Degrading Bacteria in Deep‐
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The 2014 Golden Gate National Parks Bioblitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event
National Park Service U.S. Department of the Interior Natural Resource Stewardship and Science The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 ON THIS PAGE Photograph of BioBlitz participants conducting data entry into iNaturalist. Photograph courtesy of the National Park Service. ON THE COVER Photograph of BioBlitz participants collecting aquatic species data in the Presidio of San Francisco. Photograph courtesy of National Park Service. The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 Elizabeth Edson1, Michelle O’Herron1, Alison Forrestel2, Daniel George3 1Golden Gate Parks Conservancy Building 201 Fort Mason San Francisco, CA 94129 2National Park Service. Golden Gate National Recreation Area Fort Cronkhite, Bldg. 1061 Sausalito, CA 94965 3National Park Service. San Francisco Bay Area Network Inventory & Monitoring Program Manager Fort Cronkhite, Bldg. 1063 Sausalito, CA 94965 March 2016 U.S. Department of the Interior National Park Service Natural Resource Stewardship and Science Fort Collins, Colorado The National Park Service, Natural Resource Stewardship and Science office in Fort Collins, Colorado, publishes a range of reports that address natural resource topics. These reports are of interest and applicability to a broad audience in the National Park Service and others in natural resource management, including scientists, conservation and environmental constituencies, and the public. The Natural Resource Report Series is used to disseminate comprehensive information and analysis about natural resources and related topics concerning lands managed by the National Park Service. -
The Hydrocarbon Biodegradation Potential of Faroe-Shetland Channel Bacterioplankton
THE HYDROCARBON BIODEGRADATION POTENTIAL OF FAROE-SHETLAND CHANNEL BACTERIOPLANKTON Angelina G. Angelova Submitted for the degree of Doctor of Philosophy Heriot Watt University School of Engineering and Physical Sciences July 2017 The copyright in this thesis is owned by the author. Any quotation from the thesis or use of any of the information contained in it must acknowledge this thesis as the source of the quotation or information. ABSTRACT The Faroe-Shetland Channel (FSC) is an important gateway for dynamic water exchange between the North Atlantic Ocean and the Nordic Seas. In recent years it has also become a frontier for deep-water oil exploration and petroleum production, which has raised the risk of oil pollution to local ecosystems and adjacent waterways. In order to better understand the factors that influence the biodegradation of spilled petroleum, a prerequisite has been recognized to elucidate the complex dynamics of microbial communities and their relationships to their ecosystem. This research project was a pioneering attempt to investigate the FSC’s microbial community composition, its response and potential to degrade crude oil hydrocarbons under the prevailing regional temperature conditions. Three strategies were used to investigate this. Firstly, high throughput sequencing and 16S rRNA gene-based community profiling techniques were utilized to explore the spatiotemporal patterns of the FSC bacterioplankton. Monitoring proceeded over a period of 2 years and interrogated the multiple water masses flowing through the region producing 2 contrasting water cores: Atlantic (surface) and Nordic (subsurface). Results revealed microbial profiles more distinguishable based on water cores (rather than individual water masses) and seasonal variability patterns within each core. -
Pinpointing the Origin of Mitochondria Zhang Wang Hanchuan, Hubei
Pinpointing the origin of mitochondria Zhang Wang Hanchuan, Hubei, China B.S., Wuhan University, 2009 A Dissertation presented to the Graduate Faculty of the University of Virginia in Candidacy for the Degree of Doctor of Philosophy Department of Biology University of Virginia August, 2014 ii Abstract The explosive growth of genomic data presents both opportunities and challenges for the study of evolutionary biology, ecology and diversity. Genome-scale phylogenetic analysis (known as phylogenomics) has demonstrated its power in resolving the evolutionary tree of life and deciphering various fascinating questions regarding the origin and evolution of earth’s contemporary organisms. One of the most fundamental events in the earth’s history of life regards the origin of mitochondria. Overwhelming evidence supports the endosymbiotic theory that mitochondria originated once from a free-living α-proteobacterium that was engulfed by its host probably 2 billion years ago. However, its exact position in the tree of life remains highly debated. In particular, systematic errors including sparse taxonomic sampling, high evolutionary rate and sequence composition bias have long plagued the mitochondrial phylogenetics. This dissertation employs an integrated phylogenomic approach toward pinpointing the origin of mitochondria. By strategically sequencing 18 phylogenetically novel α-proteobacterial genomes, using a set of “well-behaved” phylogenetic markers with lower evolutionary rates and less composition bias, and applying more realistic phylogenetic models that better account for the systematic errors, the presented phylogenomic study for the first time placed the mitochondria unequivocally within the Rickettsiales order of α- proteobacteria, as a sister clade to the Rickettsiaceae and Anaplasmataceae families, all subtended by the Holosporaceae family. -
Deciphering a Marine Bone Degrading Microbiome Reveals a Complex Community Effort
bioRxiv preprint doi: https://doi.org/10.1101/2020.05.13.093005; this version posted November 18, 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 4.0 International license. 1 Deciphering a marine bone degrading microbiome reveals a complex community effort 2 3 Erik Borcherta,#, Antonio García-Moyanob, Sergio Sanchez-Carrilloc, Thomas G. Dahlgrenb,d, 4 Beate M. Slabya, Gro Elin Kjæreng Bjergab, Manuel Ferrerc, Sören Franzenburge and Ute 5 Hentschela,f 6 7 aGEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Research Unit Marine Symbioses, 8 Kiel, Germany 9 bNORCE Norwegian Research Centre, Bergen, Norway 10 cCSIC, Institute of Catalysis, Madrid, Spain 11 dDepartment of Marine Sciences, University of Gothenburg, Gothenburg, Sweden 12 eIKMB, Institute of Clinical Molecular Biology, University of Kiel, Kiel, Germany 13 fChristian-Albrechts University of Kiel, Kiel, Germany 14 15 Running Head: Marine bone degrading microbiome 16 #Address correspondence to Erik Borchert, [email protected] 17 Abstract word count: 229 18 Text word count: 4908 (excluding Abstract, Importance, Materials and Methods) 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.05.13.093005; this version posted November 18, 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 4.0 International license. 19 Abstract 20 The marine bone biome is a complex assemblage of macro- and microorganisms, however the 21 enzymatic repertoire to access bone-derived nutrients remains unknown. -
Cultivation-Dependent and Cultivation-Independent Characterization of Hydrocarbon-Degrading Bacteria in Guaymas Basin Sediments
ORIGINAL RESEARCH published: 07 July 2015 doi: 10.3389/fmicb.2015.00695 Cultivation-dependent and cultivation-independent characterization of hydrocarbon-degrading bacteria in Guaymas Basin sediments Tony Gutierrez1,2*, Jennifer F. Biddle3, Andreas Teske4 and Michael D. Aitken1 1 Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA, 2 School of Life Sciences, Heriot-Watt University, Edinburgh, UK, 3 College of Earth, Ocean, and Environment, University of Delaware, Lewes, DE, USA, 4 Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA Marine hydrocarbon-degrading bacteria perform a fundamental role in the biodegradation of crude oil and its petrochemical derivatives in coastal and open Edited by: ocean environments. However, there is a paucity of knowledge on the diversity and Peter Dunfield, University of Calgary, Canada function of these organisms in deep-sea sediment. Here we used stable-isotope Reviewed by: probing (SIP), a valuable tool to link the phylogeny and function of targeted microbial Martin Krüger, groups, to investigate polycyclic aromatic hydrocarbon (PAH)-degrading bacteria under Federal Institute for Geosciences 13 and Natural Resources, Germany aerobic conditions in sediments from Guaymas Basin with uniformly labeled [ C]- 13 Casey R. J. Hubert, phenanthrene (PHE). The dominant sequences in clone libraries constructed from C- Newcastle University, UK enriched bacterial DNA (from PHE enrichments) were identified to belong to the genus *Correspondence: Cycloclasticus. We used quantitative PCR primers targeting the 16S rRNA gene of Tony Gutierrez, School of Life Sciences, Heriot-Watt the SIP-identified Cycloclasticus to determine their abundance in sediment incubations University, Edinburgh EH14 4AS, amended with unlabeled PHE and showed substantial increases in gene abundance Scotland, UK [email protected] during the experiments. -
The Role of Charcoal and Dietary Crude Protein Supplemented with Probiotic Escherchia Coli Strains UM2 and UM7
Gut microbiome analysis in piglet models infected with Escherchia coli K88: The role of charcoal and dietary crude protein supplemented with probiotic Escherchia coli strains UM2 and UM7. by Shahab Meshkibaf A Thesis submitted to the Faculty of Graduate Studies of The University of Manitoba in partial fulfillment of the requirements of the degree of MASTER OF SCIENCE Department of Medical Microbiology and Infectious Diseases University of Manitoba Winnipeg Copyright © 2011 by Shahab Meshkibaf ABSTRACT Entrotoxigenic Escherichia coli (ETEC) K88 is a causative agent of post-weaning diarrhea (PWD) in early-weaned pigs. This study investigated the efficacy of two alternative diets, charcoal (0.1, 0.5, 1, and 2%) and a low crude protein (CP) diet (17%) supplemented with probiotic E. coli strains (UM2 and UM7), against PWD infection in ETEC K88 challenged piglets. The present study found that charcoal had no effect on the challenged piglets’ performance, ileal and colonic microbiota or their fermentation end products. There was, however, a correlation between charcoal dosage and fecal consistency score. Charcoal reduced the ileal mucosal attached ETEC K88. Feeding a low-CP diet resulted in a lower ileal ammonia concentration. The low-CP diet reduced the E. coli populations in the ileal digesta as well as lowered mRNA expression of the IL-1ß. We concluded that the use of both 1-2% charcoal diet and a low-CP diet supplemented with probiotic E. coli strains were effective in reducing the incidence and severity of PWD infection. ACKNOWLEDGEMENTS I would like to thank all people who have helped and inspired me during my graduate study. -
Roseisalinus Antarcticus Gen. Nov., Sp. Nov., a Novel Aerobic Bacteriochlorophyll A-Producing A-Proteobacterium Isolated from Hypersaline Ekho Lake, Antarctica
International Journal of Systematic and Evolutionary Microbiology (2005), 55, 41–47 DOI 10.1099/ijs.0.63230-0 Roseisalinus antarcticus gen. nov., sp. nov., a novel aerobic bacteriochlorophyll a-producing a-proteobacterium isolated from hypersaline Ekho Lake, Antarctica Matthias Labrenz,13 Paul A. Lawson,2 Brian J. Tindall,3 Matthew D. Collins2 and Peter Hirsch1 Correspondence 1Institut fu¨r Allgemeine Mikrobiologie, Christian-Albrechts-Universita¨t, Kiel, Germany Matthias Labrenz 2School of Food Biosciences, University of Reading, PO Box 226, Reading RG6 6AP, UK matthias.labrenz@ 3DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Mascheroder io-warnemuende.de Weg 1b, D-38124 Braunschweig, Germany A Gram-negative, aerobic to microaerophilic rod was isolated from 10 m depths of the hypersaline, heliothermal and meromictic Ekho Lake (East Antarctica). The strain was oxidase- and catalase-positive, metabolized a variety of carboxylic acids and sugars and produced lipase. Cells had an absolute requirement for artificial sea water, which could not be replaced by NaCl. A large in vivo absorption band at 870 nm indicated production of bacteriochlorophyll a. The predominant fatty acids of this organism were 16 : 0 and 18 : 1v7c, with 3-OH 10 : 0, 16 : 1v7c and 18 : 0 in lower amounts. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylcholine. Ubiquinone 10 was produced. The DNA G+C content was 67 mol%. 16S rRNA gene sequence comparisons indicated that the isolate represents a member of the Roseobacter clade within the a-Proteobacteria. The organism showed no particular relationship to any members of this clade but clustered on the periphery of the genera Jannaschia, Octadecabacter and ‘Marinosulfonomonas’ and the species Ruegeria gelatinovorans. -
Comparative Proteomic Profiling of Newly Acquired, Virulent And
www.nature.com/scientificreports OPEN Comparative proteomic profling of newly acquired, virulent and attenuated Neoparamoeba perurans proteins associated with amoebic gill disease Kerrie Ní Dhufaigh1*, Eugene Dillon2, Natasha Botwright3, Anita Talbot1, Ian O’Connor1, Eugene MacCarthy1 & Orla Slattery4 The causative agent of amoebic gill disease, Neoparamoeba perurans is reported to lose virulence during prolonged in vitro maintenance. In this study, the impact of prolonged culture on N. perurans virulence and its proteome was investigated. Two isolates, attenuated and virulent, had their virulence assessed in an experimental trial using Atlantic salmon smolts and their bacterial community composition was evaluated by 16S rRNA Illumina MiSeq sequencing. Soluble proteins were isolated from three isolates: a newly acquired, virulent and attenuated N. perurans culture. Proteins were analysed using two-dimensional electrophoresis coupled with liquid chromatography tandem mass spectrometry (LC–MS/MS). The challenge trial using naïve smolts confrmed a loss in virulence in the attenuated N. perurans culture. A greater diversity of bacterial communities was found in the microbiome of the virulent isolate in contrast to a reduction in microbial community richness in the attenuated microbiome. A collated proteome database of N. perurans, Amoebozoa and four bacterial genera resulted in 24 proteins diferentially expressed between the three cultures. The present LC–MS/ MS results indicate protein synthesis, oxidative stress and immunomodulation are upregulated in a newly acquired N. perurans culture and future studies may exploit these protein identifcations for therapeutic purposes in infected farmed fsh. Neoparamoeba perurans is an ectoparasitic protozoan responsible for the hyperplastic gill infection of marine cultured fnfsh referred to as amoebic gill disease (AGD)1. -
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 -
Fig. S1 Diatom Abundance and Nutrient (Silicate, Nitrogen, Phosphate) Concentrations from March 1St to May 30Th 2016 at the Helgoland Sampling Site
Supplemental Figure Legends: Fig. S1 Diatom abundance and nutrient (silicate, nitrogen, phosphate) concentrations from March 1st to May 30th 2016 at the Helgoland sampling site. Fig. S2: Bubble plots showing normalized read abundance of members of the Bacteroidetes (a), Gammaproteobacteria (b), and Rhodobacteriaceae (minimum read abundance 0.005%) for each substrate incubation and the unamended incubation at t0, 3d, and 6d for Hel_1 to Hel_4. NMDS plots (right) based on Bray-Curtis dissimilarity reveal separation in Bacteroidetes, Gammaproteobacteria, and Rhodobacteriaceae composition across bloom phases with time. ANOSIM (R:Vegan) indicates significant difference between dissimilarity across bloom phases. Fig. S3: Shifts in microbial communities (1% minimum abundance) during incubation with FLA-PS. Percentage change in relative read abundance of bacterial genera (and phyla) are shown; the bar chart compares t0 abundances of each genus to 3d and 6d abundances and shows increase or decrease in each genus. ARA = arabinogalactan, CA = carrageenan, CH = chondroitin sulfate, LA = laminarin, XY = xylan, NA = no addition control. (a) Hel_1; note there are no data for CA at 6d (b) Hel_2; Note there are no data for xylan because there are no data from the t0 sample; (c) Hel_3; there are no data for the NA at 6d. Note also that there are no chondroitin data because this substrate was not used at the Hel_3 sample point. (d) Hel_4. Fig. S4: Relative abundance (% of DAPI stained cells) of Alteromonas (black; ALT1413) and Bacteroidetes (gray; CF319a) during incubations Hel_1 to Hel_4 enumerated by FISH. Fig. S5: Percentage of total DAPI-stainable cells at t0 timepoint (~ 15 minutes after substrate addition) showing staining by laminarin, xylan, chondroitin sulfate, and arabinogalactan for Hel_1 to Hel_4. -
Microbial Communities Responding to Deep-Sea Hydrocarbon Spills Molly C. Redmond1 and David L. Valentine2 1. Department of Biolo
Microbial Communities Responding to Deep-Sea Hydrocarbon Spills Molly C. Redmond1 and David L. Valentine2 1. Department of Biological Sciences, University of North Carolina at Charlotte, [email protected] 2. Department of Earth Science and Marine Science Institute, University of California, Santa Barbara, [email protected] Abstract The 2010 Deepwater Horizon oil spill in the Gulf of Mexico can be considered the world’s first deep-sea hydrocarbon spill. Deep-sea hydrocarbon spills occur in a different setting than surface oil spills and the organisms that respond must be adapted to this low temperature, high pressure environment. The hydrocarbon composition can also be quite different than at the sea surface, with high concentrations of dissolved hydrocarbons, including natural gas, and suspended droplets of petroleum. We discuss the bacteria that may respond to these spills and factors that affect their abundance, based on data collected during the Deepwater Horizon spill and in microcosm experiments in the following years. 1. Introduction When the Deepwater Horizon mobile offshore drilling unit exploded on April 20, 2010 and sank two days later, it caused the world’s first major deep-sea oil spill. Previous well blowouts such as Ixtoc I in the Gulf Mexico in 1979 and Platform A in the Santa Barbara Channel in 1969 also caused significant undersea spills, but the shallower depths of these spills (50-60 m) resulted in most of oil reaching the sea surface. In contrast, the Deepwater Horizon well was 1500 m below the sea surface and ~25% the hydrocarbons emitted remained dissolved or suspended in a deep-sea intrusion layer at depths between 900 and 1300 m (Ryerson et al. -
87-Fernanda-Cid.Pdf
UNIVERSIDAD DE LA FRONTERA Facultad de Ingeniería y Ciencias Doctorado en Ciencias de Recursos Naturales Characterization of bacterial communities from Deschampsia antarctica phyllosphere and genome sequencing of culturable bacteria with ice recrystallization inhibition activity DOCTORAL THESIS IN FULFILLMENT OF THE REQUERIMENTS FOR THE DEGREE DOCTOR OF SCIENCES IN NATURAL RESOURCES FERNANDA DEL PILAR CID ALDA TEMUCO-CHILE 2018 “Characterization of bacterial communities from Deschampsia antarctica phyllosphere and genome sequencing of culturable bacteria with ice recrystallization inhibition activity” Esta tesis fue realizada bajo la supervisión del Director de tesis, Dr. Milko A. Jorquera Tapia, profesor asociado del Departamento de Ciencias Químicas y Recursos Naturales, Facultad de Ingeniería y Ciencias, Universidad de La Frontera y co-dirigida por el Dr. León A. Bravo Ramírez, profesor titular del Departamento de Ciencias Agronómicas y Recursos Naturales, Facultad de Ciencias Agropecuarias y Forestales, Universidad de La Frontera. Esta tesis ha sido además aprobada por la comisión examinadora. Fernanda del Pilar Cid Alda …………………………………………… ……………………………………. Dr. MILKO JORQUERA T. Dr. Francisco Matus DIRECTOR DEL PROGRAMA DE …………………………………………. DOCTORADO EN CIENCIAS DE Dr. LEON BRAVO R. RECURSOS NATURALES …………………………………………. Dra. MARYSOL ALVEAR Z. ............................................................ Dr. Juan Carlos Parra ………………………………………… DIRECTOR DE POSTGRADO Dra. PAULINA BULL S. UNIVERSIDAD DE LA FRONTERA ………………………………………… Dr. LUIS COLLADO G. ………………………………………… Dra. ANA MUTIS T Dedico esta tesis a mis padres, Lillie Alda Leiva y Fernando Cid Verdugo quienes dedicaron sus vidas a la tarea de enseñar en la Universidad de La Frontera, Temuco-Chile. Abril, 2018 Agradecimientos /Acknowledgements Agradecimientos /Acknowledgements This study was supported by the following research projects: Doctoral Scholarship from Conicyt (no. 21140534) and La Frontera University.