Deciphering a Marine Bone Degrading Microbiome Reveals a Complex Community Effort
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Zygote Gene Expression and Plasmodial Development in Didymium Iridis
DePaul University Via Sapientiae College of Science and Health Theses and Dissertations College of Science and Health Summer 8-25-2019 Zygote gene expression and plasmodial development in Didymium iridis Sean Schaefer DePaul University, [email protected] Follow this and additional works at: https://via.library.depaul.edu/csh_etd Part of the Biology Commons Recommended Citation Schaefer, Sean, "Zygote gene expression and plasmodial development in Didymium iridis" (2019). College of Science and Health Theses and Dissertations. 322. https://via.library.depaul.edu/csh_etd/322 This Thesis is brought to you for free and open access by the College of Science and Health at Via Sapientiae. It has been accepted for inclusion in College of Science and Health Theses and Dissertations by an authorized administrator of Via Sapientiae. For more information, please contact [email protected]. Zygote gene expression and plasmodial development in Didymium iridis A Thesis presented in Partial fulfillment of the Requirements for the Degree of Master of Biology By Sean Schaefer 2019 Advisor: Dr. Margaret Silliker Department of Biological Sciences College of Liberal Arts and Sciences DePaul University Chicago, IL Abstract: Didymium iridis is a cosmopolitan species of plasmodial slime mold consisting of two distinct life stages. Haploid amoebae and diploid plasmodia feed on microscopic organisms such as bacteria and fungi through phagocytosis. Sexually compatible haploid amoebae act as gametes which when fused embark on an irreversible developmental change resulting in a diploid zygote. The zygote can undergo closed mitosis resulting in a multinucleated plasmodium. Little is known about changes in gene expression during this developmental transition. Our principal goal in this study was to provide a comprehensive list of genes likely to be involved in plasmodial development. -
Microbiome Exploration of Deep-Sea Carnivorous Cladorhizidae Sponges
Microbiome exploration of deep-sea carnivorous Cladorhizidae sponges by Joost Theo Petra Verhoeven A Thesis submitted to the School of Graduate Studies in partial fulfillment of the requirements for the degree of Doctor of Philosophy Department of Biology Memorial University of Newfoundland March 2019 St. John’s, Newfoundland and Labrador ABSTRACT Members of the sponge family Cladorhizidae are unique in having replaced the typical filter-feeding strategy of sponges by a predatory lifestyle, capturing and digesting small prey. These carnivorous sponges are found in many different environments, but are particularly abundant in deep waters, where they constitute a substantial component of the benthos. Sponges are known to host a wide range of microbial associates (microbiome) important for host health, but the extent of the microbiome in carnivorous sponges has never been extensively investigated and their importance is poorly understood. In this thesis, the microbiome of two deep-sea carnivorous sponge species (Chondrocladia grandis and Cladorhiza oxeata) is investigated for the first time, leveraging recent advances in high-throughput sequencing and through custom developed bioinformatic and molecular methods. Microbiome analyses showed that the carnivorous sponges co-occur with microorganisms and large differences in the composition and type of associations were observed between sponge species. Tissues of C. grandis hosted diverse bacterial communities, similar in composition between individuals, in stark contrast to C. oxeata where low microbial diversity was found with a high host-to-host variability. In C. grandis the microbiome was not homogeneous throughout the host tissue, and significant shifts occured within community members across anatomical regions, with the enrichment of specific bacterial taxa in particular anatomical niches, indicating a potential symbiotic role of such taxa within processes like prey digestion and chemolithoautotrophy. -
Arxiv:2105.11503V2 [Physics.Bio-Ph] 26 May 2021 3.1 Geometry and Swimming Speeds of the Cells
The Bank Of Swimming Organisms at the Micron Scale (BOSO-Micro) Marcos F. Velho Rodrigues1, Maciej Lisicki2, Eric Lauga1,* 1 Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge CB3 0WA, United Kingdom. 2 Faculty of Physics, University of Warsaw, Warsaw, Poland. *Email: [email protected] Abstract Unicellular microscopic organisms living in aqueous environments outnumber all other creatures on Earth. A large proportion of them are able to self-propel in fluids with a vast diversity of swimming gaits and motility patterns. In this paper we present a biophysical survey of the available experimental data produced to date on the characteristics of motile behaviour in unicellular microswimmers. We assemble from the available literature empirical data on the motility of four broad categories of organisms: bacteria (and archaea), flagellated eukaryotes, spermatozoa and ciliates. Whenever possible, we gather the following biological, morphological, kinematic and dynamical parameters: species, geometry and size of the organisms, swimming speeds, actuation frequencies, actuation amplitudes, number of flagella and properties of the surrounding fluid. We then organise the data using the established fluid mechanics principles for propulsion at low Reynolds number. Specifically, we use theoretical biophysical models for the locomotion of cells within the same taxonomic groups of organisms as a means of rationalising the raw material we have assembled, while demonstrating the variability for organisms of different species within the same group. The material gathered in our work is an attempt to summarise the available experimental data in the field, providing a convenient and practical reference point for future studies. Contents 1 Introduction 2 2 Methods 4 2.1 Propulsion at low Reynolds number . -
Which Organisms Are Used for Anti-Biofouling Studies
Table S1. Semi-systematic review raw data answering: Which organisms are used for anti-biofouling studies? Antifoulant Method Organism(s) Model Bacteria Type of Biofilm Source (Y if mentioned) Detection Method composite membranes E. coli ATCC25922 Y LIVE/DEAD baclight [1] stain S. aureus ATCC255923 composite membranes E. coli ATCC25922 Y colony counting [2] S. aureus RSKK 1009 graphene oxide Saccharomycetes colony counting [3] methyl p-hydroxybenzoate L. monocytogenes [4] potassium sorbate P. putida Y. enterocolitica A. hydrophila composite membranes E. coli Y FESEM [5] (unspecified/unique sample type) S. aureus (unspecified/unique sample type) K. pneumonia ATCC13883 P. aeruginosa BAA-1744 composite membranes E. coli Y SEM [6] (unspecified/unique sample type) S. aureus (unspecified/unique sample type) graphene oxide E. coli ATCC25922 Y colony counting [7] S. aureus ATCC9144 P. aeruginosa ATCCPAO1 composite membranes E. coli Y measuring flux [8] (unspecified/unique sample type) graphene oxide E. coli Y colony counting [9] (unspecified/unique SEM sample type) LIVE/DEAD baclight S. aureus stain (unspecified/unique sample type) modified membrane P. aeruginosa P60 Y DAPI [10] Bacillus sp. G-84 LIVE/DEAD baclight stain bacteriophages E. coli (K12) Y measuring flux [11] ATCC11303-B4 quorum quenching P. aeruginosa KCTC LIVE/DEAD baclight [12] 2513 stain modified membrane E. coli colony counting [13] (unspecified/unique colony counting sample type) measuring flux S. aureus (unspecified/unique sample type) modified membrane E. coli BW26437 Y measuring flux [14] graphene oxide Klebsiella colony counting [15] (unspecified/unique sample type) P. aeruginosa (unspecified/unique sample type) graphene oxide P. aeruginosa measuring flux [16] (unspecified/unique sample type) composite membranes E. -
Mechanistic Strategies of Microbial Communities Regulating Lignocellulose Deconstruction in a UK Salt Marsh
This is a repository copy of Mechanistic strategies of microbial communities regulating lignocellulose deconstruction in a UK salt marsh. White Rose Research Online URL for this paper: https://eprints.whiterose.ac.uk/168430/ Version: Accepted Version Article: Leadbeater, Daniel Raymond, Oates, Nicola Claire, Bennett, Joe orcid.org/0000-0001- 7065-1536 et al. (9 more authors) (Accepted: 2020) Mechanistic strategies of microbial communities regulating lignocellulose deconstruction in a UK salt marsh. Microbiome. ISSN 2049-2618 (In Press) Reuse Items deposited in White Rose Research Online are protected by copyright, with all rights reserved unless indicated otherwise. They may be downloaded and/or printed for private study, or other acts as permitted by national copyright laws. The publisher or other rights holders may allow further reproduction and re-use of the full text version. This is indicated by the licence information on the White Rose Research Online record for the item. Takedown If you consider content in White Rose Research Online to be in breach of UK law, please notify us by emailing [email protected] including the URL of the record and the reason for the withdrawal request. [email protected] https://eprints.whiterose.ac.uk/ Title Mechanistic strategies of microbial communities regulating lignocellulose deconstruction in a UK salt marsh Authors Daniel R. Leadbeater1§, Nicola C. Oates1, Joseph P. Bennett1, Yi Li1, Adam A. Dowle2, Joe D. Taylor4, Juliana Sanchez Alponti1, Alexander T. Setchfield1, Anna M. Alessi1, Thorunn Helgason3, Simon J. McQueen-Mason1§, Neil C. Bruce1§ 1 Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK. -
Microbial Community Diversity Within Sediments from Two Geographically Separated Hadal Trenches
ORIGINAL RESEARCH published: 15 March 2019 doi: 10.3389/fmicb.2019.00347 Microbial Community Diversity Within Sediments From Two Geographically Separated Hadal Trenches Logan M. Peoples1, Eleanna Grammatopoulou2, Michelle Pombrol1, Xiaoxiong Xu1, Oladayo Osuntokun1, Jessica Blanton1, Eric E. Allen1, Clifton C. Nunnally3, Jeffrey C. Drazen4, Daniel J. Mayor2,5 and Douglas H. Bartlett1* 1 Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States, 2 Oceanlab, The Institute of Biological and Environmental Sciences, King’s College, The University of Aberdeen, Aberdeen, United Kingdom, 3 Louisiana Universities Marine Consortium (LUMCON), Chauvin, LA, United States, 4 Department of Oceanography, University of Hawai’i at Ma-noa, Honolulu, HI, United States, 5 National Oceanography Centre, University of Southampton Waterfront Campus European Way, Southampton, United Kingdom Hadal ocean sediments, found at sites deeper than 6,000 m water depth, are thought to Edited by: contain microbial communities distinct from those at shallower depths due to high Ian Hewson, Cornell University, United States hydrostatic pressures and higher abundances of organic matter. These communities may Reviewed by: also differ from one other as a result of geographical isolation. Here we compare microbial Rulong Liu, community composition in surficial sediments of two hadal environments—the Mariana Shanghai Ocean University, China Ellard R. Hunting, and Kermadec trenches—to evaluate microbial biogeography at hadal depths. Sediment University of Bristol, United Kingdom microbial consortia were distinct between trenches, with higher relative sequence *Correspondence: abundances of taxa previously correlated with organic matter degradation present in the Douglas H. Bartlett Kermadec Trench. In contrast, the Mariana Trench, and deeper sediments in both trenches, [email protected] were enriched in taxa predicted to break down recalcitrant material and contained other Specialty section: uncharacterized lineages. -
Bacterial Biofilms on Microplastics in the Baltic Sea – Composition, Influences, and Interactions with Their Environment
Bacterial biofilms on microplastics in the Baltic Sea – Composition, influences, and interactions with their environment kumulative Dissertation zur Erlangung des akademischen Grades Doctor rerum naturalium (Dr. rer. nat.) der Mathematisch-Naturwissenschaftlichen Fakultät der Universität Rostock vorgelegt von Katharina Kesy, geb. am 06.11.1985 in Berlin aus Rostock Rostock, 17.09.2019 https://doi.org/10.18453/rosdok_id00002636 Gutachter: Prof. Dr. Matthias Labrenz, Sektion Biologische Meereskunde, Leibniz-Institut für Ostseeforschug Warnemünde Assist. Prof. Dr. Melissa Duhaime, Department of Computational Medicine and Bioinformatics, University of Michigan, USA Jahr der Einreichung: 2019 Jahr der Verteidigung: 2020 Table of contents i Table of contents Summary/Zusammenfassung ............................................................................................. 1 General introduction ........................................................................................................... 6 Biofilms, their formation, and influential factors ............................................................. 6 The ecological importance of biofilms in aquatic systems ............................................... 8 Microplastics in aquatic environments: a newly available habitat for surface associated microorganisms and possible vector for potential pathogens ........................................... 9 Description of research aims ............................................................................................ 15 Summary -
A Comparison of Bacterial Communities from OMZ Sediments in the Arabian Sea and the Bay of Bengal
1 Manuscript title: 2 A comparison of bacterial communities from OMZ sediments in the Arabian Sea and the Bay of Bengal 3 reveals major differences in nitrogen turnover and carbon recycling potential 4 5 Author names: 6 1, 2Jovitha Lincy * and 1Cathrine Sumathi Manohar 7 8 Author affiliation(s): 9 1 Biological Oceanography Division, CSIR-National Institute of Oceanography (NIO), Goa-403004, India. 10 2 Academy of Scientific and Innovative Research (AcSIR), CSIR-NIO Campus, Goa, India. 11 12 Correspondence: 13 JL: [email protected]; +91-9847871900 (*corresponding author). 14 CSM: [email protected]; +91-832-245-0441. 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 1 31 ABSTRACT: 32 The Northern Indian Ocean hosts two Oxygen Minimum Zones (OMZ), one in the Arabian Sea and the 33 other in the Bay of Bengal. High-throughput sequencing was used to understand the total bacterial diversity in, 34 the surface sediment off Goa within the OMZ of the Arabian Sea, and from off Paradip within the OMZ of the 35 Bay of Bengal. The dominant phyla identified included Firmicutes (33.08%) and Proteobacteria (32.59%) from 36 the Arabian Sea, and Proteobacteria (52.65%) and Planctomycetes (9.36%) from the Bay of Bengal. Only 30% 37 of OTUs were shared between the sites which make up three-fourth of the Bay of Bengal OMZ bacterial 38 community, but only one-fourth of the Arabian Sea OMZ sediment bacterial community. Statistical analysis 39 indicated the bacterial diversity from sediments of the Bay of Bengal OMZ is ~48% higher than the Arabian Sea 40 OMZ. -
Degrading Bacteria in Deep‐
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Aberdeen University Research Archive Journal of Applied Microbiology ISSN 1364-5072 ORIGINAL ARTICLE Hydrocarbon-degrading bacteria in deep-water subarctic sediments (Faroe-Shetland Channel) E. Gontikaki1 , L.D. Potts1, J.A. Anderson2 and U. Witte1 1 School of Biological Sciences, University of Aberdeen, Aberdeen, UK 2 Surface Chemistry and Catalysis Group, Materials and Chemical Engineering, School of Engineering, University of Aberdeen, Aberdeen, UK Keywords Abstract clone libraries, Faroe-Shetland Channel, hydrocarbon degradation, isolates, marine Aims: The aim of this study was the baseline description of oil-degrading bacteria, oil spill, Oleispira, sediment. sediment bacteria along a depth transect in the Faroe-Shetland Channel (FSC) and the identification of biomarker taxa for the detection of oil contamination Correspondence in FSC sediments. Evangelia Gontikaki and Ursula Witte, School Methods and Results: Oil-degrading sediment bacteria from 135, 500 and of Biological Sciences, University of Aberdeen, 1000 m were enriched in cultures with crude oil as the sole carbon source (at Aberdeen, UK. ° E-mails: [email protected] and 12, 5 and 0 C respectively). The enriched communities were studied using [email protected] culture-dependent and culture-independent (clone libraries) techniques. Isolated bacterial strains were tested for hydrocarbon degradation capability. 2017/2412: received 8 December 2017, Bacterial isolates included well-known oil-degrading taxa and several that are revised 16 May 2018 and accepted 18 June reported in that capacity for the first time (Sulfitobacter, Ahrensia, Belliella, 2018 Chryseobacterium). The orders Oceanospirillales and Alteromonadales dominated clone libraries in all stations but significant differences occurred at doi:10.1111/jam.14030 genus level particularly between the shallow and the deep, cold-water stations. -
Systema Naturae 2000 (Phylum, 6 Nov 2017)
The Taxonomicon Systema Naturae 2000 Classification of Domain Bacteria (prokaryotes) down to Phylum Compiled by Drs. S.J. Brands Universal Taxonomic Services 6 Nov 2017 Systema Naturae 2000 - Domain Bacteria - Domain Bacteria Woese et al. 1990 1 Genus †Eoleptonema Schopf 1983, incertae sedis 2 Genus †Primaevifilum Schopf 1983, incertae sedis 3 Genus †Archaeotrichion Schopf 1968, incertae sedis 4 Genus †Siphonophycus Schopf 1968, incertae sedis 5 Genus Bactoderma Tepper and Korshunova 1973 (Approved Lists 1980), incertae sedis 6 Genus Stibiobacter Lyalikova 1974 (Approved Lists 1980), incertae sedis 7.1.1.1.1.1 Superphylum "Proteobacteria" Craig et al. 2010 1.1 Phylum "Alphaproteobacteria" 1.2.1 Phylum "Acidithiobacillia" 1.2.2.1 Phylum "Gammaproteobacteria" 1.2.2.2.1 Candidate phylum Muproteobacteria (RIF23) Anantharaman et al. 2016 1.2.2.2.2 Phylum "Betaproteobacteria" 2 Phylum "Zetaproteobacteria" 7.1.1.1.1.2 Phylum "Deltaproteobacteria_1" 7.1.1.1.2.1.1.1 Phylum "Deltaproteobacteria" [polyphyletic] 7.1.1.1.2.1.1.2.1 Phylum "Deltaproteobacteria_2" 7.1.1.1.2.1.1.2.2 Phylum "Deltaproteobacteria_3" 7.1.1.1.2.1.2 Candidate phylum Dadabacteria (CSP1-2) Hug et al. 2015 7.1.1.1.2.2.1 Candidate phylum "MBNT15" 7.1.1.1.2.2.2 Candidate phylum "Uncultured Bacterial Phylum 10 (UBP10)" Parks et al. 2017 7.1.1.2.1 Phylum "Nitrospirae_1" 7.1.1.2.2 Phylum Chrysiogenetes Garrity and Holt 2001 7.1.2.1.1 Phylum "Nitrospirae" Garrity and Holt 2001 [polyphyletic] 7.1.2.1.2.1.1 Candidate phylum Rokubacteria (CSP1-6) Hug et al. -
Colwellia and Marinobacter Metapangenomes Reveal Species
bioRxiv preprint doi: https://doi.org/10.1101/2020.09.28.317438; this version posted September 28, 2020. 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 Colwellia and Marinobacter metapangenomes reveal species-specific responses to oil 2 and dispersant exposure in deepsea microbial communities 3 4 Tito David Peña-Montenegro1,2,3, Sara Kleindienst4, Andrew E. Allen5,6, A. Murat 5 Eren7,8, John P. McCrow5, Juan David Sánchez-Calderón3, Jonathan Arnold2,9, Samantha 6 B. Joye1,* 7 8 Running title: Metapangenomes reveal species-specific responses 9 10 1 Department of Marine Sciences, University of Georgia, 325 Sanford Dr., Athens, 11 Georgia 30602-3636, USA 12 13 2 Institute of Bioinformatics, University of Georgia, 120 Green St., Athens, Georgia 14 30602-7229, USA 15 16 3 Grupo de Investigación en Gestión Ecológica y Agroindustrial (GEA), Programa de 17 Microbiología, Facultad de Ciencias Exactas y Naturales, Universidad Libre, Seccional 18 Barranquilla, Colombia 19 20 4 Microbial Ecology, Center for Applied Geosciences, University of Tübingen, 21 Schnarrenbergstrasse 94-96, 72076 Tübingen, Germany 22 23 5 Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA 92037, 24 USA 25 26 6 Integrative Oceanography Division, Scripps Institution of Oceanography, UC San 27 Diego, La Jolla, CA 92037, USA 28 29 7 Department of Medicine, University of Chicago, Chicago, IL, USA 30 31 8 Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, USA 32 33 9Department of Genetics, University of Georgia, 120 Green St., Athens, Georgia 30602- 34 7223, USA 35 36 *Correspondence: Samantha B. -
Chapter 02282
Psychrophiles and Psychrotrophs$ Craig L Moyer, Western Washington University, Bellingham, WA, United States R Eric Collins, University of Alaska Fairbanks, Fairbanks, AK, United States Richard Y Morita, Oregon State University, Corvallis, OR, United States r 2017 Elsevier Inc. All rights reserved. Glossary Cryophiles Cold-loving eukaryotes. Barophiles (also known as piezophiles) Pressure-loving Homeophasic adaptation The ability of the cell bacteria and archaea. membrane to maintain a relatively constant viscosity Cryobiosis A temporary state of reduced metabolism in (fluidity) throughout the growth temperature range. which metabolic activity is absent or undetectable due to Membrane fluidity The ability of the cell membrane to freezing. To initiate cryobiosis, the organism freezes all of remain fluid in order to modulate the activity of the the water within its cell(s). This allows the organism to intrinsic proteins which perform functions such as electron endure the freezing temperatures until more transport, ion pumping, and nutrient uptake. hospitable conditions return. Studies have shown that the Psychrophiles Cold-loving bacteria and archaea. longer an organism remains in cryobiosis, the longer it takes Psychrotrophs Cold-tolerant bacteria and archaea. for the organism to come out of cryobiosis. This is because Thermocline In the stratification of warm surface water the organism must use its own energy to come out of over cold deeper water, the transition zone of rapid cryobiosis, and the longer it stays in cryobiosis the less temperature decline between two layers. energy it will retain. Introduction Psychrophiles are cold-loving bacteria or archaea, whereas cryophiles are cold-loving higher biological forms (e.g., polar fish).