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Runella Slithyformis Type Strain (LSU 4(T))
Lawrence Berkeley National Laboratory Recent Work Title Complete genome sequence of the aquatic bacterium Runella slithyformis type strain (LSU 4(T)). Permalink https://escholarship.org/uc/item/52p6k8qb Journal Standards in genomic sciences, 6(2) ISSN 1944-3277 Authors Copeland, Alex Zhang, Xiaojing Misra, Monica et al. Publication Date 2012-05-04 DOI 10.4056/sigs.2475579 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Standards in Genomic Sciences (2012) 6:145-154 DOI:10.4056/sigs.2485911 Complete genome sequence of the aquatic bacterium T Runella slithyformis type strain (LSU 4 ) Alex Copeland1, Xiaojing Zhang1,2, Monica Misra1,2, Alla Lapidus1, Matt Nolan1, Susan Lucas1, Shweta Deshpande1, Jan-Fang Cheng1, Roxanne Tapia1,2, Lynne A. Goodwin1,2, Sam Pitluck1, Konstantinos Liolios1, Ioanna Pagani1, Natalia Ivanova1, Natalia Mikhailova1, Amrita Pati1, Amy Chen3, Krishna Palaniappan3, Miriam Land1,4, Loren Hauser1,4, Chongle Pan1,4, Cynthia D. Jeffries1,4, John C. Detter1, Evelyne-Marie Brambilla5, Manfred Rohde6, Olivier D. Ngatchou Djao6, Markus Göker5, Johannes Sikorski5, Brian J. Tindall5, Tanja Woyke1, James Bristow1, Jonathan A. Eisen1,7, Victor Markowitz3, Philip Hugenholtz1,8, Nikos C. Kyrpides1, Hans-Peter Klenk5*, and Konstantinos Mavromatis1 1 DOE Joint Genome Institute, Walnut Creek, California, USA 2 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 3 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, -
The Subway Microbiome: Seasonal Dynamics and Direct Comparison Of
Gohli et al. Microbiome (2019) 7:160 https://doi.org/10.1186/s40168-019-0772-9 RESEARCH Open Access The subway microbiome: seasonal dynamics and direct comparison of air and surface bacterial communities Jostein Gohli1* , Kari Oline Bøifot1,2, Line Victoria Moen1, Paulina Pastuszek3, Gunnar Skogan1, Klas I. Udekwu4 and Marius Dybwad1,2 Abstract Background: Mass transit environments, such as subways, are uniquely important for transmission of microbes among humans and built environments, and for their ability to spread pathogens and impact large numbers of people. In order to gain a deeper understanding of microbiome dynamics in subways, we must identify variables that affect microbial composition and those microorganisms that are unique to specific habitats. Methods: We performed high-throughput 16S rRNA gene sequencing of air and surface samples from 16 subway stations in Oslo, Norway, across all four seasons. Distinguishing features across seasons and between air and surface were identified using random forest classification analyses, followed by in-depth diversity analyses. Results: There were significant differences between the air and surface bacterial communities, and across seasons. Highly abundant groups were generally ubiquitous; however, a large number of taxa with low prevalence and abundance were exclusively present in only one sample matrix or one season. Among the highly abundant families and genera, we found that some were uniquely so in air samples. In surface samples, all highly abundant groups were also well represented in air samples. This is congruent with a pattern observed for the entire dataset, namely that air samples had significantly higher within-sample diversity. We also observed a seasonal pattern: diversity was higher during spring and summer. -
Article-Associated Bac- Teria and Colony Isolation in Soft Agar Medium for Bacteria Unable to Grow at the Air-Water Interface
Biogeosciences, 8, 1955–1970, 2011 www.biogeosciences.net/8/1955/2011/ Biogeosciences doi:10.5194/bg-8-1955-2011 © Author(s) 2011. CC Attribution 3.0 License. Diversity of cultivated and metabolically active aerobic anoxygenic phototrophic bacteria along an oligotrophic gradient in the Mediterranean Sea C. Jeanthon1,2, D. Boeuf1,2, O. Dahan1,2, F. Le Gall1,2, L. Garczarek1,2, E. M. Bendif1,2, and A.-C. Lehours3 1Observatoire Oceanologique´ de Roscoff, UMR7144, INSU-CNRS – Groupe Plancton Oceanique,´ 29680 Roscoff, France 2UPMC Univ Paris 06, UMR7144, Adaptation et Diversite´ en Milieu Marin, Station Biologique de Roscoff, 29680 Roscoff, France 3CNRS, UMR6023, Microorganismes: Genome´ et Environnement, Universite´ Blaise Pascal, 63177 Aubiere` Cedex, France Received: 21 April 2011 – Published in Biogeosciences Discuss.: 5 May 2011 Revised: 7 July 2011 – Accepted: 8 July 2011 – Published: 20 July 2011 Abstract. Aerobic anoxygenic phototrophic (AAP) bac- detected in the eastern basin, reflecting the highest diver- teria play significant roles in the bacterioplankton produc- sity of pufM transcripts observed in this ultra-oligotrophic tivity and biogeochemical cycles of the surface ocean. In region. To our knowledge, this is the first study to document this study, we applied both cultivation and mRNA-based extensively the diversity of AAP isolates and to unveil the ac- molecular methods to explore the diversity of AAP bacte- tive AAP community in an oligotrophic marine environment. ria along an oligotrophic gradient in the Mediterranean Sea By pointing out the discrepancies between culture-based and in early summer 2008. Colony-forming units obtained on molecular methods, this study highlights the existing gaps in three different agar media were screened for the production the understanding of the AAP bacteria ecology, especially in of bacteriochlorophyll-a (BChl-a), the light-harvesting pig- the Mediterranean Sea and likely globally. -
Bacterial Community Change Through Drinking Water Treatment Processes
Int. J. Environ. Sci. Technol. (2015) 12:1867–1874 DOI 10.1007/s13762-014-0540-0 ORIGINAL PAPER Bacterial community change through drinking water treatment processes X. Liao • C. Chen • Z. Wang • C.-H. Chang • X. Zhang • S. Xie Received: 28 August 2012 / Revised: 30 September 2013 / Accepted: 5 March 2014 / Published online: 18 March 2014 Ó Islamic Azad University (IAU) 2014 Abstract The microbiological quality of drinking water Introduction has aroused increasing attention due to potential public health risks. Knowledge of the bacterial ecology in the The microbiological quality of drinking water has aroused effluents of drinking water treatment units will be of practical increasing attention due to potential public health risks. importance. However, the bacterial community in the The conventional treatment process, composed of coagu- effluents of drinking water filters remains poorly understood. lation–flocculation, sedimentation, rapid sand filtration, The changes of the density of viable heterotrophic bacteria and disinfection, is still widely used by drinking water and bacterial populations through a pilot-scale drinking producers to remove turbidity and pathogens. The con- water treatment process were investigated using heterotro- ventional treatment process is not efficient in removal of phic plate counts and clone library analysis, respectively. biodegradable dissolved organic carbon (BDOC) that is The pilot-scale treatment process was composed of preozo- mainly responsible for the microbial regrowth in drinking nation, rapid mixing, flocculation, sedimentation, sand fil- water distribution systems (DWDS). Biological activated tration postozonation, and biological activated carbon carbon (BAC) filtration can perform well in reduction of (BAC) filtration. The results indicated that heterotrophic organic pollutants after the attachment of the indigenous plate counts decreased dramatically through the drinking microbiota attached to the porous surface of granular water treatment processes. -
How to Cite Complete Issue More Information About This
Revista Internacional de Contaminación Ambiental ISSN: 0188-4999 [email protected] Universidad Nacional Autónoma de México México Luis-Villaseñor, Irasema E.; Zamudio-Armenta, Olga O.; Voltolina, Domenico; Rochin- Arenas, Jesús A.; Gómez-Gil, Bruno; Audelo-Naranjo, Juan M.; Flores-Higuera, Francisco A. BACTERIAL COMMUNITIES OF THE OYSTERS Crassostrea corteziensis AND C. sikamea OF COSPITA BAY, SINALOA, MEXICO Revista Internacional de Contaminación Ambiental, vol. 34, no. 2, 2018, May-July, pp. 203-213 Universidad Nacional Autónoma de México México DOI: https://doi.org/10.20937/RICA.2018.34.02.02 Available in: https://www.redalyc.org/articulo.oa?id=37056657002 How to cite Complete issue Scientific Information System Redalyc More information about this article Network of Scientific Journals from Latin America and the Caribbean, Spain and Journal's webpage in redalyc.org Portugal Project academic non-profit, developed under the open access initiative Rev. Int. Contam. Ambie. 34 (2) 203-213, 2018 DOI: 10.20937/RICA.2018.34.02.02 BACTERIAL COMMUNITIES OF THE OYSTERS Crassostrea corteziensis AND C. sikamea OF COSPITA BAY, SINALOA, MEXICO Irasema E. LUIS-VILLASEÑOR1*, Olga O. ZAMUDIO-ARMENTA1, Domenico VOLTOLINA2, Jesús A. ROCHIN-ARENAS1, Bruno GÓMEZ-GIL3, Juan M. AUDELO-NARANJO1 y Francisco A. FLORES-HIGUERA1 1 Universidad Autónoma de Sinaloa, Facultad de Ciencias del Mar, Paseo Claussen s/n, Mazatlán, Sinaloa, México 2 Centro de Investigaciones Biológicas del Noroeste, Apartado 1132, Mazatlán, Sinaloa, México 3 Centro de Investigación en Alimentación y Desarrollo, Unidad Mazatlán, Apartado 711, Mazatlán, Sinaloa, México * Author for correspondence; [email protected] (Received December 2016; accepted September 2017) Key words: bacteria, cultured oysters, wild oysters ABSTRACT This work aimed to quantify the bacterial loads and determine the taxonomic composi- tion of the microbial communities of oysters Crassostrea corteziensis and C. -
A Report of Nine Unrecorded Bacterial Species in the Phylum Bacteroidetes Collected from Freshwater Environments in Korea
Journal of Species Research 7(3):187-192, 2018 A report of nine unrecorded bacterial species in the phylum Bacteroidetes collected from freshwater environments in Korea Sanghwa Park, Kiwoon Beak, Ji-Hye Han, Yoon-Jong Nam and Mi-Hwa Lee* Bacterial Resources Research Division, Freshwater Bioresources Research Bureau, Nakdonggang National Institute of Biological Resources (NNIBR), Sangju, Gyengsangbuk-do 37242, Republic of Korea *Correspondent: [email protected] During a comprehensive study of indigenous prokaryotic species in South Korea, nine bacterial species in the phylum Bacteroidetes were isolated from freshwater environmental samples that were collected from three major rivers in the Republic of Korea. High 16S rRNA gene sequence similarity (≥98.7%) and robust phylogenetic clades with the closely related species suggest that each strain was correctly assigned to an independent and predefined bacterial species. There were no previous reports of these nine species in Korea. Within the phylum Bacteroidetes, four species were assigned to the genus Flavobacterium, order Flavobac- teriales, and five species to three genera of two families in the order Cytophagales. Gram reaction, colony and cell morphology, basic biochemical characteristics, isolation source, and strain IDs are described in the species description section. Keywords: 16S rRNA gene, Bacteroidetes, Flavobacteriales, Cytophagales, unrecorded species Ⓒ 2018 National Institute of Biological Resources DOI:10.12651/JSR.2018.7.3.187 INTRODUCTION MATERIALS AND METHODS The phylum Bacteroidetes (Ludwig and Klenk, 2001), Samples of freshwater, brackish water, and sediment also known as the Bacteroides-Cytophaga-Flexibacter were collected from the Han River, Nakdong River, and group, are widely distributed over a diverse range of eco- Seomjin River. -
Inter-Domain Horizontal Gene Transfer of Nickel-Binding Superoxide Dismutase 2 Kevin M
bioRxiv preprint doi: https://doi.org/10.1101/2021.01.12.426412; this version posted January 13, 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 Inter-domain Horizontal Gene Transfer of Nickel-binding Superoxide Dismutase 2 Kevin M. Sutherland1,*, Lewis M. Ward1, Chloé-Rose Colombero1, David T. Johnston1 3 4 1Department of Earth and Planetary Science, Harvard University, Cambridge, MA 02138 5 *Correspondence to KMS: [email protected] 6 7 Abstract 8 The ability of aerobic microorganisms to regulate internal and external concentrations of the 9 reactive oxygen species (ROS) superoxide directly influences the health and viability of cells. 10 Superoxide dismutases (SODs) are the primary regulatory enzymes that are used by 11 microorganisms to degrade superoxide. SOD is not one, but three separate, non-homologous 12 enzymes that perform the same function. Thus, the evolutionary history of genes encoding for 13 different SOD enzymes is one of convergent evolution, which reflects environmental selection 14 brought about by an oxygenated atmosphere, changes in metal availability, and opportunistic 15 horizontal gene transfer (HGT). In this study we examine the phylogenetic history of the protein 16 sequence encoding for the nickel-binding metalloform of the SOD enzyme (SodN). A comparison 17 of organismal and SodN protein phylogenetic trees reveals several instances of HGT, including 18 multiple inter-domain transfers of the sodN gene from the bacterial domain to the archaeal domain. -
Microbial Community Composition of Two Environmentally Conserved Estuaries in the Midorikawa River and Shirakawa River
Microbial Community Composition in Midorikawa and Shirakawa River 63 (Liem et al.) Microbial Community Composition of Two Environmentally Conserved Estuaries in the Midorikawa River and Shirakawa River Tran Thanh Liem1*, Mitsuaki Nakano1, Hiroto Ohta1, Takuro Niidome1, Tatsuya Masuda2, Kiyoshi Takikawa3, Shigeru Morimura1 1Graduate School of Science and Technology, Kumamoto University, Kumamoto City, Japan 2Priority Organization for Innovation and Excellence, Kumamoto University, Kumamoto City, Japan 3Center for Marine Environment Studies, Kumamoto University, Kumamoto City, Japan Abstract To provide a general overview of the microbial communities in environmentally conserved estuaries, the top 5 cm of sediment was sampled from the sandy estuary of the Shirakawa River and from the muddy estuary of the Midorikawa River. Higher amounts of organic matter were detected in the Midorikawa estuary sample than in the Shirakawa estuary sample. Measurement of redox potential revealed that the Shirakawa estuary was aerobic and the Midorikawa estuary was much less aerobic. Clone analysis was performed by targeting partial 16S rRNA gene sequences and using extracted DNA from the samples as a template. Various bacteria were detected, among which Gammaproteobacteria was dominant at both estuaries. Unclassified clones were detected in the Gammaproteobacteria group, mainly among samples from the Midorikawa estuary. Other detected bacterial groups were Alphaproteobacteria, Deltaproteobacteria, Chloroflexi, Actinobacteria, and Bacteroidetes. All the Deltaproteobacteria clones were anaerobic sulfate-reducing bacteria. Those aerobic and anaerobic bacteria coexisted in the top 5 cm of the estuary sediments indicating the surface layer have active sulfur and carbon cycle. Abundance of aerobic Gammaproteobacteria may be an indicator for conserved estuaries. Keywords: conserved environment, clone analysis, estuary, microbial community, 16S rRNA gene. -
1 Detection of Horizontal Gene Transfer in the Genome of the Choanoflagellate Salpingoeca
bioRxiv preprint doi: https://doi.org/10.1101/2020.06.28.176636; this version posted June 29, 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 Detection of Horizontal Gene Transfer in the Genome of the Choanoflagellate Salpingoeca 2 rosetta 3 4 Danielle M. Matriano1, Rosanna A. Alegado2, and Cecilia Conaco1 5 6 1 Marine Science Institute, University of the Philippines, Diliman 7 2 Department of Oceanography, Hawaiʻi Sea Grant, Daniel K. Inouye Center for Microbial 8 Oceanography: Research and Education, University of Hawai`i at Manoa 9 10 Corresponding author: 11 Cecilia Conaco, [email protected] 12 13 Author email addresses: 14 Danielle M. Matriano, [email protected] 15 Rosanna A. Alegado, [email protected] 16 Cecilia Conaco, [email protected] 17 18 19 20 21 22 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.06.28.176636; this version posted June 29, 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. 23 Abstract 24 25 Horizontal gene transfer (HGT), the movement of heritable materials between distantly related 26 organisms, is crucial in eukaryotic evolution. However, the scale of HGT in choanoflagellates, the 27 closest unicellular relatives of metazoans, and its possible roles in the evolution of animal 28 multicellularity remains unexplored. -
Life in the Cold Biosphere: the Ecology of Psychrophile
Life in the cold biosphere: The ecology of psychrophile communities, genomes, and genes Jeff Shovlowsky Bowman A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy University of Washington 2014 Reading Committee: Jody W. Deming, Chair John A. Baross Virginia E. Armbrust Program Authorized to Offer Degree: School of Oceanography i © Copyright 2014 Jeff Shovlowsky Bowman ii Statement of Work This thesis includes previously published and submitted work (Chapters 2−4, Appendix 1). The concept for Chapter 3 and Appendix 1 came from a proposal by JWD to NSF PLR (0908724). The remaining chapters and appendices were conceived and designed by JSB. JSB performed the analysis and writing for all chapters with guidance and editing from JWD and co- authors as listed in the citation for each chapter (see individual chapters). iii Acknowledgements First and foremost I would like to thank Jody Deming for her patience and guidance through the many ups and downs of this dissertation, and all the opportunities for fieldwork and collaboration. The members of my committee, Drs. John Baross, Ginger Armbrust, Bob Morris, Seelye Martin, Julian Sachs, and Dale Winebrenner provided valuable additional guidance. The fieldwork described in Chapters 2, 3, and 4, and Appendices 1 and 2 would not have been possible without the help of dedicated guides and support staff. In particular I would like to thank Nok Asker and Lewis Brower for giving me a sample of their vast knowledge of sea ice and the polar environment, and the crew of the icebreaker Oden for a safe and fascinating voyage to the North Pole. -
David López Escardó
Unveiling new molecular Opisthokonta diversity: A perspective from evolutionary genomics David López Escardó TESI DOCTORAL UPF / ANY 2017 DIRECTOR DE LA TESI Dr. Iñaki Ruiz Trillo DEPARTAMENT DE CIÈNCIES EXPERIMENTALS I DE LA SALUT ii Acknowledgements: Aquesta tesi va començar el dia que, mirant grups on poguer fer el projecte de màster, vaig trobar la web d'un grup de recerca que treballaven amb uns microorganismes, desconeguts per mi en aquell moment, per entendre l'origen dels animals. Tres o quatre assignatures de micro a la carrera, i cap d'elles tractava a fons amb protistes i menys els parents unicel·lulars dels animals. En fi, "Bitxos" raros, origen dels animals... em va semblar interessant. Així que em vaig presentar al despatx del Iñaki vestit amb el tratge de comercial de Tecnocasa, per veure si podia fer les pràctiques del Màster amb ells. El primer que vaig volguer remarcar durant l'entrevista és que no pretenia anar amb tratge a la feina, que no es pensés que jo de normal vaig tan seriós... Sigui com sigui, després de rumiar-s'ho, em va dir que endavant i em va emplaçar a fer una posterior entrevista amb els diferents membres del lab perquè tries un projecte de màster. Per tant, aquí el meu primer agraïment i molt gran, al Iñaki, per permetre'm, no només fer el màster, sinó també permetre'm fer aquesta tesis al seu laboratori. També per la llibertat alhora de triar projectes i per donar-li al MCG un ambient cordial on hi dóna gust treballar. Gràcies, doncs, per deixar-me entrar al món científic per la porta de la protistologia, la genòmica i l'evolució, que de ben segur m'acompanyaran sempre. -
Choanoflagellate Models — Monosiga Brevicollis and Salpingoeca Rosetta
Available online at www.sciencedirect.com ScienceDirect Choanoflagellate models — Monosiga brevicollis and Salpingoeca rosetta 1,2 1 Tarja T Hoffmeyer and Pawel Burkhardt Choanoflagellates are the closest single-celled relatives of choanoflagellate cells are highly polarized [1 ,6]. Choano- animals and provide fascinating insights into developmental flagellates possess a single posterior flagellum that is processes in animals. Two species, the choanoflagellates enclosed by a collar composed of microvilli (Figure 1b). Monosiga brevicollis and Salpingoeca rosetta are emerging The movement of the flagellum serves two main functions: as promising model organisms to reveal the evolutionary origin to allow motile cells to swim and to create water currents of key animal innovations. In this review, we highlight how which trap bacteria to the collar to allow phagocytosis [7,8]. choanoflagellates are used to study the origin of multicellularity Phagocytosed bacteria are digested in anterior localized in animals. The newly available genomic resources and food vacuoles (Figure 1b). The Golgi apparatus with many functional techniques provide important insights into the associated vesicles is positioned posterior to the prominent function of choanoflagellate pre- and postsynaptic proteins, nucleus. Moreover, many choanoflagellates possess anteri- cell–cell adhesion and signaling molecules and the evolution or filopodia (Figure 1b), which allow for substratum attach- of animal filopodia and thus underscore the relevance of ment of the cells [1 ,9]. choanoflagellate models for evolutionary biology, neurobiology and cell biology research. In this review, we highlight recent advances in choano- Addresses flagellate phylogeny and critically discuss the latest pro- 1 Marine Biological Association, The Laboratory, Citadel Hill, Plymouth gresses made on the establishment of choanoflagellates as PL1 2PB, UK 2 model organisms to understand the origin of multicellulari- Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK ty in animals.