DOCSLIB.ORG

MIAMI UNIVERSITY the Graduate School Certificate for Approving the Dissertation

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

MIAMI UNIVERSITY The Graduate School Certificate for Approving the Dissertation We hereby approve the Dissertation of Wei Li Candidate for the Degree: Doctor of Philosophy Dr. Rachael Morgan-Kiss, Director Dr. Annette Bollmann, Reader Dr. Thomas Crist, Reader Dr. Michael Vanni, Reader Dr. Richard Edelmann, Graduate School Representative Dr. Rebecca Gast, Distinguished Off Campus Scholar ABSTRACT INFLUENCE OF ENVIRONMENTAL DRIVERS AND INTERACTIONS ON THE MICROBIAL COMMUNITY STRUCTURE IN PERMANENTLY STRATIFIED MEROMICTIC ANTARCTIC LAKES by Wei Li The microbial loop plays important roles in the cycling of energy, carbon and elements in aquatic ecosystems. Viruses, bacteria, Archaea and microbial eukaryotes are key players in global carbon cycle and biogeochemical cycles. Investigating microbial diversity and community structure is crucial first step for understanding the ecological functioning in aquatic environment. Meromictic lakes are bodies of water and exhibit permanent stratification of major physical and chemical environmental factors. Microbial consortia residing in permanently stratified lakes exhibit relatively constant spatial stratification throughout the water column and are adapted to vastly different habitats within the same water. Pristine perennially-ice-covered lakes (Lake Bonney, Lake Fryxell and Lake Vanda) are meromictic lakes located in the McMurdo Dry Valleys (MDV) of Southern Victoria Land, Antarctica. The lakes have isolated water bodies and extremely stable strata that vary physically, chemically, and biologically within and between the water columns. The unique characteristics support microbially dominated food webs in these lakes. In the research presented here, we gathered new understanding of how environmental drivers influence microbial community structure in these aquatic ecosystems. We explored the lake microbial ecology from three major approaches: 1). Assess trophic activities in the natural environment and identify potential environmental drivers impacting heterotrophic (β Glucosaminidase) and autotrophic (Ribulose 1,5 bisphosphate carboxylase) enzyme activities; 2). Resolve the protist community composition (i.e. autotrophic, heterotrophic and mixotrophic groups) based on high throughput sequencing and bioinformatics. Identify how the community structures correlate with specific environmental and biological factors; 3). Reveal the diversity of potential microbial interactions between the microorganisms in the MDV lakes at individual cell level, and investigate how the interactions vary between organisms with different nutritional strategies. Studies of polar microbial communities on the cusp of environmental change will be important for predicting how microbial communities in low latitude aquatic systems will respond. This study expands the understanding of how environmental drivers interact with microbial communities in the Antarctica lakes, and provide new information to predict how the community structure will alter as response to climate changes. INFLUENCE OF ENVIRONMENTAL DRIVERS AND INTERACTIONS ON THE MICROBIAL COMMUNITY STRUCTURES IN PERMANENTLY STRATIFIED MEROMICTIC ANTARCTIC LAKES A DISSERTATION Submitted to the faculty of Miami University In partial fulfillment of the requirements for the degree of Doctor of Philosophy Department of Microbiology Ecology, Evolution and Environmental Biology Program by Wei Li Miami University Oxford, OH 2016 Advisor: Dr. Rachael Morgan-Kiss TABLE OF CONTENTS PAGE List of Tables v List of Figures vi Acknowledgments vii Chapter I: Introduction 1.1. introduction 2 Chapter II: Spatial heterogeneity and the impact of biotic and abiotic drivers on microbial autotrophic and heterotrophic activities in three chemically stratified Antarctic lakes 2.1. Introduction 16 2.2. Materials and methods 20 2.2.1. Field sampling and limnological parameters 20 2.2.2. Rubisco carboxylase activity assay 21 2.2.3. Glucosaminidase activity assay 21 2.2.4. Protein concentration determination 22 2.2.5. Bacterial enumeration 22 2.2.6. Statistical analyses 23 2.3. Results 24 2.3.1. Lake Bonney 24 2.3.2. Lake Fryxell 25 2.3.3. Lake Vanda 25 2.3.4. Cluster analyses of lake physicochemical parameters 26 2.3.5. Correlation of autotrophic and heterotrophic activities with physicochemical parameters 26 2.4. Discussion 28 2.5. Acknowledgements. 32 2.6. References 41 Chapter III: Influence of environmental drivers and potential interactions on the distribution of microbial communities from three permanently stratified Antarctic lakes 3.1. Introduction 45 3.2. Materials and methods 48 3.2.1. Site description and sample collection 48 3.2.2. Environmental parameter measurements 48 3.2.3. DNA library preparation and Illumina MiSeq Sequencing 49 3.2.4. Sequence analysis 49 3.2.5. Diversity assessment 50 3.2.6. Network analysis 50 3.3. Results 52 3.3.1. Environmental parameters 52 3.3.2. Ilumina MiSeq sequencing summary 52 iii 3.3.3. Bacterial community composition 53 3.3.4. Eukaryotic community composition 54 3.3.5. Co-occurrence microbial network and associated environmental factors 55 3.4. Discussion 57 3.5. Acknowledgements. 61 3.6. References 76 Chapter IV: Ultrastructural and single-cell level characterization reveals metabolic versatility in a microbial eukaryote community from an ice-covered Antarctic lake 4.1. Introduction 87 4.2. Materials and methods 90 4.2.1. Site description, sample collection and enrichment cultures 90 4.2.2. Single cell sorting 91 4.2.3. DNA template preparation for PCR 91 4.2.4. Sanger sequencing 92 4.2.5. Illumina sequencing 92 4.2.6. Analysis of the sequences 93 4.2.7. Confocal Laser Scanning Microscopy 93 4.2.8. Scanning Electron Microscopy 94 4.3. Results and discussion 95 4.3.1. Identities and trophic modes of sorted eukaryotes 95 4.3.2. Isolation and description of two key photosynthetic protists 98 4.3.3. Community composition of organisms co-sorted with Lake Bonney eukaryotes 99 4.3.4. Potential interactions between Dry Valley protists and bacteria 100 4.4. Conclusions 105 4.5. Acknowledgements 105 4.6. References 112 Chapter V: Conclusions 5.1 Conclusions 127 5.2 References 133 iv LIST OF TABLES PAGE 1. Pearson correlation coefficient values (R) for average RubisCO and βGAM activity with lake physical, chemical, and biological parameters for all samples 39 2. Linear regression models explaining the enzyme activities in different portions of water columns 40 3. Summary of major physicochemical parameters in the studied lakes 68 4. Pairwise comparison of species richness between lakes using Tukey’s HSD test 69 5. ANOSIM of communities from different lakes and layers 70 6. List of nodes in co-occurrence network 72 7. Basic growth physiology of Chlamydomonas sp. ICE-MDV and Isochrysis sp. MDV isolates 121 8. Diversity of major algal classes in Lake Bonney enrichment cultures 122 v LIST OF FIGURES PAGE 1. Schematic of Microbial loop and energy flows in aquatic environment 7 2. Map showing locations of study sites within the McMurdo Dry Valleys, Antarctica 8 3. Depth profiles of physical and chemical characteristics for the MDV lakes in this study 9 4. Map showing locations of study sites within the McMurdo Dry Valleys, Antarctica 33 5. Salinity profiles for Lake Bonney (east lobe, ELB; west lobe, WLB), Lake Fryxell (FRX) and Lake Vanda (VAN) 34 6. Depth profiles of physical and chemical characteristics for the three lakes in this study 35 7. Depth profiles for phytoplankton biomass (Chl a) and bacterial abundance for study sites 36 8. Spatial variability in enzyme activity of RubisCO and β-Glucosaminidase (B-GAM) in study sites 37 9. Hierarchical clustering analysis (HCA) and principal component analysis (PCA) 38 10. Observed and estimated alpha diversity of 16S and 18S OTUs. 62 11. 16S OTUs relative abundance at phylum level 63 12. 18S OTUs relative abundance at phylum level 64 13. NMDS plot of bacterial communities 65 14. NMDS plot of eukaryal communities 66 15. Association network of concurrent of bacteria, eukaryotes and correlation with environmental parameters 67 16. Rarefaction curves of 16S and 18S OTUs 84 17. Representive SEM micrographs of protists found in studied lakes 85 18. Sample cytogram showing flow cytometric sort regions for microbial eukaryotes from an enrichment culture (MDV87) generated from the Antarctic Dry Valley Lake Bonney. 106 19. Maximum-likelihood tree (1000 bootstrap) showing identity of Lake Bonney microbial eukaryote single amplified genomes (EUK-SAGS) recovered from enrichment culture MDV87 107 20. Confocal microscopic images of Chlamydomonas sp. ICE-MDV and Isochrysis sp. MDV isolates 108 21. Principle Coordinates Analysis (PCoA) 109 22. SEM micrographs and the diversity of microbial partners associated with the heterotrophic nanoflagellate Pteridomonas 110 23. Evidence of parasite-host interactions between Lake Bonney microbial eukaryotes. a, Diversity of 16S rRNA gene OTUs recovered from Pirsonia EUK-SAGs 111 24. Confocal microscopic images of Isochrysis sp. MDV isolates without LysoTracker Green staining 123 25. Confocal microscopic images of Chlamydomonas sp. ICE-MDV isolates without LysoTracker Green staining 124 26. Heat map of communities associated with sorted eukaryotic organisms based on 16s rRNA sequence abundance 125 27. Working models of our current understanding of major carbon and energy cycles in Lake Bonney (west) vs. Lake Fryxell 132 vi Acknowledgements I would like to express my sincere appreciation and thanks to my mentor and Team Protist leader, Dr. Rachael Morgan-Kiss, who has been extremely
Recommended publications
  • Management Plan For

    Management Plan For

    Measure 8 (2013) Annex Management Plan for Antarctic Specially Protected Area (ASPA) No.138 Linnaeus Terrace, Asgard Range, Victoria Land Introduction Linnaeus Terrace is an elevated bench of weathered Beacon Sandstone located at the western end of the Asgard Range, 1.5km north of Oliver Peak, at 161° 05.0' E 77° 35.8' S,. The terrace is ~ 1.5 km in length by ~1 km in width at an elevation of about 1600m. Linnaeus Terrace is one of the richest known localities for the cryptoendolithic communities that colonize the Beacon Sandstone. The sandstones also exhibit rare physical and biological weathering structures, as well as trace fossils. The excellent examples of cryptoendolithic communities are of outstanding scientific value, and are the subject of some of the most detailed Antarctic cryptoendolithic descriptions. The site is vulnerable to disturbance by trampling and sampling, and is sensitive to the importation of non-native plant, animal or microbial species and requires long-term special protection. Linnaeus Terrace was originally designated as Site of Special Scientific Interest (SSSI) No. 19 through Recommendation XIII-8 (1985) after a proposal by the United States of America. The SSSI expiry date was extended by Resolution 7 (1995), and the Management Plan was adopted in Annex V format through Measure 1 (1996). The site was renamed and renumbered as ASPA No 138 by Decision 1 (2002). The Management Plan was updated through Measure 10 (2008) to include additional provisions to reduce the risk of non-native species introductions into the Area. The Area is situated in Environment S – McMurdo – South Victoria Land Geologic based on the Environmental Domains Analysis for Antarctica and in Region 9 – South Victoria Land based on the Antarctic Conservation Biogeographic Regions.
  • Bacterial Epibiotic Communities of Ubiquitous and Abundant Marine Diatoms Are Distinct in Short- and Long-Term Associations

    Bacterial Epibiotic Communities of Ubiquitous and Abundant Marine Diatoms Are Distinct in Short- and Long-Term Associations

    fmicb-09-02879 December 1, 2018 Time: 14:0 # 1 ORIGINAL RESEARCH published: 04 December 2018 doi: 10.3389/fmicb.2018.02879 Bacterial Epibiotic Communities of Ubiquitous and Abundant Marine Diatoms Are Distinct in Short- and Long-Term Associations Klervi Crenn, Delphine Duffieux and Christian Jeanthon* CNRS, Sorbonne Université, Station Biologique de Roscoff, Adaptation et Diversité en Milieu Marin, Roscoff, France Interactions between phytoplankton and bacteria play a central role in mediating biogeochemical cycling and food web structure in the ocean. The cosmopolitan diatoms Thalassiosira and Chaetoceros often dominate phytoplankton communities in marine systems. Past studies of diatom-bacterial associations have employed community- level methods and culture-based or natural diatom populations. Although bacterial assemblages attached to individual diatoms represents tight associations little is known on their makeup or interactions. Here, we examined the epibiotic bacteria of 436 Thalassiosira and 329 Chaetoceros single cells isolated from natural samples and Edited by: collection cultures, regarded here as short- and long-term associations, respectively. Matthias Wietz, Epibiotic microbiota of single diatom hosts was analyzed by cultivation and by cloning- Alfred Wegener Institut, Germany sequencing of 16S rRNA genes obtained from whole-genome amplification products. Reviewed by: The prevalence of epibiotic bacteria was higher in cultures and dependent of the host Lydia Jeanne Baker, Cornell University, United States species. Culture approaches demonstrated that both diatoms carry distinct bacterial Bryndan Paige Durham, communities in short- and long-term associations. Bacterial epibonts, commonly University of Washington, United States associated with phytoplankton, were repeatedly isolated from cells of diatom collection *Correspondence: cultures but were not recovered from environmental cells.
  • The Planktonic Protist Interactome: Where Do We Stand After a Century of Research?

    The Planktonic Protist Interactome: Where Do We Stand After a Century of Research?

    bioRxiv preprint doi: https://doi.org/10.1101/587352; this version posted May 2, 2019. 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. Bjorbækmo et al., 23.03.2019 – preprint copy - BioRxiv The planktonic protist interactome: where do we stand after a century of research? Marit F. Markussen Bjorbækmo1*, Andreas Evenstad1* and Line Lieblein Røsæg1*, Anders K. Krabberød1**, and Ramiro Logares2,1** 1 University of Oslo, Department of Biosciences, Section for Genetics and Evolutionary Biology (Evogene), Blindernv. 31, N- 0316 Oslo, Norway 2 Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta, 37-49, ES-08003, Barcelona, Catalonia, Spain * The three authors contributed equally ** Corresponding authors: Ramiro Logares: Institute of Marine Sciences (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Catalonia, Spain. Phone: 34-93-2309500; Fax: 34-93-2309555. [email protected] Anders K. Krabberød: University of Oslo, Department of Biosciences, Section for Genetics and Evolutionary Biology (Evogene), Blindernv. 31, N-0316 Oslo, Norway. Phone +47 22845986, Fax: +47 22854726. [email protected] Abstract Microbial interactions are crucial for Earth ecosystem function, yet our knowledge about them is limited and has so far mainly existed as scattered records. Here, we have surveyed the literature involving planktonic protist interactions and gathered the information in a manually curated Protist Interaction DAtabase (PIDA). In total, we have registered ~2,500 ecological interactions from ~500 publications, spanning the last 150 years.
  • University of Oklahoma

    University of Oklahoma

    UNIVERSITY OF OKLAHOMA GRADUATE COLLEGE MACRONUTRIENTS SHAPE MICROBIAL COMMUNITIES, GENE EXPRESSION AND PROTEIN EVOLUTION A DISSERTATION SUBMITTED TO THE GRADUATE FACULTY in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY By JOSHUA THOMAS COOPER Norman, Oklahoma 2017 MACRONUTRIENTS SHAPE MICROBIAL COMMUNITIES, GENE EXPRESSION AND PROTEIN EVOLUTION A DISSERTATION APPROVED FOR THE DEPARTMENT OF MICROBIOLOGY AND PLANT BIOLOGY BY ______________________________ Dr. Boris Wawrik, Chair ______________________________ Dr. J. Phil Gibson ______________________________ Dr. Anne K. Dunn ______________________________ Dr. John Paul Masly ______________________________ Dr. K. David Hambright ii © Copyright by JOSHUA THOMAS COOPER 2017 All Rights Reserved. iii Acknowledgments I would like to thank my two advisors Dr. Boris Wawrik and Dr. J. Phil Gibson for helping me become a better scientist and better educator. I would also like to thank my committee members Dr. Anne K. Dunn, Dr. K. David Hambright, and Dr. J.P. Masly for providing valuable inputs that lead me to carefully consider my research questions. I would also like to thank Dr. J.P. Masly for the opportunity to coauthor a book chapter on the speciation of diatoms. It is still such a privilege that you believed in me and my crazy diatom ideas to form a concise chapter in addition to learn your style of writing has been a benefit to my professional development. I’m also thankful for my first undergraduate research mentor, Dr. Miriam Steinitz-Kannan, now retired from Northern Kentucky University, who was the first to show the amazing wonders of pond scum. Who knew that studying diatoms and algae as an undergraduate would lead me all the way to a Ph.D.
  • Identification of Active Methylotroph Populations in an Acidic Forest Soil

    Identification of Active Methylotroph Populations in an Acidic Forest Soil

    Microbiology (2002), 148, 2331–2342 Printed in Great Britain Identification of active methylotroph populations in an acidic forest soil by stable- isotope probing Stefan Radajewski,1 Gordon Webster,2† David S. Reay,3‡ Samantha A. Morris,1 Philip Ineson,4 David B. Nedwell,3 James I. Prosser2 and J. Colin Murrell1 Author for correspondence: J. Colin Murrell. Tel: j44 24 7652 2553. Fax: j44 24 7652 3568. e-mail: cmurrell!bio.warwick.ac.uk 1 Department of Biological Stable-isotope probing (SIP) is a culture-independent technique that enables Sciences, University of the isolation of DNA from micro-organisms that are actively involved in a Warwick, Coventry CV4 7AL, UK specific metabolic process. In this study, SIP was used to characterize the active methylotroph populations in forest soil (pH 35) microcosms that were exposed 2 Department of Molecular 13 13 13 13 and Cell Biology, to CH3OH or CH4. Distinct C-labelled DNA ( C-DNA) fractions were resolved University of Aberdeen, from total community DNA by CsCl density-gradient centrifugation. Analysis of Institute of Medical 16S rDNA sequences amplified from the 13C-DNA revealed that bacteria related Sciences, Foresterhill, Aberdeen AB25 2ZD, UK to the genera Methylocella, Methylocapsa, Methylocystis and Rhodoblastus had assimilated the 13C-labelled substrates, which suggested that moderately 3 Department of Biological Sciences, University of acidophilic methylotroph populations were active in the microcosms. Essex, Wivenhoe Park, Enrichments targeted towards the active proteobacterial CH3OH utilizers were Colchester, Essex CO4 3SQ, successful, although none of these bacteria were isolated into pure culture. A UK parallel analysis of genes encoding the key enzymes methanol dehydrogenase 4 Department of Biology, and particulate methane monooxygenase reflected the 16S rDNA analysis, but University of York, PO Box 373, YO10 5YW, UK unexpectedly revealed sequences related to the ammonia monooxygenase of ammonia-oxidizing bacteria (AOB) from the β-subclass of the Proteobacteria.
  • Adaptive Laboratory Evolution Enhances Methanol Tolerance and Conversion in Engineered Corynebacterium Glutamicum

    Adaptive Laboratory Evolution Enhances Methanol Tolerance and Conversion in Engineered Corynebacterium Glutamicum

    ARTICLE https://doi.org/10.1038/s42003-020-0954-9 OPEN Adaptive laboratory evolution enhances methanol tolerance and conversion in engineered Corynebacterium glutamicum Yu Wang 1, Liwen Fan1,2, Philibert Tuyishime1, Jiao Liu1, Kun Zhang1,3, Ning Gao1,3, Zhihui Zhang1,3, ✉ ✉ 1234567890():,; Xiaomeng Ni1, Jinhui Feng1, Qianqian Yuan1, Hongwu Ma1, Ping Zheng1,2,3 , Jibin Sun1,3 & Yanhe Ma1 Synthetic methylotrophy has recently been intensively studied to achieve methanol-based biomanufacturing of fuels and chemicals. However, attempts to engineer platform micro- organisms to utilize methanol mainly focus on enzyme and pathway engineering. Herein, we enhanced methanol bioconversion of synthetic methylotrophs by improving cellular tolerance to methanol. A previously engineered methanol-dependent Corynebacterium glutamicum is subjected to adaptive laboratory evolution with elevated methanol content. Unexpectedly, the evolved strain not only tolerates higher concentrations of methanol but also shows improved growth and methanol utilization. Transcriptome analysis suggests increased methanol con- centrations rebalance methylotrophic metabolism by down-regulating glycolysis and up- regulating amino acid biosynthesis, oxidative phosphorylation, ribosome biosynthesis, and parts of TCA cycle. Mutations in the O-acetyl-L-homoserine sulfhydrylase Cgl0653 catalyzing formation of L-methionine analog from methanol and methanol-induced membrane-bound transporter Cgl0833 are proven crucial for methanol tolerance. This study demonstrates the importance of
  • Biology and Systematics of Heterokont and Haptophyte Algae1

    Biology and Systematics of Heterokont and Haptophyte Algae1

    American Journal of Botany 91(10): 1508±1522. 2004. BIOLOGY AND SYSTEMATICS OF HETEROKONT AND HAPTOPHYTE ALGAE1 ROBERT A. ANDERSEN Bigelow Laboratory for Ocean Sciences, P.O. Box 475, West Boothbay Harbor, Maine 04575 USA In this paper, I review what is currently known of phylogenetic relationships of heterokont and haptophyte algae. Heterokont algae are a monophyletic group that is classi®ed into 17 classes and represents a diverse group of marine, freshwater, and terrestrial algae. Classes are distinguished by morphology, chloroplast pigments, ultrastructural features, and gene sequence data. Electron microscopy and molecular biology have contributed signi®cantly to our understanding of their evolutionary relationships, but even today class relationships are poorly understood. Haptophyte algae are a second monophyletic group that consists of two classes of predominately marine phytoplankton. The closest relatives of the haptophytes are currently unknown, but recent evidence indicates they may be part of a large assemblage (chromalveolates) that includes heterokont algae and other stramenopiles, alveolates, and cryptophytes. Heter- okont and haptophyte algae are important primary producers in aquatic habitats, and they are probably the primary carbon source for petroleum products (crude oil, natural gas). Key words: chromalveolate; chromist; chromophyte; ¯agella; phylogeny; stramenopile; tree of life. Heterokont algae are a monophyletic group that includes all (Phaeophyceae) by Linnaeus (1753), and shortly thereafter, photosynthetic organisms with tripartite tubular hairs on the microscopic chrysophytes (currently 5 Oikomonas, Anthophy- mature ¯agellum (discussed later; also see Wetherbee et al., sa) were described by MuÈller (1773, 1786). The history of 1988, for de®nitions of mature and immature ¯agella), as well heterokont algae was recently discussed in detail (Andersen, as some nonphotosynthetic relatives and some that have sec- 2004), and four distinct periods were identi®ed.
  • The Plankton Lifeform Extraction Tool: a Digital Tool to Increase The

    The Plankton Lifeform Extraction Tool: a Digital Tool to Increase The

    Discussions https://doi.org/10.5194/essd-2021-171 Earth System Preprint. Discussion started: 21 July 2021 Science c Author(s) 2021. CC BY 4.0 License. Open Access Open Data The Plankton Lifeform Extraction Tool: A digital tool to increase the discoverability and usability of plankton time-series data Clare Ostle1*, Kevin Paxman1, Carolyn A. Graves2, Mathew Arnold1, Felipe Artigas3, Angus Atkinson4, Anaïs Aubert5, Malcolm Baptie6, Beth Bear7, Jacob Bedford8, Michael Best9, Eileen 5 Bresnan10, Rachel Brittain1, Derek Broughton1, Alexandre Budria5,11, Kathryn Cook12, Michelle Devlin7, George Graham1, Nick Halliday1, Pierre Hélaouët1, Marie Johansen13, David G. Johns1, Dan Lear1, Margarita Machairopoulou10, April McKinney14, Adam Mellor14, Alex Milligan7, Sophie Pitois7, Isabelle Rombouts5, Cordula Scherer15, Paul Tett16, Claire Widdicombe4, and Abigail McQuatters-Gollop8 1 10 The Marine Biological Association (MBA), The Laboratory, Citadel Hill, Plymouth, PL1 2PB, UK. 2 Centre for Environment Fisheries and Aquacu∑lture Science (Cefas), Weymouth, UK. 3 Université du Littoral Côte d’Opale, Université de Lille, CNRS UMR 8187 LOG, Laboratoire d’Océanologie et de Géosciences, Wimereux, France. 4 Plymouth Marine Laboratory, Prospect Place, Plymouth, PL1 3DH, UK. 5 15 Muséum National d’Histoire Naturelle (MNHN), CRESCO, 38 UMS Patrinat, Dinard, France. 6 Scottish Environment Protection Agency, Angus Smith Building, Maxim 6, Parklands Avenue, Eurocentral, Holytown, North Lanarkshire ML1 4WQ, UK. 7 Centre for Environment Fisheries and Aquaculture Science (Cefas), Lowestoft, UK. 8 Marine Conservation Research Group, University of Plymouth, Drake Circus, Plymouth, PL4 8AA, UK. 9 20 The Environment Agency, Kingfisher House, Goldhay Way, Peterborough, PE4 6HL, UK. 10 Marine Scotland Science, Marine Laboratory, 375 Victoria Road, Aberdeen, AB11 9DB, UK.
  • Perchlorate and Chlorate Biogeochemistry in Ice-Covered Lakes of the Mcmurdo Dry Valleys, Antarctica

    Perchlorate and Chlorate Biogeochemistry in Ice-Covered Lakes of the Mcmurdo Dry Valleys, Antarctica

    Available online at www.sciencedirect.com Geochimica et Cosmochimica Acta 98 (2012) 19–30 www.elsevier.com/locate/gca Perchlorate and chlorate biogeochemistry in ice-covered lakes of the McMurdo Dry Valleys, Antarctica W. Andrew Jackson a,⇑, Alfonso F. Davila b,c, Nubia Estrada a, W. Berry Lyons d, John D. Coates e, John C. Priscu f a Department of Civil and Environmental Engineering, Texas Tech University, Lubbock, TX 79409, USA b NASA Ames Research Center, Moffett Field, CA 95136, USA c SETI Institute, 189 Bernardo Ave., Suite 100, Mountain View, CA 94043-5203, USA d Byrd Polar Research Center, The Ohio State University, Columbus, OH 43210, USA e Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA f Department of Land Resources & Environmental Sciences, Montana State University, Bozeman, MT 59717, USA Received 15 February 2012; accepted in revised form 5 September 2012; available online 19 September 2012 Abstract À À We measured chlorate (ClO3 ) and perchlorate (ClO4 ) concentrations in ice covered lakes of the McMurdo Dry Valleys À À (MDVs) of Antarctica, to evaluate their role in the ecology and geochemical evolution of the lakes. ClO3 and ClO4 are À À present throughout the MDV Lakes, streams, and other surface water bodies. ClO3 and ClO4 originate in the atmosphere and are transported to the lakes by surface inflow of glacier melt that has been differentially impacted by interaction with soils À À and aeolian matter. Concentrations of ClO3 and ClO4 in the lakes and between lakes vary based on both total evaporative concentration, as well as biological activity within each lake.
  • Fig.S1. the Pairwise Aligments of High Scoring Pairs of Recognizable Pseudogenes

    Fig.S1. the Pairwise Aligments of High Scoring Pairs of Recognizable Pseudogenes

    LysR transcriptional regulator Identities = 57/164 (35%), Positives = 82/164 (50%), Gaps = 13/164 (8%) 70530- SNQAIKTYLMPK*LRLLRQK*SPVEFQLQVHLIKKIRLNIVIRDINLTIIEN-TPVKLKI -70354 ++Q TYLMP+ + L RQK V QLQVH ++I ++ INL II P++LK 86251- ASQTTGTYLMPRLIGLFRQKYPQVAVQLQVHSTRRIAWSVANGHINLAIIGGEVPIELKN -86072 70353- FYTLLRMKERI*H*YCLGFL------FQFLIAYKKKNLYGLRLIKVDIPFPIRGIMNNP* -70192 + E L + F L + +K++LY LR I +D IR +++ 86071- MLQVTSYAED-----ELALILPKSHPFSMLRSIQKEDLYRLRFIALDRQSTIRKVIDKVL -85907 70191- IKTELIPRNLN-EMELSLFKPIKNAV*PGLNVTLIFVSAIAKEL -70063 + + EMEL+ + IKNAV GL + VSAIAKEL 85906- NQNGIDSTRFKIEMELNSVEAIKNAVQSGLGAAFVSVSAIAKEL -85775 ycf3 Photosystem I assembly protein Identities = 25/59 (42%), Positives = 39/59 (66%), Gaps = 3/59 (5%) 19162- NRSYML-SIQCM-PNNSDYVNTLKHCR*ALDLSSKL-LAIRNVTISYYCQDIIFSEKKD -19329 +RSY+L +I + +N +YV L++ ALDL+S+L AI N+ + Y+ Q + SEKKD 19583- DRSYILYNIGLIYASNGEYVKALEYYHQALDLNSRLPPAINNIAVIYHYQGVKASEKKD -19759 Fig.S1. The pairwise aligments of high scoring pairs of recognizable pseudogenes. The upper amino acid sequences indicates Cryptomonas sp. SAG977-2f. The lower sequences are corresponding amino acid sequences of homologs in C. curvata CCAP979/52. Table S1. Presence/absence of protein genes in the plastid genomes of Cryptomonas and representative species of Cryptomonadales. Note; y indicates pseudogenes. Photosynthetic Non-Photosynthetic Guillardia Rhodomonas Cryptomonas C. C. curvata C. curvata parameciu Guillardia Rhodomonas FBCC300 CCAP979/ SAG977 CCAC1634 m theta salina -2f B 012D 52 CCAP977/2 a rps2 + + + +
  • Community in a Eutrophic Coastal Mesocosm Experiment

    Community in a Eutrophic Coastal Mesocosm Experiment

    Biogeosciences Discuss., doi:10.5194/bg-2017-10, 2017 Manuscript under review for journal Biogeosciences Published: 30 January 2017 c Author(s) 2017. CC-BY 3.0 License. 1 Insignificant effects of elevated CO2 on bacterioplankton 2 community in a eutrophic coastal mesocosm experiment 3 Xin Lin†*1, Ruiping Huang†1, Yan Li1, Yaping Wu1,2, David A. Hutchins3, Minhan Dai1, 4 Kunshan Gao*1 5 6 Institutions: 7 1State Key Laboratory of Marine Environmental Science, Xiamen University (Xiang An Campus), 8 Xiamen 361102, China. 9 2College of oceanography, Hohai university, No.1 Xikang road, Nanjing 210000, China. 10 3Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, AHF 11 301, Los Angeles, CA 90089-0371, USA. 12 13 † These authors contribute equally to this work. 14 Correspondence to: Xin Lin ([email protected], TEL: +865922880171); 15 Kunshan Gao ([email protected], TEL: +865922187963) 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 1 Biogeosciences Discuss., doi:10.5194/bg-2017-10, 2017 Manuscript under review for journal Biogeosciences Published: 30 January 2017 c Author(s) 2017. CC-BY 3.0 License. 1 Abstract 2 There is increasing concern about the effects of ocean acidification on marine biogeochemical and 3 ecological processes and the organisms that drive them, including marine bacteria. Here, we examine the 4 effects of elevated CO2 on bacterioplankton community during a mesocosm experiment using an 5 artificial phytoplankton community in subtropical, eutrophic coastal waters of Xiamen, Southern China. 6 We found that the elevated CO2 hardly altered the network structure of the bacterioplankton taxa present 7 with high abundance but appeared to reassemble the community network of taxa present with low 8 abundance by sequencing of the bacterial 16S rRNA gene V3-V4 region and ecological network analysis.
  • Mixotrophic Protists Among Marine Ciliates and Dinoflagellates: Distribution, Physiology and Ecology

    Mixotrophic Protists Among Marine Ciliates and Dinoflagellates: Distribution, Physiology and Ecology

    FACULTY OF SCIENCE UNIVERSITY OF COPENHAGEN PhD thesis Woraporn Tarangkoon Mixotrophic Protists among Marine Ciliates and Dinoflagellates: Distribution, Physiology and Ecology Academic advisor: Associate Professor Per Juel Hansen Submitted: 29/04/10 Contents List of publications 3 Preface 4 Summary 6 Sammenfating (Danish summary) 8 สรุป (Thai summary) 10 The sections and objectives of the thesis 12 Introduction 14 1) Mixotrophy among marine planktonic protists 14 1.1) The role of light, food concentration and nutrients for 17 the growth of marine mixotrophic planktonic protists 1.2) Importance of marine mixotrophic protists in the 20 planktonic food web 2) Marine symbiont-bearing dinoflagellates 24 2.1) Occurrence of symbionts in the order Dinophysiales 24 2.2) The spatial distribution of symbiont-bearing dinoflagellates in 27 marine waters 2.3) The role of symbionts and phagotrophy in dinoflagellates with symbionts 28 3) Symbiosis and mixotrophy in the marine ciliate genus Mesodinium 30 3.1) Occurrence of symbiosis in Mesodinium spp. 30 3.2) The distribution of marine Mesodinium spp. 30 3.3) The role of symbionts and phagotrophy in marine Mesodinium rubrum 33 and Mesodinium pulex Conclusion and future perspectives 36 References 38 Paper I Paper II Paper III Appendix-Paper IV Appendix-I Lists of publications The thesis consists of the following papers, referred to in the synthesis by their roman numerals. Co-author statements are attached to the thesis (Appendix-I). Paper I Tarangkoon W, Hansen G Hansen PJ (2010) Spatial distribution of symbiont-bearing dinoflagellates in the Indian Ocean in relation to oceanographic regimes. Aquat Microb Ecol 58:197-213.