Carotenoid Distribution in Nature
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Developing a Genetic Manipulation System for the Antarctic Archaeon, Halorubrum Lacusprofundi: Investigating Acetamidase Gene Function
www.nature.com/scientificreports OPEN Developing a genetic manipulation system for the Antarctic archaeon, Halorubrum lacusprofundi: Received: 27 May 2016 Accepted: 16 September 2016 investigating acetamidase gene Published: 06 October 2016 function Y. Liao1, T. J. Williams1, J. C. Walsh2,3, M. Ji1, A. Poljak4, P. M. G. Curmi2, I. G. Duggin3 & R. Cavicchioli1 No systems have been reported for genetic manipulation of cold-adapted Archaea. Halorubrum lacusprofundi is an important member of Deep Lake, Antarctica (~10% of the population), and is amendable to laboratory cultivation. Here we report the development of a shuttle-vector and targeted gene-knockout system for this species. To investigate the function of acetamidase/formamidase genes, a class of genes not experimentally studied in Archaea, the acetamidase gene, amd3, was disrupted. The wild-type grew on acetamide as a sole source of carbon and nitrogen, but the mutant did not. Acetamidase/formamidase genes were found to form three distinct clades within a broad distribution of Archaea and Bacteria. Genes were present within lineages characterized by aerobic growth in low nutrient environments (e.g. haloarchaea, Starkeya) but absent from lineages containing anaerobes or facultative anaerobes (e.g. methanogens, Epsilonproteobacteria) or parasites of animals and plants (e.g. Chlamydiae). While acetamide is not a well characterized natural substrate, the build-up of plastic pollutants in the environment provides a potential source of introduced acetamide. In view of the extent and pattern of distribution of acetamidase/formamidase sequences within Archaea and Bacteria, we speculate that acetamide from plastics may promote the selection of amd/fmd genes in an increasing number of environmental microorganisms. -
LUNDY FUNGI: FURTHER SURVEYS 2004-2008 by JOHN N
Journal of the Lundy Field Society, 2, 2010 LUNDY FUNGI: FURTHER SURVEYS 2004-2008 by JOHN N. HEDGER1, J. DAVID GEORGE2, GARETH W. GRIFFITH3, DILUKA PEIRIS1 1School of Life Sciences, University of Westminster, 115 New Cavendish Street, London, W1M 8JS 2Natural History Museum, Cromwell Road, London, SW7 5BD 3Institute of Biological Environmental and Rural Sciences, University of Aberystwyth, SY23 3DD Corresponding author, e-mail: [email protected] ABSTRACT The results of four five-day field surveys of fungi carried out yearly on Lundy from 2004-08 are reported and the results compared with the previous survey by ourselves in 2003 and to records made prior to 2003 by members of the LFS. 240 taxa were identified of which 159 appear to be new records for the island. Seasonal distribution, habitat and resource preferences are discussed. Keywords: Fungi, ecology, biodiversity, conservation, grassland INTRODUCTION Hedger & George (2004) published a list of 108 taxa of fungi found on Lundy during a five-day survey carried out in October 2003. They also included in this paper the records of 95 species of fungi made from 1970 onwards, mostly abstracted from the Annual Reports of the Lundy Field Society, and found that their own survey had added 70 additional records, giving a total of 156 taxa. They concluded that further surveys would undoubtedly add to the database, especially since the autumn of 2003 had been exceptionally dry, and as a consequence the fruiting of the larger fleshy fungi on Lundy, especially the grassland species, had been very poor, resulting in under-recording. Further five-day surveys were therefore carried out each year from 2004-08, three in the autumn, 8-12 November 2004, 4-9 November 2007, 3-11 November 2008, one in winter, 23-27 January 2006 and one in spring, 9-16 April 2005. -
Beobachtungen Zur Gattung Sowerbyeüa in Österreich
ZOBODAT - www.zobodat.at Zoologisch-Botanische Datenbank/Zoological-Botanical Database Digitale Literatur/Digital Literature Zeitschrift/Journal: Österreichische Zeitschrift für Pilzkunde Jahr/Year: 2003 Band/Volume: 12 Autor(en)/Author(s): Klofac Wolfgang, Voglmayr Hermann Artikel/Article: Beobachtungen zur Gattung Sowerbyella in Österreich. 141-151 ©Österreichische Mykologische Gesellschaft, Austria, download unter www.biologiezentrum.at Osten. Z. Pilzk. 12(2003) 141 Beobachtungen zur Gattung Sowerbyeüa in Österreich WOLFGANG KLOFAC Mayerhöfen 28 A-3074 Michelbach, Österreich HERMANN VOGLMAYR Institut fur Botanik, Universität Wien Rennweg 14 A-1030 Wien, Österreich Email: [email protected] Eingelangt am 16. 9. 2003 Key words: Ascomycetes, Pezizales, Pyronemataceae, Sowerbyella. - Mycoflora of Austria Abstract: Five species of the genus Sowerbyella (S. brevispora, S. fagicola, S. radiculata, S. reguisii and S. rhenana) collected in Austria are described and illustrated, including scanning electron micros- copy pictures of spores. Colour plates of all species except Sowerbyella rhenana are given. Species characteristics, delimitation from similar species and ecology are briefely discussed. Zusammenfassung: Fünf in Österreich beobachtete Arten der Gattung Sowerbyella (S. brevispora, S. Jagicola, S. radiculata, S. reguisii und S. rhenana) werden kurz vorgestellt und mit rasterelektronen- mikroskopischen Fotos illustriert. Zusätzlich werden alle Arten außer Sowerbyella rhenana mit Farb- fotos dokumentiert. Die charakteristischen -
Mycologist News
MYCOLOGIST NEWS The newsletter of the British Mycological Society 2012 (4) Edited by Prof. Pieter van West and Dr Anpu Varghese 2013 BMS Council BMS Council and Committee Members 2013 President Prof. Geoffrey D. Robson Vice-President Prof. Bruce Ing President Elect Prof Nick Read Treasurer Prof. Geoff M Gadd Secretary Position vacant Publications Officer Dr. Pieter van West International Initiatives Adviser Prof. AJ Whalley Fungal Biology Research Committee representatives: Dr. Elaine Bignell; Prof Nick Read Fungal Education and Outreach Committee: Dr. Paul S. Dyer; Dr Ali Ashby Field Mycology and Conservation: Dr. Stuart Skeates, Mrs Dinah Griffin Fungal Biology Research Committee Prof. Nick Read (Chair) retiring 31.12. 2013 Dr. Elaine Bignell retiring 31.12. 2013 Dr. Mark Ramsdale retiring 31.12. 2013 Dr. Pieter van West retiring 31.12. 2013 Dr. Sue Crosthwaite retiring 31.12. 2014 Prof. Mick Tuite retiring 31.12. 2014 Dr Alex Brand retiring 31.12. 2015 Fungal Education and Outreach Committee Dr. Paul S. Dyer (Chair and FBR link) retiring 31.12. 2013 Dr. Ali Ashby retiring 31.12. 2013 Ms. Carol Hobart (FMC link) retiring 31.12. 2012 Dr. Sue Assinder retiring 31.12. 2013 Dr. Kay Yeoman retiring 31.12. 2013 Alan Williams retiring 31.12. 2014 Prof Lynne Boddy (Media Liaison) retiring 31.12. 2014 Dr. Elaine Bignell retiring 31.12. 2015 Field Mycology and Conservation Committee Dr. Stuart Skeates (Chair, website & FBR link) retiring 31.12. 2014 Prof Richard Fortey retiring 31.12. 2013 Mrs. Sheila Spence retiring 31.12. 2013 Mrs Dinah Griffin retiring 31.12. 2014 Dr. -
Molecular Phylogenetic and Scanning Electron Microscopical Analyses
Acta Biologica Hungarica 59 (3), pp. 365–383 (2008) DOI: 10.1556/ABiol.59.2008.3.10 MOLECULAR PHYLOGENETIC AND SCANNING ELECTRON MICROSCOPICAL ANALYSES PLACES THE CHOANEPHORACEAE AND THE GILBERTELLACEAE IN A MONOPHYLETIC GROUP WITHIN THE MUCORALES (ZYGOMYCETES, FUNGI) KERSTIN VOIGT1* and L. OLSSON2 1 Institut für Mikrobiologie, Pilz-Referenz-Zentrum, Friedrich-Schiller-Universität Jena, Neugasse 24, D-07743 Jena, Germany 2 Institut für Spezielle Zoologie und Evolutionsbiologie, Friedrich-Schiller-Universität Jena, Erbertstr. 1, D-07743 Jena, Germany (Received: May 4, 2007; accepted: June 11, 2007) A multi-gene genealogy based on maximum parsimony and distance analyses of the exonic genes for actin (act) and translation elongation factor 1 alpha (tef ), the nuclear genes for the small (18S) and large (28S) subunit ribosomal RNA (comprising 807, 1092, 1863, 389 characters, respectively) of all 50 gen- era of the Mucorales (Zygomycetes) suggests that the Choanephoraceae is a monophyletic group. The monotypic Gilbertellaceae appears in close phylogenetic relatedness to the Choanephoraceae. The mono- phyly of the Choanephoraceae has moderate to strong support (bootstrap proportions 67% and 96% in distance and maximum parsimony analyses, respectively), whereas the monophyly of the Choanephoraceae-Gilbertellaceae clade is supported by high bootstrap values (100% and 98%). This suggests that the two families can be joined into one family, which leads to the elimination of the Gilbertellaceae as a separate family. In order to test this hypothesis single-locus neighbor-joining analy- ses were performed on nuclear genes of the 18S, 5.8S, 28S and internal transcribed spacer (ITS) 1 ribo- somal RNA and the translation elongation factor 1 alpha (tef ) and beta tubulin (βtub) nucleotide sequences. -
Table S5. the Information of the Bacteria Annotated in the Soil Community at Species Level
Table S5. The information of the bacteria annotated in the soil community at species level No. Phylum Class Order Family Genus Species The number of contigs Abundance(%) 1 Firmicutes Bacilli Bacillales Bacillaceae Bacillus Bacillus cereus 1749 5.145782459 2 Bacteroidetes Cytophagia Cytophagales Hymenobacteraceae Hymenobacter Hymenobacter sedentarius 1538 4.52499338 3 Gemmatimonadetes Gemmatimonadetes Gemmatimonadales Gemmatimonadaceae Gemmatirosa Gemmatirosa kalamazoonesis 1020 3.000970902 4 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas indica 797 2.344876284 5 Firmicutes Bacilli Lactobacillales Streptococcaceae Lactococcus Lactococcus piscium 542 1.594633558 6 Actinobacteria Thermoleophilia Solirubrobacterales Conexibacteraceae Conexibacter Conexibacter woesei 471 1.385742446 7 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas taxi 430 1.265115184 8 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas wittichii 388 1.141545794 9 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas sp. FARSPH 298 0.876754244 10 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sorangium cellulosum 260 0.764953367 11 Proteobacteria Deltaproteobacteria Myxococcales Polyangiaceae Sorangium Sphingomonas sp. Cra20 260 0.764953367 12 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas panacis 252 0.741416341 -
Tile Geoglossaceae of Sweden **
ARKIV FOR· BOTANIK. BAND 30 A. N:o 4. Tile Geoglossaceae of Sweden (with Regard also to the Surrounding CQuntries). By J. A. NANNFELDT. With 5 plates and 6 figures in the text. Communicated June 4th, 1941, by NILS E. SVEDELIUS and ROB. E. FRIES. There are hardly any Discomycetes that have been the subject of so many monographs as the Geoglossaceae. Already in 1875, COOKE (1875 a, 1875 b) published two monographic studies, and some years later he described and illustrated in his Mycographia (COOKE 1879) the majority of the species known at that time. In 1897, MAssEE published a world monograph of the family, though this paper - as so many other publications by the same author - is mainly a compi lation. DURA.ND'S monog-raph (1908, with a supplement in 19~1) of the North American species is a model of accuracy and thoroughness, and indispensable also for other parts of the world. This monograph was the base for a pamphlet by LLOYD (1916) on the Geoglossaceae of the world. If we add v. LUYK'S revision (1919) of the Geoglossaceae in the Rijks herbarium at Leiden, with all PERSOON'S specimens, SINDEN & FITZPATRICK'S paper (1930) on a new species of T1'ichoglos8ttrli, IMAI'S studies (1934, 1936 a, 1936 b, 1938) on Japanese species of certain genera, his list of the Norwegian Geoglos8aceae (IMA.I 1940), and MAIN'S papers (1936, 19~0) with descriptions of several new American species, the most important contri butions of recent date to the taxonomy of the family have been mentioned. -
Previously Uncultured Marine Bacteria Linked to Novel Alkaloid Production
UC San Diego UC San Diego Previously Published Works Title Previously Uncultured Marine Bacteria Linked to Novel Alkaloid Production. Permalink https://escholarship.org/uc/item/6263h6gw Journal Chemistry & biology, 22(9) ISSN 1074-5521 Authors Choi, Eun Ju Nam, Sang-Jip Paul, Lauren et al. Publication Date 2015-09-01 DOI 10.1016/j.chembiol.2015.07.014 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Resource Previously Uncultured Marine Bacteria Linked to Novel Alkaloid Production Graphical Abstract Authors Eun Ju Choi, Sang-Jip Nam, Lauren Paul, ..., Christopher A. Kauffman, Paul R. Jensen, William Fenical Correspondence [email protected] In Brief Choi et al. illustrate that low-nutrient media and long incubation times lead to the isolation of rare, previously uncultured marine bacteria that produce new antibacterial metabolites. Their work demonstrates that unique marine bacteria are easier to cultivate than previously suggested. Highlights Accession Numbers d Simple methods allow the isolation of rare, previously JN703500 KJ572269 uncultured marine bacteria JN703501 KJ572270 JN703502 KJ572271 d Previously uncultured marine bacteria produce new JN703503 KJ572272 antibacterial metabolites JN368460 KJ572273 JN368461 KJ572274 KJ572262 KJ572275 KJ572263 KJ572264 KJ572265 KJ572266 KJ572267 KJ572268 Choi et al., 2015, Chemistry & Biology 22, 1–10 September 17, 2015 ª2015 Elsevier Ltd All rights reserved http://dx.doi.org/10.1016/j.chembiol.2015.07.014 Please cite this article in press as: Choi et al., Previously Uncultured Marine Bacteria Linked to Novel Alkaloid Production, Chemistry & Biology (2015), http://dx.doi.org/10.1016/j.chembiol.2015.07.014 Chemistry & Biology Resource Previously Uncultured Marine Bacteria Linked to Novel Alkaloid Production Eun Ju Choi,1,2,3 Sang-Jip Nam,1,2,4 Lauren Paul,1 Deanna Beatty,1 Christopher A. -
Pyronemataceae, Pezizales) Based on Molecular and Morphological Data
Mycol Progress (2012) 11:699–710 DOI 10.1007/s11557-011-0779-5 ORIGINAL ARTICLE The taxonomic position of the genus Heydenia (Pyronemataceae, Pezizales) based on molecular and morphological data Adrian Leuchtmann & Heinz Clémençon Received: 12 May 2011 /Revised: 19 July 2011 /Accepted: 21 July 2011 /Published online: 9 August 2011 # German Mycological Society and Springer 2011 Abstract Molecular and morphological data indicate that easily becomes accepted as true, without proof, in the the genus Heydenia is closely related to the cleistothecial mycological literature. One case of such questionable ascomycete Orbicula (Pyronemataceae, Pezizales). Obser- reasoning is exemplified by the genus Heydenia. vations on the disposition and the immediate surroundings Since fungi with fruiting bodies of unusual or misleading of immature spores within the spore capsule suggest that form are difficult to fit into a classification based on the Heydenia fruiting bodies are teleomorphs producing morphology alone, many genera were left unclassified early evanescent asci in stipitate cleistothecia. The once («incertae sedis») or were assigned by guesswork to a advocated identity of Heydenia with Onygena is refuted on taxonomic group until more objective criteria based on molecular grounds. Onygena arietina E. Fischer is trans- analyses of DNA sequences indicated a firm phylogenetic ferred to Heydenia. relationship. Examples of such genera are Torrendia (stipitate gasteromycete-like, Hallen et al. 2004), Thaxter- Keywords Ascomycota . Beta tubulin . Cleistothecium . ogaster (stipitate sequestrate, Peintner et al. 2002)and Histology. nuLSU . Orbicula . Phylogeny Physalacria (columnar hollow, Wilson and Desjardin 2005) among the basidiomycetes, and Neolecta (columnar, Landvik et al. 2001), Trichocoma (cup-shaped with a Introduction protruding tuft, Berbee et al. -
Lycopene Overproduction in Saccharomyces Cerevisiae Through
Chen et al. Microb Cell Fact (2016) 15:113 DOI 10.1186/s12934-016-0509-4 Microbial Cell Factories RESEARCH Open Access Lycopene overproduction in Saccharomyces cerevisiae through combining pathway engineering with host engineering Yan Chen1,2, Wenhai Xiao1,2* , Ying Wang1,2, Hong Liu1,2, Xia Li1,2 and Yingjin Yuan1,2 Abstract Background: Microbial production of lycopene, a commercially and medically important compound, has received increasing concern in recent years. Saccharomyces cerevisiae is regarded as a safer host for lycopene production than Escherichia coli. However, to date, the lycopene yield (mg/g DCW) in S. cerevisiae was lower than that in E. coli and did not facilitate downstream extraction process, which might be attributed to the incompatibility between host cell and heterologous pathway. Therefore, to achieve lycopene overproduction in S. cerevisiae, both host cell and heterologous pathway should be delicately engineered. Results: In this study, lycopene biosynthesis pathway was constructed by integration of CrtE, CrtB and CrtI in S. cerevisiae CEN.PK2. When YPL062W, a distant genetic locus, was deleted, little acetate was accumulated and approxi- mately 100 % increase in cytosolic acetyl-CoA pool was achieved relative to that in parental strain. Through screening CrtE, CrtB and CrtI from diverse species, an optimal carotenogenic enzyme combination was obtained, and CrtI from Blakeslea trispora (BtCrtI) was found to have excellent performance on lycopene production as well as lycopene pro- portion in carotenoid. Then, the expression level of BtCrtI was fine-tuned and the effect of cell mating types was also evaluated. Finally, potential distant genetic targets (YJL064W, ROX1, and DOS2) were deleted and a stress-responsive transcription factor INO2 was also up-regulated. -
On the Structure, Ecology and Distribution of the Species of Mitrula S.Lat
On the structure, ecology and distribution of the species of Mitrula s.lat. (Ascomycetes, Geoglossaceae) Esteri Kankainen The Subarctic Research Station of the University of Turku, Turku. Finland Introduction the notes of KALLIO & KANKAINEN ( 1964, 1966) are also plotted on the maps (Figs. 1, The matter under consideration is a part 3). of my research including the larger fungi in I express my best thanks. for direction and arctic and subarctic regions. For eight years I advice of great value to my teacher Prof. Paa have also collected Mitrula material, and so vo Kallio, for valuable notes and discussion me notes are published in KALLIO & KANKAI to Phil. lie. Tauno Ulvinen, for determinat NEN (1964, 1966 ). I have had the opportunity ion of the mosses in question to Phil. mag. to participate on the excursions of Kevo, the Unto Laine, and for the linguistic revision to Subarctic Research Station of the University Mrs. Linna Miiller-Wille. I have received of Turku under the leadership of Prof. Paavo financial support from Suomen. Kulttuurira Kallio. Our Mitrula collections from these hasto. trips to Spitsbergen in 1966 and northeastern Mit r u l a Fr., Syst. Myc. 1, p. 491. 1821. Canada in 1967 are taken into consideration (sensu strict.) in the present paper. The specimens studied lMAI ( 1941 ) and MAAS GEESTERANUS are preserved in the following herbariums: ( 1964) have unravelled the history of the genus Mitrula, and we only ascertain the lar H Botanical Museum of the Univer ge variation in its content from one extreme sity of Helsinki to the other, from the wide opinion of HFR Finnish Forest Research Institute, KARSTEN ( 1871) and MASSEE ( 1897) to the Helsinki narrow one of IMAI (1941, 1956) and MAAS HPP Department of Phytopathology, GEESTERANUS ( 1964). -
Sept. (Ascom Ycetes) Rijksherbarium, Leiden Pyronemataceae (Merkus
PERSOONIA Published by the Rijksherbarium, Leiden Volume Part 8, 3, pp. 227-247 (1975) Ultrastructure of the ascospore wall in Pezizales (Ascomycetes) —III. Otideaceae and Pezizaceae Emily Merkus Rijksherbarium, Leiden (With Plates 34-45) The of wall and ornamentation of is studied development layers ascospores with the electron microscope in members of the Otideaceae and Pezizaceae. and the in Ascodesmis Primary wall, endospore, epispore developin sameway as and the Pyronemataceae; the development of the secondary wall and the formation of the patterns ofornamentation resemble that in the Pyronemata- attention is ceae. Special paid to specialized plasmic structures. Introduction earlier I of In papers (Merkus, 1973, 1974) reported my electron microscopy the ultrastructure ofthe wall in Pezizales and discussed theresults Ascodesmis ascospore on and the Pyronemataceae sensu Eckblad (1968). The continuationof this and the results in present paper represents a study gives the Otideaceae and which identical species belonging to Pezizaceae, are practically with the Otideae and Aleurieae ofthe Aleuriaceae of Le Gal (1947: 284). REVIEW OF EARLIER WORK brief review is Like in my paper on the Pyronemataceae (Merkus, 1974), a given of Gal's of ornamentation of the of Le light microscopy the patterns ascospores the Pezizaceae (1947). Though this involves duplication of some of the data, it gives a better overall insight and makes it easier to interpret new results. According to the rules of the international code of botanicalnomenclature some of the names used by Le Gal (see footnotes) had to be changed. ornamentation. The species of Pezizaceae studied by Le Gal develop simple spore In all the wall arises and it is the species a primary ornamentation on present; orna- mentation consists of callose and pectine formations and is of sporal origin.