study is given encouraging results for further studies on other distribution with abundance of Sea cucumber species H.edulis (a) (b) bottom species such as sea urchins, gastropods and cephalopods. with abundance of Sea Cucumber. -
SPC Beche-De-Mer Information Bulletin
Secretariat of the Pacific Community ISSN 1025-4943 Issue 34 – May 2014 BECHE-DE-MER information bulletin Inside this issue Editorial The IUCN Red List assessment of th aspidochirotid sea cucumbers and its The 34 issue of the Beche-de-mer Information Bulletin includes, as implications always, a considerable amount of information on the biology, ecology and C. Conand et al. p. 3 bio-management of sea cucumbers. The status of the sea cucumber fishery in Batiki District, Lomaiviti, Fiji In the first article, Chantal Conand and co-authors describe the process used W. Lalavanua, I. Tuinasavusavu and the results obtained in an assessment of sea cucumber species for the and P. Seru p. 8 International Union for Conservation of Nature (IUCN) Red List; 16 threatened species, out of 377 known aspidochirotids examined, are presented. An Indonesian sea cucumber fishing village: The case of Pulau Misa The second article comes from Fiji. Watisoni Lalavanua and colleagues P.G. Navarro et al. p. 14 undertook a sea cucumber assessment survey in Batiki District in October An assessment of holothurian diversity, 2012. The results indicate that the sea cucumber fishery there is under abundance and distribution in the shallow lagoons of Mauritius stress from overexploitation and requires effective management. K. Lampe-Ramdoo, R. Moothien Pillay Pablo Navarro and co-authors provide some information on beche-de- and C. Conand p. 17 mer activities at Pulau Misa, a small island in Indonesia’s Flores Sea. The Some data on the diversity and people from Pulau Misa carry out a semi-traditional sea cucumber fishery. -
Genomic Analysis of a Freshwater Actinobacterium, “Candidatus
J. Microbiol. Biotechnol. (2017), 27(4), 825–833 https://doi.org/10.4014/jmb.1701.01047 Research Article Review jmb Genomic Analysis of a Freshwater Actinobacterium, “Candidatus Limnosphaera aquatica” Strain IMCC26207, Isolated from Lake Soyang Suhyun Kim, Ilnam Kang, and Jang-Cheon Cho* Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea Received: January 16, 2017 Revised: February 3, 2017 Strain IMCC26207 was isolated from the surface layer of Lake Soyang in Korea by the dilution- Accepted: February 6, 2017 to-extinction culturing method, using a liquid medium prepared with filtered and autoclaved lake water. The strain could neither be maintained in a synthetic medium other than natural freshwater medium nor grown on solid agar plates. Phylogenetic analysis of 16S rRNA gene First published online sequences indicated that strain IMCC26207 formed a distinct lineage in the order February 7, 2017 Acidimicrobiales of the phylum Actinobacteria. The closest relative among the previously *Corresponding author identified bacterial taxa was “Candidatus Microthrix parvicella” with 16S rRNA gene sequence Phone: +82-32-860-7711; similarity of 91.7%. Here, the draft genome sequence of strain IMCC26207, a freshwater Fax: +82-32-232-0541; actinobacterium, is reported with the description of the genome properties and annotation E-mail: [email protected] summary. The draft genome consisted of 10 contigs with a total size of 3,316,799 bp and an average G+C content of 57.3%. The IMCC26207 genome was predicted to contain 2,975 protein-coding genes and 51 non-coding RNA genes, including 45 tRNA genes. Approximately 76.8% of the protein coding genes could be assigned with a specific function. -
Egibacter Rhizosphaerae Gen. Nov., Sp. Nov., an Obligately Halophilic, Facultatively Alkaliphilic Actinobacterium and Proposal of Egibaceraceae Fam
International Journal of Systematic and Evolutionary Microbiology (2016), 66, 283–289 DOI 10.1099/ijsem.0.000713 Egibacter rhizosphaerae gen. nov., sp. nov., an obligately halophilic, facultatively alkaliphilic actinobacterium and proposal of Egibaceraceae fam. nov. and Egibacterales ord. nov. Yong-Guang Zhang,1 Hong-Fei Wang,1,2 Ling-Ling Yang,3 Xing-Kui Zhou,4 Xiao-Yang Zhi,3 Yan-Qing Duan,4 Min Xiao,5 Yuan-Ming Zhang1 and Wen-Jun Li1,3,5 Correspondence 1Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Wen-Jun Li Geography, Chinese Academy of Sciences, U¨ ru´mqi 830011, PR China [email protected] or 2College of Life Science, Liaoning Normal University, Dalian, 116029, PR China [email protected] 3Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, PR China 4China Tobacco Yunnan Industrial Co., Ltd, Kunming 650231, PR China 5State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou, 510275, PR China A novel obligately halophilic, facultatively alkaliphilic actinobacterium, designated EGI 80759T,was isolated from the rhizosphere of Tamarix hispida Willd, Karamay, Xinjiang province, north-west China. Cells of strain EGI 80759T were Gram-stain-positive, non-motile and non-endospore-forming rods. Strain EGI 80759T showed obligately halophilic growth with a tolerance to 8–25 % (w/v) NaCl (optimum growth at 10–12 %, w/v) and facultatively alkaliphilic growth within the pH range 7.0–11.0 (optimum growth at pH 9.0–10.0). Cell-wall hydrolysates of the isolate contained meso- diaminopimelic acid (peptidoglycan type A1c), with glucose, glucosamine, ribose and mannose as the major sugars. -
Chemical Defense Mechanisms and Ecological Implications of Indo-Pacific Holothurians
molecules Article Chemical Defense Mechanisms and Ecological Implications of Indo-Pacific Holothurians Elham Kamyab 1,* , Sven Rohde 1 , Matthias Y. Kellermann 1 and Peter J. Schupp 1,2,* 1 Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl-von-Ossietzky University Oldenburg, Schleusenstrasse 1, 26382 Wilhelmshaven, Germany; [email protected] (S.R.); [email protected] (M.Y.K.) 2 Helmholtz Institute for Functional Marine Biodiversity, University of Oldenburg, Ammerländer Heerstrasse 231, D-26129 Oldenburg, Germany * Correspondence: [email protected] (E.K.); [email protected] (P.J.S.); Tel.: +49-4421-944-100 (P.J.S.) Academic Editor: David Popovich Received: 14 August 2020; Accepted: 13 October 2020; Published: 19 October 2020 Abstract: Sea cucumbers are slow-moving organisms that use morphological, but also a diverse combination of chemical defenses to improve their overall fitness and chances of survival. Since chemical defense compounds are also of great pharmaceutical interest, we pinpoint the importance of biological screenings that are a relatively fast, informative and inexpensive way to identify the most bioactive organisms prior to further costly and elaborate pharmacological screenings. In this study, we investigated the presence and absence of chemical defenses of 14 different sea cucumber species from three families (Holothuriidae, Stichopodidae and Synaptidae) against ecological factors such as predation and pathogenic attacks. We used the different sea cucumber crude extracts as well as purified fractions and pure saponin compounds in a portfolio of ecological activity tests including fish feeding assays, cytotoxicity tests and antimicrobial assays against environmental pathogenic and non-pathogenic bacteria. -
Species Composition, Density and Distribution of Sea Cucumbers (Holothuroidea) at Arreceffi Island, Honda Bay, Palawan, Philippines Jean Beth S
SPC Beche-de-mer Information Bulletin #37 – March 2017 21 Species composition, density and distribution of sea cucumbers (Holothuroidea) at Arreceffi Island, Honda Bay, Palawan, Philippines Jean Beth S. Jontila,1* Rodulf Anthony T. Balisco1 and Glesselle T. Batin2 Abstract This study was conducted to determine the species composition, distribution, density and size structure of sea cucumbers at Arreceffi Island in Honda Bay, Palawan, Philippines. Three stations covering different habitats (intertidal flats, seagrass beds, and coral reefs) were surveyed during the day and night by walking, snorkeling and scuba diving. In total, 15 species in the families Holothuriidae (11 species), Stichopodidae (3 species) and Synaptidae (1 species) were recorded. Some rare Stichopus and high-value species were recorded along with other aggregating species of the family Holothuriidae. Density generally ranged from 0.3 to 19.0 ind. 100 m-2, and greatly varied depending on habitat. Introduction remains unregulated. Initial assessments in Pala- wan have revealed that areas open to harvesting Sea cucumbers are among the heavily exploited have very little populations remaining, or popula- invertebrates in the Philippines although their col- tions have been depleted (Jontila et al. 2013). High- lection is unregulated due to poor implementation value species were seldom encountered in shallow of pertinent laws. Information on sea cucumber sites of Bataraza, Quezon, El Nido and Roxas in populations is also very limited. Most of the earlier Palawan except around Arreceffi Island in Honda works focused on taxonomy and species inventories Bay, Puerto Princesa City, where viable populations (Domantay 1934, 1960; Reyes-Leonardo 1984; Tan were noted (Jontila et al.