Characterization of Root-Associated Bacterial Community Structures In
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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. -
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 -
Flavobacterium Gliding Motility: from Protein Secretion to Cell Surface Adhesin Movements
University of Wisconsin Milwaukee UWM Digital Commons Theses and Dissertations August 2019 Flavobacterium Gliding Motility: From Protein Secretion to Cell Surface Adhesin Movements Joseph Johnston University of Wisconsin-Milwaukee Follow this and additional works at: https://dc.uwm.edu/etd Part of the Biology Commons, Microbiology Commons, and the Molecular Biology Commons Recommended Citation Johnston, Joseph, "Flavobacterium Gliding Motility: From Protein Secretion to Cell Surface Adhesin Movements" (2019). Theses and Dissertations. 2202. https://dc.uwm.edu/etd/2202 This Dissertation is brought to you for free and open access by UWM Digital Commons. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of UWM Digital Commons. For more information, please contact [email protected]. FLAVOBACTERIUM GLIDING MOTILITY: FROM PROTEIN SECRETION TO CELL SURFACE ADHESIN MOVEMENTS by Joseph J. Johnston A Dissertation Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Biological Sciences at The University of Wisconsin-Milwaukee August 2019 ABSTRACT FLAVOBACTERIUM GLIDING MOTILITY: FROM PROTEIN SECRETION TO CELL SURFACE ADHESIN MOVEMENTS by Joseph J. Johnston The University of Wisconsin-Milwaukee, 2019 Under the Supervision of Dr. Mark J. McBride Flavobacterium johnsoniae exhibits rapid gliding motility over surfaces. At least twenty genes are involved in this process. Seven of these, gldK, gldL, gldM, gldN, sprA, sprE, and sprT encode proteins of the type IX protein secretion system (T9SS). The T9SS is required for surface localization of the motility adhesins SprB and RemA, and for secretion of the soluble chitinase ChiA. This thesis demonstrates that the gliding motility proteins GldA, GldB, GldD, GldF, GldH, GldI and GldJ are also essential for secretion. -
Halophilic Bacteroidetes As an Example on How Their Genomes Interact with the Environment
DOCTORAL THESIS 2020 PHYLOGENOMICS OF BACTEROIDETES; HALOPHILIC BACTEROIDETES AS AN EXAMPLE ON HOW THEIR GENOMES INTERACT WITH THE ENVIRONMENT Raúl Muñoz Jiménez DOCTORAL THESIS 2020 Doctoral Programme of Environmental and Biomedical Microbiology PHYLOGENOMICS OF BACTEROIDETES; HALOPHILIC BACTEROIDETES AS AN EXAMPLE ON HOW THEIR GENOMES INTERACT WITH THE ENVIRONMENT Raúl Muñoz Jiménez Thesis Supervisor: Ramon Rosselló Móra Thesis Supervisor: Rudolf Amann Thesis tutor: Elena I. García-Valdés Pukkits Doctor by the Universitat de les Illes Balears Publications resulted from this thesis Munoz, R., Rosselló-Móra, R., & Amann, R. (2016). Revised phylogeny of Bacteroidetes and proposal of sixteen new taxa and two new combinations including Rhodothermaeota phyl. nov. Systematic and Applied Microbiology, 39(5), 281–296 Munoz, R., Rosselló-Móra, R., & Amann, R. (2016). Corrigendum to “Revised phylogeny of Bacteroidetes and proposal of sixteen new taxa and two new combinations including Rhodothermaeota phyl. nov.” [Syst. Appl. Microbiol. 39 (5) (2016) 281–296]. Systematic and Applied Microbiology, 39, 491–492. Munoz, R., Amann, R., & Rosselló-Móra, R. (2019). Ancestry and adaptive radiation of Bacteroidetes as assessed by comparative genomics. Systematic and Applied Microbiology, 43(2), 126065. Dr. Ramon Rosselló Móra, of the Institut Mediterrani d’Estudis Avançats, Esporles and Dr. Rudolf Amann, of the Max-Planck-Institute für Marine Mikrobiologie, Bremen WE DECLARE: That the thesis titled Phylogenomics of Bacteroidetes; halophilic Bacteroidetes as an example on how their genomes interact with the environment, presented by Raúl Muñoz Jiménez to obtain a doctoral degree, has been completed under our supervision and meets the requirements to opt for an International Doctorate. For all intents and purposes, we hereby sign this document. -
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. -
Taibaiella Smilacinae Gen. Nov., Sp. Nov., an Endophytic Member of The
International Journal of Systematic and Evolutionary Microbiology (2013), 63, 3769–3776 DOI 10.1099/ijs.0.051607-0 Taibaiella smilacinae gen. nov., sp. nov., an endophytic member of the family Chitinophagaceae isolated from the stem of Smilacina japonica, and emended description of Flavihumibacter petaseus Lei Zhang,1,2 Yang Wang,3 Linfang Wei,1 Yao Wang,1 Xihui Shen1 and Shiqing Li1,2 Correspondence 1State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Xihui Shen Northwest A&F University, Yangling, Shaanxi 712100, PR China [email protected] 2State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Sciences and Northwest A&F University, Yangling, Shaanxi 712100, PR China 3Hubei Institute for Food and Drug Control, Wuhan 430072, PR China A light-yellow-coloured bacterium, designated strain PTJT-5T, was isolated from the stem of Smilacina japonica A. Gray collected from Taibai Mountain in Shaanxi Province, north-west China, and was subjected to a taxonomic study by using a polyphasic approach. The novel isolate grew optimally at 25–28 6C and pH 6.0–7.0. Flexirubin-type pigments were produced. Cells were Gram-reaction-negative, strictly aerobic, rod-shaped and non-motile. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain PTJT-5T was a member of the phylum Bacteroidetes, exhibiting the highest sequence similarity to Lacibacter cauensis NJ-8T (87.7 %). The major cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 and iso-C17 : 0 3-OH. -
Dinghuibacter Silviterrae Gen. Nov., Sp. Nov., Isolated from Forest Soil Ying-Ying Lv, Jia Wang, Mei-Hong Chen, Jia You and Li-Hong Qiu
International Journal of Systematic and Evolutionary Microbiology (2016), 66, 1785–1791 DOI 10.1099/ijsem.0.000940 Dinghuibacter silviterrae gen. nov., sp. nov., isolated from forest soil Ying-Ying Lv, Jia Wang, Mei-Hong Chen, Jia You and Li-Hong Qiu Correspondence State Key Laboratory of Biocontrol, School of Life Science, Sun Yat-sen University, Li-Hong Qiu Guangzhou, 510275, PR China [email protected] A novel Gram-stain negative, non-motile, rod-shaped, aerobic bacterial strain, designated DHOA34T, was isolated from forest soil of Dinghushan Biosphere Reserve, Guangdong Province, China. Comparative 16S rRNA gene sequence analysis showed that it exhibited highest similarity with Flavisolibacter ginsengiterrae Gsoil 492T and Flavitalea populi HY-50RT, at 90.89 and 90.83 %, respectively. In the neighbour-joining phylogenetic tree based on 16S rRNA gene sequences, DHOA34T formed an independent lineage within the family Chitinophagaceae but was distinct from all recognized species and genera of the family. T The major cellular fatty acids of DHOA34 included iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1v6c and/or C16 : 1v7c). The DNA G+C content was 51.6 mol% and the predominant quinone was menaquinone 7 (MK-7). Flexirubin pigments were produced. The phenotypic, chemotaxonomic and phylogenetic data demonstrate consistently that strain DHOA34T represents a novel species of a new genus in the family Chitinophagaceae, for which the name Dinghuibacter silviterrae gen. nov., sp. nov. is proposed. The type strain of Dinghuibacter silviterrae is DHOA34T (5CGMCC 1.15023T5KCTC 42632T). The family Chitinophagaceae, belonging to the class Sphingo- For isolation of DHOA34T, the soil sample was thoroughly bacteriia of the phylum Bacteroidetes, was proposed by suspended with 100 mM PBS (pH 7.0) and the suspension Ka¨mpfer et al. -
Rice Plant–Soil Microbiome Interactions Driven by Root and Shoot Biomass
diversity Article Rice Plant–Soil Microbiome Interactions Driven by Root and Shoot Biomass Cristina P. Fernández-Baca 1, Adam R. Rivers 2 , Jude E. Maul 3 , Woojae Kim 1,4, Ravin Poudel 2, Anna M. McClung 1, Daniel P. Roberts 3, Vangimalla R. Reddy 5 and Jinyoung Y. Barnaby 1,* 1 Dale Bumpers National Rice Research Center, USDA Agricultural Research Service, Stuttgart, AR 72160, USA; [email protected] (C.P.F.-B.); [email protected] (W.K.); [email protected] (A.M.M.) 2 Genomics and Bioinformatics Research Unit, USDA Agricultural Research Service, Gainesville, FL 32608, USA; [email protected] (A.R.R.); [email protected] (R.P.) 3 Beltsville Agricultural Research Center, Sustainable Agricultural Systems Laboratory, USDA Agricultural Research Service, Beltsville, MD 20705, USA; [email protected] (J.E.M.); [email protected] (D.P.R.) 4 Rural Development Administration, National Institute of Crop Science, Wanju 55365, Korea 5 Beltsville Agricultural Research Center, Adaptive Cropping Systems Laboratory, USDA Agricultural Research Service, Beltsville, MD 20705, USA; [email protected] * Correspondence: [email protected]; Tel.: 1-301-504-8436 Abstract: Plant–soil microbe interactions are complex and affected by many factors including soil type, edaphic conditions, plant genotype and phenotype, and developmental stage. The rice rhizo- sphere microbial community composition of nine recombinant inbred lines (RILs) and their parents, Francis and Rondo, segregating for root and shoot biomass, was determined using metagenomic Citation: Fernández-Baca, C.P.; sequencing as a means to examine how biomass phenotype influences the rhizosphere community. Rivers, A.R.; Maul, J.E.; Kim, W.; Two plant developmental stages were studied, heading and physiological maturity, based on root Poudel, R.; McClung, A.M.; Roberts, and shoot biomass growth patterns across the selected genotypes. -
Unraveling a Lignocellulose-Decomposing Bacterial Consortium from Soil Associated with Dry Sugarcane Straw by Genomic-Centered Metagenomics
microorganisms Article Unraveling a Lignocellulose-Decomposing Bacterial Consortium from Soil Associated with Dry Sugarcane Straw by Genomic-Centered Metagenomics Bruno Weiss 1,2,†, Anna Carolina Oliveira Souza 1,2,†, Milena Tavares Lima Constancio 1,2, Danillo Oliveira Alvarenga 1 , Victor S. Pylro 3 , Lucia M. Carareto Alves 1,* and Alessandro M. Varani 1,* 1 Departament of Technology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, São Paulo 14884-900, Brazil; [email protected] (B.W.); [email protected] (A.C.O.S.); [email protected] (M.T.L.C.); [email protected] (D.O.A.) 2 Graduate Program in Agricultural and Livestock Microbiology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, São Paulo 14884-900, Brazil 3 Microbial Ecology and Bioinformatics Laboratory, Department of Biology, Federal University of Lavras (UFLA), Lavras, Minas Gerais 37200-000, Brazil; victor.pylro@ufla.br * Correspondence: [email protected] (L.M.C.A.); [email protected] (A.M.V.) † Both authors contributed equally to this work. Abstract: Second-generation biofuel production is in high demand, but lignocellulosic biomass’ complexity impairs its use due to the vast diversity of enzymes necessary to execute the complete saccharification. In nature, lignocellulose can be rapidly deconstructed due to the division of Citation: Weiss, B.; Souza, A.C.O.; biochemical labor effectuated in bacterial communities. Here, we analyzed the lignocellulolytic Constancio, M.T.L.; Alvarenga, D.O.; potential of a bacterial consortium obtained from soil and dry straw leftover from a sugarcane milling Pylro, V.S.; Alves, L.M.C.; Varani, plant. -
Consortia of Anti-Nematode Fungi and Bacteria in the Rhizosphere Of
bioRxiv preprint doi: https://doi.org/10.1101/332403; this version posted May 28, 2018. 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 Consortia of anti-nematode fungi and bacteria in the 2 rhizosphere of soybean plants attacked by root-knot 3 nematodes 4 5 Hirokazu Toju1,2* and Yu Tanaka2,3 6 7 1Center for Ecological Research, Kyoto University, Otsu, Shiga 520-2133, Japan 8 2Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and 9 Technology Agency, Kawaguchi, Saitama 332-0012, Japan 10 3Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo, Kyoto, 11 606-8502, Japan 12 13 *Correspondence: Hirokazu Toju ([email protected]). 14 15 This article includes 5 Figures, 4 Tables, 5 Supplementary Figures, and 5 Supplementary 16 Data. 17 Running head: Anti-nematode microbiomes 18 bioRxiv preprint doi: https://doi.org/10.1101/332403; this version posted May 28, 2018. 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. 19 Abstract. 20 Cyst and root-knot nematodes are major risk factors of agroecosystem management, often 21 causing devastating impacts on crop production. The use of microbes that parasitize or prey 22 on nematodes has been considered as a promising approach for suppressing phytopathogenic 23 nematode populations. -
Nauny, Philippe É. M. (2019) Interpretation of Biosignatures in Extreme Environments, and Their Potential Impact for the Search for Life on Mars
Nauny, Philippe É. M. (2019) Interpretation of biosignatures in extreme environments, and their potential impact for the search for life on Mars. PhD thesis. http://theses.gla.ac.uk/77875/ Copyright and moral rights for this work are retained by the author A copy can be downloaded for personal non-commercial research or study, without prior permission or charge This work cannot be reproduced or quoted extensively from without first obtaining permission in writing from the author The content must not be changed in any way or sold commercially in any format or medium without the formal permission of the author When referring to this work, full bibliographic details including the author, title, awarding institution and date of the thesis must be given Enlighten: Theses https://theses.gla.ac.uk/ [email protected] Interpretation of biosignatures in extreme environments, and their potential impact for the search for life on Mars Philippe É. M. Nauny Master en Chimie et Biologie Université Louis Pasteur, Strasbourg Submitted in fulfilment of the requirements for the Degree of Doctor of Philosophy School of Geographical and Earth Sciences College of Science and Engineering University of Glasgow Viva: 21st February 2019 Abstract The search for life beyond Earth, and on Mars in particular, is one of the key points of astrobiology research. However, space missions are expensive and time-consuming. Simu- lating such missions at analogue sites on Earth can thus save time and money whilst working in natural settings. This thesis presents three studies of biosignatures from three different martian analogues. These biosignatures were linked — when possible — to environmental parameters observed at their sampling sites. -
Supporting Online Information
Supplementary Table 1 Initial PyOM and corn stover properties Property (units) Value PyOM Stover Total C (%) 61.0 41.9 Total N (%) 2.7 1.96 C:N (by mass) 22 21 C isotope signature (δ13C, ‰) +37.5 +1.7 Total H (%) 3.9 Total O (%) 15 pHDIW (1:20 w/v) 10.0 Feedstock Corn Particle size (mm) < 2 Heating rate (°C min-1) 5 Final temp (°C) 350 Residence time (min) 45 Surface area (m2 g-1) 92.8 ASTM Ash (%) 17 ASTM Volatiles (%) 35 ASTM Fixed C (%) 48 Supplementary Table 2 Initial soil properties Property (units) Value Texture (Channery) silt loam Bulk density (g cm-3) pHDIW 6.0 % sand 28.1 % silt 54.7 % clay 17.2 Total C (%) 1.48 Total N (%) 0.16 C:N (mass) 9.39 C isotope signature (δ13C, ‰) -25.5 Microbial biomass N* (mg kg-1 dry soil) (Vance et 8.5 al., 1987) *Microbial biomass C data were compromised, but based on a measured C:N ratio of 10.2 in the DOM, we predict roughly 87 mg MB-C kg-1 dry soil. Supplementary Table 3 Forward primer (full) sequences (adapterbarcodepad&link16Sfwdprimer) AATGATACGGCGACCACCGAGATCTACACATCGTACGAATGTTTTAATGGTG YCAGCMGCMGCGGTRA AATGATACGGCGACCACCGAGATCTACACACTATCTGAATGTTTTAATGGTG YCAGCMGCMGCGGTRA AATGATACGGCGACCACCGAGATCTACACTAGCGAGTAATGTTTTAATGGTG YCAGCMGCMGCGGTRA AATGATACGGCGACCACCGAGATCTACACCTGCGTGTAATGTTTTAATGGTG YCAGCMGCMGCGGTRA AATGATACGGCGACCACCGAGATCTACACTCATCGAGAATGTTTTAATGGTG YCAGCMGCMGCGGTRA AATGATACGGCGACCACCGAGATCTACACCGTGAGTGAATGTTTTAATGGTG YCAGCMGCMGCGGTRA AATGATACGGCGACCACCGAGATCTACACGGATATCTAATGTTTTAATGGTG YCAGCMGCMGCGGTRA AATGATACGGCGACCACCGAGATCTACACGACACCGTAATGTTTTAATGGTG YCAGCMGCMGCGGTRA Supplementary