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Osl Dating of High-Elevation Alluvial Sediments: Mcmurdo Dry
OSL DATING OF HIGH-ELEVATION ALLUVIAL SEDIMENTS: MCMURDO DRY VALLEYS, ANTARCTICA A Thesis Submitted to the Graduate Faculty of the North Dakota State University of Agriculture and Applied Science By Meridith Ann Ramsey In Partial Fulfillment of the Requirements for the Degree of MASTER OF SCIENCE Major Program: Environmental and Conservation Science November 2014 Fargo, North Dakota North Dakota State University Graduate School Title OSL DATING OF HIGH-ELEVATION ALLUVIAL SEDIMENTS: MCMURDO DRY VALLEYS, ANTARCTICA By Meridith Ann Ramsey The Supervisory Committee certifies that this disquisition complies with North Dakota State University’s regulations and meets the accepted standards for the degree of MASTER OF SCIENCE SUPERVISORY COMMITTEE: Kenneth Lepper Chair Adam Lewis Lisa Montplaisir Approved: 04/16/2015 Eakalak Khan Date Department Chair ABSTRACT High-elevation alluvial fans in the McMurdo Dry Valleys are a record of short-term, occasional melting events along the margins of the East Antarctic Ice Sheet. Sediment samples were dated from five fans using Optically Stimulated Luminescence (OSL) dating. OSL dates the time since quartz grains were last exposed to sunlight; all sample preparation takes place in a dark room. Thirteen samples were dated for this thesis, the ages were stratigraphically consistent and ranged from 1.1 ka to 105.9 ka. Clusters of fan activity occurred between 1.1 and 3.1 ka and 8.1 and 11.1 ka. The melting events appear to be linked to insolation, with periods of fan activity occurring usually at times of increased mean annual insolation. The alluvial fans show promise as a possible archive for climate proxies in this region of Antarctica. -
Leaf-Associated Shifts in Bacterial and Fungal Communities in Response to Chicken Rearing Under Moso Bamboo Forests in Subtropical China
Article Leaf-Associated Shifts in Bacterial and Fungal Communities in Response to Chicken Rearing Under Moso Bamboo Forests in Subtropical China Xiaoping Zhang 1, Zheke Zhong 1,*, Xu Gai 1, Jiafu Ying 2, Weifen Li 2, Xuhua Du 1, Fangyuan Bian 1 and Chuanbao Yang 1 1 China National Bamboo Research Center, Key Laboratory of Resources and Utilization of Bamboo of State Forestry Administration, Hangzhou 310012, China; [email protected] (X.Z.); [email protected] (X.G.); [email protected] (X.D.); [email protected] (F.B.); [email protected] (C.Y.) 2 College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; [email protected] (J.Y.); wfl[email protected] (W.L.) * Correspondence: [email protected]; Tel.: +86-0571-88860734 Received: 25 January 2019; Accepted: 25 February 2019; Published: 1 March 2019 Abstract: Integrated bamboo-chicken farming (BCF) systems are a traditional agroforestry pattern with large economic benefits in subtropical China. However, little is known regarding the effect of this integration on the bamboo leaf-associated microbiome, which can be very important for disease control and nutrient turnover. In the present study, we compared the leaf-associated bacterial and fungal communities of moso bamboo (Phyllostachys edulis) in a BCF system and an adjacent moso bamboo forest (MBF). The results showed that Cyanobacteria and Ascomycota were the predominant microbial phyla associated with bamboo leaves. Chicken farming under the bamboo forest significantly increased the bacterial and fungal alpha diversity (observed operational taxonomic units (OTUs) and Simpson’s index) associated with bamboo leaves. Principal components analysis (PCoA) further confirmed the shifts in the bacterial and fungal communities caused by chicken farming. -
Microbial Dispersal Limitation to Isolated Soil Habitats in the Mcmurdo Dry Valleys
bioRxiv preprint doi: https://doi.org/10.1101/493411; this version posted December 13, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Microbial dispersal limitation to isolated soil habitats in the McMurdo Dry Valleys 2 of Antarctica 3 4 Stephen D.J. Archer1,2, Kevin C. Lee2, Tancredi Caruso3, Teruya Maki4, Charles K. Lee5, 5 Don A. Cowan6, Fernando T. Maestre7, Stephen B. Pointing1,8 6 7 1 Yale-NUS College, National University of Singapore, Singapore 138527 8 2 Institute for Applied Ecology New Zealand, Auckland University of Technology, Auckland 9 1142, New Zealand 10 3 School of Biological Sciences and Global Institute for Food Security, Queen's University 11 Belfast, Belfast BT9 7BL, Northern Ireland, UK 12 4 Department of Chemical Engineering, Kanazawa University, Kanazawa 920-1192, Japan 13 5 International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton 14 3240, New Zealand 15 6 Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria 0002, South 16 Africa 17 7 Departamento de Biología y Geología, Física y Química Inorgánica, Escuela Superior de 18 Ciencias Experimentales y Tecnología, Universidad Rey Juan Carlos, C/ Tulipán s/n, 28933 19 Móstoles, Spain 20 8 Department of Biological Sciences, National University of Singapore, Singapore 117558 21 1 bioRxiv preprint doi: https://doi.org/10.1101/493411; this version posted December 13, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. -
Catalogue of Bacteria Shapes
We first tried to use the most general shape associated with each genus, which are often consistent across species (spp.) (first choice for shape). If there was documented species variability, either the most common species (second choice for shape) or well known species (third choice for shape) is shown. Corynebacterium: pleomorphic bacilli. Due to their snapping type of division, cells often lie in clusters resembling chinese letters (https://microbewiki.kenyon.edu/index.php/Corynebacterium) Shown is Corynebacterium diphtheriae Figure 1. Stained Corynebacterium cells. The "barred" appearance is due to the presence of polyphosphate inclusions called metachromatic granules. Note also the characteristic "Chinese-letter" arrangement of cells. (http:// textbookofbacteriology.net/diphtheria.html) Lactobacillus: Lactobacilli are rod-shaped, Gram-positive, fermentative, organotrophs. They are usually straight, although they can form spiral or coccobacillary forms under certain conditions. (https://microbewiki.kenyon.edu/index.php/ Lactobacillus) Porphyromonas: A genus of small anaerobic gram-negative nonmotile cocci and usually short rods thatproduce smooth, gray to black pigmented colonies the size of which varies with the species. (http:// medical-dictionary.thefreedictionary.com/Porphyromonas) Shown: Porphyromonas gingivalis Moraxella: Moraxella is a genus of Gram-negative bacteria in the Moraxellaceae family. It is named after the Swiss ophthalmologist Victor Morax. The organisms are short rods, coccobacilli or, as in the case of Moraxella catarrhalis, diplococci in morphology (https://en.wikipedia.org/wiki/Moraxella). *This one could be changed to a diplococcus shape because of moraxella catarrhalis, but i think the short rods are fair given the number of other moraxella with them. Jeotgalicoccus: Jeotgalicoccus is a genus of Gram-positive, facultatively anaerobic, and halotolerant to halophilicbacteria. -
The RDP-II Backbone Tree for Release 8.0. the Tree Was Inferred from a Distance Matrix Generated in PAUP* with the Weighbor (Weighted Neighbor Joining) Algorithm
Methylococcus capsulatus ACM 1292 (T) Oceanospirillum linum ATCC 11336 (T) Halomonas halodenitrificans ATCC 13511 (T) Legionella lytica PCM 2298 (T) Francisella tularensis subsp. tularensis ATCC 6223 (T) Coxiella burnetii Q177 Moraxella catarrhalis ATCC 25238 (T) Pseudomonas fluorescens IAM 12022 (T) Piscirickettsia salmonis LF-89 (T) Thiothrix nivea DSM 5205 (T) Allochromatium minutissimum DSM 1376 (T) Alteromonas macleodii IAM 12920 (T) Aeromonas salmonicida subsp. smithia CCM 4103 (T) Pasteurella multocida NCTC 10322 (T) Enterobacter nimipressuralis LMG 10245 (T) Vibrio vulnificus ATCC 27562 (T) Ectothiorhodospira mobilis DSM237 (T) Xanthomonas campestris LMG 568 (T) Cardiobacterium hominis ATCC 15826 (T) Methylophilus methylotrophus ATCC 53528 (T) Rhodocyclus tenuis DSM 109 (T) Hydrogenophilus thermoluteolus TH-1 (T) Neisseria gonorrhoeae NCTC 8375 (T) Comamonas testosteroni ATCC 11996 (T) Nitrosospira multiformis ATCC 25196 (T) Spirillum volutans ATCC 19554 (T) Burkholderia glathei LMG 14190 (T) Alcaligenes defragrans DSM 12141 (T) Oxalobacter formigenes ATCC 35274 (T) Acetobacter oboediens DSM 11826 (T) clone CS93 PROTEOBACTERIA Caedibacter caryophilus 221 (T) Rhodobacter sphaeroides ATCC 17023 (T) Rickettsia rickettsii ATCC VR-891 (T) Ehrlichia risticii ATCC VR-986 (T) Sphingomonas paucimobilis GIFU 2395 (T) Caulobacter fusiformis ATCC 15257 (T) Rhodospirillum rubrum ATCC 11170 (T) Brucella melitensis ATCC 23459 (T) Rhizobium tropici IFO 15247 (T) Bartonella vinsonii subsp. vinsonii ATCC VR-152 (T) Phyllobacterium myrsinacearum -
Bacterial Community Structure in High-Arctic Snow and Freshwater As Revealed by Pyrosequencing of 16S Rrna Genes and Cultivation Annette K
RESEARCH/REVIEW ARTICLE Bacterial community structure in High-Arctic snow and freshwater as revealed by pyrosequencing of 16S rRNA genes and cultivation Annette K. Møller,1 Ditte A. Søborg,1 Waleed Abu Al-Soud,2 Søren J. Sørensen2 & Niels Kroer1 1 Department of Environmental Science, Aarhus University, Frederiksborgvej 399, DK-4000 Roskilde, Denmark 2 Department of Biology, University of Copenhagen, Sølvgade 83H, DK-1307 K Copenhagen, Denmark Keywords Abstract Taxonomic diversity; microbial assemblages; bacterial density; DOC. The bacterial community structures in High-Arctic snow over sea ice and an ice-covered freshwater lake were examined by pyrosequencing of 16S rRNA Correspondence genes and 16S rRNA gene sequencing of cultivated isolates. Both the Niels Kroer, pyrosequence and cultivation data indicated that the phylogenetic composition Department of Environmental Science, of the microbial assemblages was different within the snow layers and between Aarhus University, snow and freshwater. The highest diversity was seen in snow. In the middle Frederiksborgvej 399, and top snow layers, , and dominated, DK-4000 Roskilde, Denmark. Proteobacteria Bacteroidetes Cyanobacteria E-mail: [email protected] although Actinobacteria and Firmicutes were relatively abundant also. High numbers of chloroplasts were also observed. In the deepest snow layer, large percentages of Firmicutes and Fusobacteria were seen. In freshwater, Bacter- oidetes, Actinobacteria and Verrucomicrobia were the most abundant phyla while relatively few Proteobacteria and Cyanobacteria were present. Possibly, light intensity controlled the distribution of the Cyanobacteria and algae in the snow while carbon and nitrogen fixed by these autotrophs in turn fed the heterotrophic bacteria. In the lake, a probable lower light input relative to snow resulted in low numbers of Cyanobacteria and chloroplasts and, hence, limited input of organic carbon and nitrogen to the heterotrophic bacteria. -
Microclimate and Weathering Processes in the Area of Darwin
relationship between the folds reported by Burgess (in Findlay, R. H. 1978. Provisional report on the geology of the region press) and those described here cannot be determined from between the Renegar and Blue Glaciers, Antarctica. New Zealand present evidence. Antarctic Record, 1, 39-44. Skinner (1964, 1965) named the rocks at Mt. Madison the Grindley, G. W., McGregor, V. R., and Walcott, R. I. 1964. Outline Selborne Marble and distinguished them from the Shack- of the geology of the Nimrod-Beardmore-Axel Heiberg Glaciers region, Ross dependency. In Adie (Ed.), leton Limestone due to their higher metamorphic grade. He R. J. Antarctic geology. Amsterdam: North-Holland Publishing. suggested that they may be Precambrian in age, correlative with the Nimrod Group in the Miller Range (Grindley, Skinner, D. N. B. 1964, A summary of the geology of the region McGregor, and Walcott 1964). If this is the case, deforma- between Byrd and Starshot glaciers, south Victoria Land, In Adie (Ed.), Antarctic geology. Amsterdam: North-Holland tion at Mt. Madison is probably not related to the Shackle- R. J. Publishing. ton Limestone south of Byrd Glacier. Skinner, D. N. B. 1965. Petrographic criteria of the rock units To me, lithologies at Mt. Madison appear similar to those between the Byrd and Starshot Glaciers, south Victoria Land, of the Shackleton Limestone and pelitic Dick Formation Antarctica. New Zealand Journal of Geology and Geophysics, 8, (Skinner 1965), and I would suggest that the Selborne Mar- 292-303. ble is a metamorphosed equivalent of those two formations. Skinner, D. N. B. In press. Stratigraphy and structure of lower The metamorphic grade suggests an adjacent granitic pluton grade metasediments of Skelton Group, McMurdo Sound—Does north of Mt. -
University Microfilms, a XEROX Company, Ann Arbor, Michigan
I I 72-15,173 BEHLING, Robert Edward, 1941- PEDOLOGICAL DEVELOPMENT ON MORAINES OF THE MESERVE GLACIER, ANTARCTICA. The Ohio State University in cooperation with Miami (Ohio) University, Ph.D., 1971 Geology University Microfilms,A XEROX Company , Ann Arbor, Michigan PEDOLOGICAL DEVELOPMENT ON MORAINES OF THE MESERVE GLACIER, ANTARCTICA DISSERTATION Presented In Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Robert E. Behling, B.Sc., M*Sc. ***** The Ohio State University 1971 Approved by Adv Department f Geology PLEASE NOTE: Some pages have indistinct print. Filmed as received. University Microfilms, A Xerox Education Company ACKNOWLEDGEMENTS This study could not have been possible without the cooperation of faculty members of the departments of agronomy, mineralogy, and geology, I wish to thank Dr. R. P. Goldthwait as chairman of my committee, Dr. L. P. Wilding and Dr. R. T. Tettenhorst as members of my reading committee, as well as Dr. C. B. Bull and Dr. K. R. Everett for valuable assistance and criticism of the manuscript. A special thanks is due Dr. K. R. Everett for guidance during that first field season, and to Dr. F. Ugolini who first introduced me to the problems of weathering in cold deserts. Numerous people contributed to this end result through endless discussions: Dr. Lois Jones and Dr. P. Calkin receive special thanks, as do Dr. G. Holdsworth and Maurice McSaveney. Laboratory assistance was given by Mr. Paul Mayewski and R. W. Behling. Field logistic support in Antarctica was supplied by the U.S. -
Within-Arctic Horizontal Gene Transfer As a Driver of Convergent Evolution in Distantly Related 2 Microalgae
bioRxiv preprint doi: https://doi.org/10.1101/2021.07.31.454568; this version posted August 2, 2021. 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 Within-Arctic horizontal gene transfer as a driver of convergent evolution in distantly related 2 microalgae 3 Richard G. Dorrell*+1,2, Alan Kuo3*, Zoltan Füssy4, Elisabeth Richardson5,6, Asaf Salamov3, Nikola 4 Zarevski,1,2,7 Nastasia J. Freyria8, Federico M. Ibarbalz1,2,9, Jerry Jenkins3,10, Juan Jose Pierella 5 Karlusich1,2, Andrei Stecca Steindorff3, Robyn E. Edgar8, Lori Handley10, Kathleen Lail3, Anna Lipzen3, 6 Vincent Lombard11, John McFarlane5, Charlotte Nef1,2, Anna M.G. Novák Vanclová1,2, Yi Peng3, Chris 7 Plott10, Marianne Potvin8, Fabio Rocha Jimenez Vieira1,2, Kerrie Barry3, Joel B. Dacks5, Colomban de 8 Vargas2,12, Bernard Henrissat11,13, Eric Pelletier2,14, Jeremy Schmutz3,10, Patrick Wincker2,14, Chris 9 Bowler1,2, Igor V. Grigoriev3,15, and Connie Lovejoy+8 10 11 1 Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, 12 INSERM, Université PSL, 75005 Paris, France 13 2CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, 14 FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France 15 3 US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 16 Cyclotron Road, Berkeley, -
CALIFORNIA STATE UNIVERSITY, NORTHRIDGE Comparative
CALIFORNIA STATE UNIVERSITY, NORTHRIDGE Comparative Genomics and Epigenomics of Sporosarcina ureae A thesis submitted in partial fulfillment of the requirement for the degree of Master of Science in Biology By Andrew Oliver August 2016 The thesis of Andrew Oliver is approved by: _________________________________________ ____________ Sean Murray, Ph.D. Date _________________________________________ ____________ Gilberto Flores, Ph.D. Date _________________________________________ ____________ Kerry Cooper, Ph.D., Chair Date California State University, Northridge ii Acknowledgments First and foremost, a special thanks to my advisor, Dr. Kerry Cooper, for his advice and, above all, his patience. If I can be half the scientist you are someday, I would be thrilled. I would like to also thank everyone in the Cooper lab, especially my colleagues Courtney Sams and Tabitha Bayangnos. It was a privilege to work along side you. More thanks to my committee members, Dr. Gilberto Flores and Dr. Sean Murray. Dr. Flores, you were instrumental in guiding me to ask the right questions regarding bacterial taxonomy. Dr. Murray, your contributions to my graduate studies would make this section run on for pages. I thank you for taking me under your wing from the beginning. Acknowledgement and thanks to the Baresi lab, especially Dr. Larry Baresi and Tania Kurbessoian for their partnership in this research. Also to Bernardine Pregerson for all the work that lays at the foundation of this study. This research would not be what it is without the help of my childhood friend, Matthew Kay. You wrote programs, taught me coding languages, and challenged me to go digging for answers to very difficult questions. -
Sporosarcina Aquimarina Sjam16103 Isolated from the Pneumatophores of Avicennia Marina L
Hindawi Publishing Corporation International Journal of Microbiology Volume 2012, Article ID 532060, 10 pages doi:10.1155/2012/532060 Research Article Plant Growth Promoting of Endophytic Sporosarcina aquimarina SjAM16103 Isolated from the Pneumatophores of Avicennia marina L. S. Rylo Sona Janarthine1 and P. Eganathan2 1 Faculty of Marine Science, Annamalai University, Chidambaram 608 502, India 2 Biotechnology Division, M S Swaminathan Research Foundation, Chennai 600 113, India Correspondence should be addressed to S. Rylo Sona Janarthine, jana [email protected] Received 17 October 2011; Revised 12 January 2012; Accepted 20 April 2012 AcademicEditor:A.J.M.Stams Copyright © 2012 S. R. S. Janarthine and P. Eganathan. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Endophytic Sporosarcina aquimarina SjAM16103 was isolated from the inner tissues of pneumatophores of mangrove plant Avicennia marina along with Bacillus sp. and Enterobacter sp. Endophytic S. aquimarina SjAM16103 was Gram variable, and motile bacterium measured 0.6–0.9 μm wide by 1.7–2.0 μm long and light orange-brown coloured in 3-day cultures on tryptone broth at 26◦C. Nucleotide sequence of this strain has been deposited in the GenBank under accession number GU930359. This endophytic bacterium produced 2.37 μMol/mL of indole acetic acid and siderophore as it metabolites. This strain could solubilize phosphate molecules and fixes atmospheric nitrogen. Endophytic S. aquimarina SjAM16103 was inoculated into four different plants under in vitro method to analyse its growth-promoting activity and role inside the host plants. -
The Two-Domain Tree of Life Is Linked to a New Root for the Archaea
The two-domain tree of life is linked to a new root for the Archaea Kasie Raymanna, Céline Brochier-Armanetb, and Simonetta Gribaldoa,1 aInstitut Pasteur, Department of Microbiology, Unit Biologie Moléculaire du Gène chez les Extrêmophiles, 75015 Paris, France; and bUniversité de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, 69622 Villeurbanne, France Edited by W. Ford Doolittle, Dalhousie University, Halifax, NS, Canada, and approved April 17, 2015 (received for review November 02, 2014) One of the most fundamental questions in evolutionary biology is restricted taxonomic sampling, notably for the outgroup, may also the origin of the lineage leading to eukaryotes. Recent phyloge- generate or mask potential tree reconstruction artifacts (16). All nomic analyses have indicated an emergence of eukaryotes from these considerations emphasize that we have not yet found a way within the radiation of modern Archaea and specifically from a group out of the phylogenomic impasse caused by the use of universal comprising Thaumarchaeota/“Aigarchaeota” (candidate phylum)/ trees to investigate the relationships among Archaea and eu- Crenarchaeota/Korarchaeota (TACK). Despite their major im- karyotes (12). plications, these studies were all based on the reconstruction of Here, we have applied an original two-step strategy that we universal trees and left the exact placement of eukaryotes with re- proposed a few years ago which involves separately analyzing the spect to the TACK lineage unclear. Here we have applied an original markers shared between Archaea and eukaryotes and between two-step approach that involves the separate analysis of markers Archaea and Bacteria (12). This strategy allowed us to use a larger shared between Archaea and eukaryotes and between Archaea and taxonomic sampling, more markers and thus more positions, have Bacteria.