Characterization of the Microbial Community in the Anaerobic/Oxic/Anoxic Process Combined with Sludge Ozonation and Phosphorus Adsorption
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
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 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. -
Eelgrass Sediment Microbiome As a Nitrous Oxide Sink in Brackish Lake Akkeshi, Japan
Microbes Environ. Vol. 34, No. 1, 13-22, 2019 https://www.jstage.jst.go.jp/browse/jsme2 doi:10.1264/jsme2.ME18103 Eelgrass Sediment Microbiome as a Nitrous Oxide Sink in Brackish Lake Akkeshi, Japan TATSUNORI NAKAGAWA1*, YUKI TSUCHIYA1, SHINGO UEDA1, MANABU FUKUI2, and REIJI TAKAHASHI1 1College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, 252–0880, Japan; and 2Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, 060–0819, Japan (Received July 16, 2018—Accepted October 22, 2018—Published online December 1, 2018) Nitrous oxide (N2O) is a powerful greenhouse gas; however, limited information is currently available on the microbiomes involved in its sink and source in seagrass meadow sediments. Using laboratory incubations, a quantitative PCR (qPCR) analysis of N2O reductase (nosZ) and ammonia monooxygenase subunit A (amoA) genes, and a metagenome analysis based on the nosZ gene, we investigated the abundance of N2O-reducing microorganisms and ammonia-oxidizing prokaryotes as well as the community compositions of N2O-reducing microorganisms in in situ and cultivated sediments in the non-eelgrass and eelgrass zones of Lake Akkeshi, Japan. Laboratory incubations showed that N2O was reduced by eelgrass sediments and emitted by non-eelgrass sediments. qPCR analyses revealed that the abundance of nosZ gene clade II in both sediments before and after the incubation as higher in the eelgrass zone than in the non-eelgrass zone. In contrast, the abundance of ammonia-oxidizing archaeal amoA genes increased after incubations in the non-eelgrass zone only. Metagenome analyses of nosZ genes revealed that the lineages Dechloromonas-Magnetospirillum-Thiocapsa and Bacteroidetes (Flavobacteriia) within nosZ gene clade II were the main populations in the N2O-reducing microbiome in the in situ sediments of eelgrass zones. -
Runella Slithyfurmis Gen. Nov., Sp. Nov., a Curved, Nonflexible, Pink Bacterium
0020-77 13/78/0028-0032$02.00/0 INTERNA'I'IONAI, JOIIRNA~.OF SYSTI.:MATI(' BA(TTEHIOI,OGY, Jan. 1978, p. 32-36 Vol. 28, No. 1 Copyright 0 1978 International Association of Microbiological Societies Printed in U.S. A. Runella slithyfurmis gen. nov., sp. nov., a Curved, Nonflexible, Pink Bacterium JOHN M. LARKIN AND PATRICIA M. WILLIAMS Department of Microbiology, Louisiana State University, Baton Rouge, Louisiana 70803 Two strains of bacteria regarded as belonging to a new species were isolated from bodies of water near Baton Rouge, La. The cells of these strains were gram-negative, curved rods, the degree of curvature varying among cells in a single culture. A pink pigment was produced on glucose-peptone-yeast extract agar. The strains were nonmotile and nonfermentative, and the guanine-plus- cytosine contents of their deoxyribonucleic acids varied from 49.3 to 49.6 mol%. The species cannot be assigned to any known genus, and therefore a new genus, Runella, is proposed, with R. slzthyformis as the type species. The type strain of this species is strain 4 (= ATCC 29530). At present, it is difficult to place the genus Runella in a family. During examination of the bacteria that in- eosin-methylene blue agar, phenol red-mannitol-salt habit the bodies of fresh water in southern agar, phenyl ethyl alcohol agar, nutrient agar, nutrient Louisiana, we repeatedly encountered bacteria agar plus 5% sucrose, Trypticase soy agar, Trypticase soy agar plus 3% glucose, peptonized milk agar, MS that resembled those of the newly described agar, yeast extract-acetate-tryptoneagar, McConkey genus Flectobucillus (2). -
Taxonomy JN869023
Species that differentiate periods of high vs. low species richness in unattached communities Species Taxonomy JN869023 Bacteria; Actinobacteria; Actinobacteria; Actinomycetales; ACK-M1 JN674641 Bacteria; Bacteroidetes; [Saprospirae]; [Saprospirales]; Chitinophagaceae; Sediminibacterium JN869030 Bacteria; Actinobacteria; Actinobacteria; Actinomycetales; ACK-M1 U51104 Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Comamonadaceae; Limnohabitans JN868812 Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Comamonadaceae JN391888 Bacteria; Planctomycetes; Planctomycetia; Planctomycetales; Planctomycetaceae; Planctomyces HM856408 Bacteria; Planctomycetes; Phycisphaerae; Phycisphaerales GQ347385 Bacteria; Verrucomicrobia; [Methylacidiphilae]; Methylacidiphilales; LD19 GU305856 Bacteria; Proteobacteria; Alphaproteobacteria; Rickettsiales; Pelagibacteraceae GQ340302 Bacteria; Actinobacteria; Actinobacteria; Actinomycetales JN869125 Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Comamonadaceae New.ReferenceOTU470 Bacteria; Cyanobacteria; ML635J-21 JN679119 Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Comamonadaceae HM141858 Bacteria; Acidobacteria; Holophagae; Holophagales; Holophagaceae; Geothrix FQ659340 Bacteria; Verrucomicrobia; [Pedosphaerae]; [Pedosphaerales]; auto67_4W AY133074 Bacteria; Elusimicrobia; Elusimicrobia; Elusimicrobiales FJ800541 Bacteria; Verrucomicrobia; [Pedosphaerae]; [Pedosphaerales]; R4-41B JQ346769 Bacteria; Acidobacteria; [Chloracidobacteria]; RB41; Ellin6075 -
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 -
Spirosoma Endophyticum Sp. Nov., Isolated from Zn- and Cd-Accumulating Salix Caprea
International Journal of Systematic and Evolutionary Microbiology (2013), 63, 4586–4590 DOI 10.1099/ijs.0.052654-0 Spirosoma endophyticum sp. nov., isolated from Zn- and Cd-accumulating Salix caprea Julia Fries, Stefan Pfeiffer, Melanie Kuffner and Angela Sessitsch Correspondence AIT Austrian Institute of Technology GmbH, Bioresources Unit, Tulln, Austria Angela Sessitsch [email protected] A Gram-reaction-negative, yellow-pigmented strain, designated EX36T, was characterized using a polyphasic approach comprising phylogenetic, morphological and genotypic analyses. The endophytic strain was isolated from Zn/Cd-accumulating Salix caprea in Arnoldstein, Austria. Analysis of the 16S rRNA gene demonstrated that the novel strain is most closely related to members of the genus Spirosoma (95 % sequence similarity with Spirosoma linguale). The genomic DNA G+C content was 47.2 mol%. The predominant quinone was and the major cellular fatty acids were summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1v7c), C16 : 1v5c, iso- T C17 : 0 3-OH and iso-C15 : 0. On the basis of its phenotypic and genotypic properties, strain EX36 should be classified as a novel species of the genus Spirosoma, for which the name Spirosoma endophyticum sp. nov. is proposed. The type strain is EX36T (5DSM 26130T5LMG 27272T). The genus Spirosoma was first proposed by Larkin & Borrall rRNA gene was amplified by PCR using the primers 8f (59- (1984) and belongs to the family Flexibacteraceae in the AGAGTTTGATCCTGGCTCAG-39)(Weisburget al., 1991) phylum Bacteroidetes. At the time of writing the genus and 1520r (59-AAGGAGGTGATCCAGCCGCA-39)(Edwards Spirosoma includes five species, the type species Spirosoma et al., 1989). -
Horizontal Operon Transfer, Plasmids, and the Evolution of Photosynthesis in Rhodobacteraceae
The ISME Journal (2018) 12:1994–2010 https://doi.org/10.1038/s41396-018-0150-9 ARTICLE Horizontal operon transfer, plasmids, and the evolution of photosynthesis in Rhodobacteraceae 1 2 3 4 1 Henner Brinkmann ● Markus Göker ● Michal Koblížek ● Irene Wagner-Döbler ● Jörn Petersen Received: 30 January 2018 / Revised: 23 April 2018 / Accepted: 26 April 2018 / Published online: 24 May 2018 © The Author(s) 2018. This article is published with open access Abstract The capacity for anoxygenic photosynthesis is scattered throughout the phylogeny of the Proteobacteria. Their photosynthesis genes are typically located in a so-called photosynthesis gene cluster (PGC). It is unclear (i) whether phototrophy is an ancestral trait that was frequently lost or (ii) whether it was acquired later by horizontal gene transfer. We investigated the evolution of phototrophy in 105 genome-sequenced Rhodobacteraceae and provide the first unequivocal evidence for the horizontal transfer of the PGC. The 33 concatenated core genes of the PGC formed a robust phylogenetic tree and the comparison with single-gene trees demonstrated the dominance of joint evolution. The PGC tree is, however, largely incongruent with the species tree and at least seven transfers of the PGC are required to reconcile both phylogenies. 1234567890();,: 1234567890();,: The origin of a derived branch containing the PGC of the model organism Rhodobacter capsulatus correlates with a diagnostic gene replacement of pufC by pufX. The PGC is located on plasmids in six of the analyzed genomes and its DnaA- like replication module was discovered at a conserved central position of the PGC. A scenario of plasmid-borne horizontal transfer of the PGC and its reintegration into the chromosome could explain the current distribution of phototrophy in Rhodobacteraceae. -
Key Role of Alphaproteobacteria and Cyanobacteria in the Formation of Stromatolites of Lake Dziani Dzaha (Mayotte, Western Indian Ocean)
fmicb-09-00796 May 18, 2018 Time: 17:53 # 1 ORIGINAL RESEARCH published: 22 May 2018 doi: 10.3389/fmicb.2018.00796 Key Role of Alphaproteobacteria and Cyanobacteria in the Formation of Stromatolites of Lake Dziani Dzaha (Mayotte, Western Indian Ocean) Emmanuelle Gérard1*, Siham De Goeyse1, Mylène Hugoni2, Hélène Agogué3, Laurent Richard4, Vincent Milesi1, François Guyot5, Léna Lecourt1, Stephan Borensztajn1, Marie-Béatrice Joseph1, Thomas Leclerc1, Gérard Sarazin1, Didier Jézéquel1, Christophe Leboulanger6 and Magali Ader1 1 UMR CNRS 7154 Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Université Paris Diderot, Centre National de la Recherche Scientifique, Paris, France, 2 Université Lyon 1, UMR CNRS 5557 / INRA 1418, Ecologie Microbienne, Villeurbanne, France, 3 UMR 7266 CNRS-Université de la Rochelle, LIttoral ENvironnement Et Sociétés, La Rochelle, France, Edited by: 4 School of Mining and Geosciences, Nazarbayev University, Astana, Kazakhstan, 5 Museum National d’Histoire Naturelle, Christophe Dupraz, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, UMR 7590 CNRS Sorbonne Universités, Université Stockholm University, Sweden Pierre et Marie Curie, Institut de Recherche pour le Développement UMR 206, Paris, France, 6 UMR MARBEC, IRD, Ifremer, Reviewed by: CNRS, Université de Montpellier, Sète, France Trinity L. Hamilton, University of Minnesota Twin Cities, United States Lake Dziani Dzaha is a thalassohaline tropical crater lake located on the “Petite Terre” Virginia Helena Albarracín, Island of Mayotte (Comoros archipelago, Western Indian Ocean). Stromatolites are Center for Electron Microscopy (CIME), Argentina actively growing in the shallow waters of the lake shores. These stromatolites are *Correspondence: mainly composed of aragonite with lesser proportions of hydromagnesite, calcite, Emmanuelle Gérard dolomite, and phyllosilicates. -
Limibaculum Halophilum Gen. Nov., Sp. Nov., a New Member of the Family Rhodobacteraceae
TAXONOMIC DESCRIPTION Shin et al., Int J Syst Evol Microbiol 2017;67:3812–3818 DOI 10.1099/ijsem.0.002200 Limibaculum halophilum gen. nov., sp. nov., a new member of the family Rhodobacteraceae Yong Ho Shin,1 Jong-Hwa Kim,1 Ampaitip Suckhoom,2 Duangporn Kantachote2 and Wonyong Kim1,* Abstract A Gram-stain-negative, cream-pigmented, aerobic, non-motile, non-spore-forming and short-rod-shaped bacterial strain, designated CAU 1123T, was isolated from mud from reclaimed land. The strain’s taxonomic position was investigated by using a polyphasic approach. Strain CAU 1123T grew optimally at 37 C and at pH 7.5 in the presence of 2 % (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain CAU 1123T formed a monophyletic lineage within the family Rhodobacteraceae with 93.8 % or lower sequence similarity to representatives of the genera Rubrimonas, Oceanicella, Pleomorphobacterium, Rhodovulum and Albimonas. The major fatty acids were C18 : 1 !7c and 11-methyl C18 : 1 !7c and the predominant respiratory quinone was Q-10. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, two unidentified phospholipids, one unidentified aminolipid and one unidentified lipid. The DNA G+C content was 71.1 mol%. Based on the data from phenotypic, chemotaxonomic and phylogenetic studies, it is proposed that strain CAU 1123T represents a novel genus and novel species of the family Rhodobacteraceae, for which the name Limibaculumhalophilum gen. nov., sp. nov. The type strain is CAU 1123T (=KCTC 52187T, =NBRC 112522T). The family Rhodobacteraceae was first established by Garr- chemotaxonomic properties along with a detailed phyloge- ity et al. -
Metagenomics Unveils the Attributes of the Alginolytic Guilds of Sediments from Four Distant Cold Coastal Environments
Metagenomics unveils the attributes of the alginolytic guilds of sediments from four distant cold coastal environments Marina N Matos1, Mariana Lozada1, Luciano E Anselmino1, Matías A Musumeci1, Bernard Henrissat2,3,4, Janet K Jansson5, Walter P Mac Cormack6,7, JoLynn Carroll8,9, Sara Sjöling10, Leif Lundgren11 and Hebe M Dionisi1* 1Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CONICET), Puerto Madryn, U9120ACD, Chubut, Argentina 2Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 13288 Marseille, France 3INRA, USC 1408 AFMB, F-13288 Marseille, France 4Department of Biological Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia 5Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA 6Instituto Antártico Argentino, Ciudad Autónoma de Buenos Aires, C1064ABR, Argentina 7Instituto Nanobiotec, CONICET- Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, C1113AAC, Argentina 8Akvaplan-niva, Fram – High North Research Centre for Climate and the Environment, NO- 9296 Tromsø, Norway 9CAGE - Centre for Arctic Gas Hydrate, Environment and Climate, UiT The Arctic University of Norway, N-9037 Tromsø, Norway 10School of Natural Sciences and Environmental Studies, Södertörn University, 141 89 Huddinge, Sweden 11Stockholm University, SE-106 91 Stockholm, Sweden This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process which may lead to differences between this version and the Version of Record. Please cite this article as an ‘Accepted Article’, doi: 10.1111/1462-2920.13433 This article is protected by copyright. All rights reserved. Page 2 of 41 Running title: Alginolytic guilds from cold sediments *Correspondence: Hebe M. -
Detection of Microbial 16S Rrna Gene in the Blood of Patients with Parkinson’S Disease
ORIGINAL RESEARCH published: 24 May 2018 doi: 10.3389/fnagi.2018.00156 Detection of Microbial 16S rRNA Gene in the Blood of Patients With Parkinson’s Disease Yiwei Qian 1†, Xiaodong Yang 1†, Shaoqing Xu 1, Chunyan Wu 2, Nan Qin 2*, Sheng-Di Chen 1* and Qin Xiao 1* 1Department of Neurology & Collaborative Innovation Center for Brain Science, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China, 2Department of Bioinformatics, Realbio Genomics Institute, Shanghai, China Emerging evidence suggests that the microbiota present in feces plays a role in Parkinson’s disease (PD). However, the alterations of the microbiome in the blood of PD patients remain unknown. To test this hypothesis, we conducted this case-control study to explore the microbiota compositions in the blood of Chinese PD patients. Microbiota communities in the blood of 45 patients and their healthy spouses were investigated using high-throughput Illumina HiSeq sequencing targeting the V3-V4 region of 16S ribosomal RNA (rRNA) gene. The relationships between the microbiota in the blood and Edited by: PD clinical characteristics were analyzed. No difference was detected in the structure Jiawei Zhou, and richness between PD patients and healthy controls. The following genera were Institute of Neuroscience, Shanghai Institutes for Biological Sciences enriched in the blood of PD patients: Isoptericola, Cloacibacterium, Enhydrobacter (CAS), China and Microbacterium; whereas genus Limnobacter was enriched in the healthy controls Reviewed by: after adjusting for age, gender, body mass index (BMI) and constipation. Additionally, Liu Zhihua, University of Chinese Academy of the findings regarding these genera were validated in another independent group of Sciences (UCAS), China 58 PD patients and 57 healthy controls using real-time PCR targeting genus-specific Shuo Yang, Nanjing Medical University, China 16S rRNA genes.