Soil Bacteria Show Different Tolerance Ranges
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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. -
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. -
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. -
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 -
Tochko Colostate 0053N 15136.Pdf (4.934Mb)
THESIS PROCESSES GOVERNING THE PERFORMANCE OF OLEOPHILIC BIO-BARRIERS (OBBS) – LABORATORY AND FIELD STUDIES Submitted by Laura Tochko Department of Civil and Environmental Engineering In partial fulfillment of the requirements For the Degree of Master of Science Colorado State University Fort Collins, Colorado Fall 2018 Master’s Committee: Advisor: Tom Sale Joe Scalia Sally Sutton Copyright by Laura Elizabeth Tochko 2018 All Rights Reserved ABSTRACT PROCESSES GOVERNING THE PERFORMANCE OF OLEOPHILIC BIO-BARRIERS (OBBS) – LABORATORY AND FIELD STUDIES Petroleum sheens, a potential Clean Water Act violation, can occur at petroleum refining, distribution, and storage facilities located near surface water. In general, sheen remedies can be prone to failure due to the complex processes controlling the flow of light non-aqueous phase liquid (LNAPL) at groundwater/surface water interfaces (GSIs). Even a small gap in a barrier designed to resist the movement of LNAPL can result in a sheen of large areal extent. The cost of sheen remedies, exacerbated by failure, has led to research into processes governing sheens and development of the oleophilic bio-barrier (OBB). OBBs involve 1) an oleophilic (oil-loving) plastic geocomposite which intercepts and retains LNAPL and 2) cyclic delivery of oxygen and nutrients via tidally driven water level fluctuations. The OBB retains LNAPL that escapes the natural attenuation system through oleophilic retention and enhances the natural biodegradation capacity such that LNAPL is retained or degraded instead of discharging to form a sheen. Sand tank experiments were conducted to visualize the movement of LNAPL as a wetting and non-wetting fluid in a water-saturated tank. -
Diversity of Methylobacterium Species Associated with New Zealand Native Plants
http://researchcommons.waikato.ac.nz/ Research Commons at the University of Waikato Copyright Statement: The digital copy of this thesis is protected by the Copyright Act 1994 (New Zealand). The thesis may be consulted by you, provided you comply with the provisions of the Act and the following conditions of use: Any use you make of these documents or images must be for research or private study purposes only, and you may not make them available to any other person. Authors control the copyright of their thesis. You will recognise the author’s right to be identified as the author of the thesis, and due acknowledgement will be made to the author where appropriate. You will obtain the author’s permission before publishing any material from the thesis. Diversity of Methylobacterium Species Associated with New Zealand Native Plants A thesis submitted in partial fulfilment of the requirements for the degree of Masters of Science in Biological Sciences at the University of Waikato by Rowshan Jahan _________ The University of Waikato 2013 Abstract The genus Methylobacterium are pink-pigmented facultative methylotrophs (PPFMs), and are abundant colonizers of the phyllosphere, due to the availability of methanol, a waste product of pectin metabolism during plant cell division. Besides methanol cycling, Methylobacterium has important effects on plant health. The phyllosphere is an extreme environment with a landscape that is heterogeneous, continuously changing as the plant grows, and is exposed to very high ultra violet irradiation. Geographically, New Zealand has been isolated for over a million years, has a biologically diverse group of species, and is considered a biodiversity hotspot, with most of the native plants being endemic. -
Linking Microbial Community Structure to Β-Glucosidic
The ISME Journal (2013) 7, 2044–2053 & 2013 International Society for Microbial Ecology All rights reserved 1751-7362/13 www.nature.com/ismej ORIGINAL ARTICLE Linking microbial community structure to b-glucosidic function in soil aggregates Vanessa L Bailey1, Sarah J Fansler1, James C Stegen1 and Lee Ann McCue2 1Microbiology, Pacific Northwest National Laboratory, Richland, WA, USA and 2Computational Biology and Bioinformatics, Pacific Northwest National Laboratory, Richland, WA, USA To link microbial community 16S structure to a measured function in a natural soil, we have scaled both DNA and b-glucosidase assays down to a volume of soil that may approach a unique microbial community. b-Glucosidase activity was assayed in 450 individual aggregates, which were then sorted into classes of high or low activities, from which groups of 10 or 11 aggregates were identified and grouped for DNA extraction and pyrosequencing. Tandem assays of ATP were conducted for each aggregate in order to normalize these small groups of aggregates for biomass size. In spite of there being no significant differences in the richness or diversity of the microbial communities associated with high b-glucosidase activities compared with the communities associated with low b-glucosidase communities, several analyses of variance clearly show that the communities of these two groups differ. The separation of these groups is partially driven by the differential abundances of members of the Chitinophagaceae family. It may be observed that functional differences in otherwise similar soil aggregates can be largely attributed to differences in resource availability, rather than to the presence or absence of particular taxonomic groups. -
Different Microbial Strategies in the Handling Temperature
Handling Temperature Bursts Reaching 464°C: Different Microbial Strategies in the Sisters Peak Hydrothermal Chimney Mirjam Perner, Giorgio Gonnella, Stefan Kurtz and Julie LaRoche Appl. Environ. Microbiol. 2014, 80(15):4585. DOI: 10.1128/AEM.01460-14. Downloaded from Published Ahead of Print 16 May 2014. Updated information and services can be found at: http://aem.asm.org/content/80/15/4585 http://aem.asm.org/ These include: SUPPLEMENTAL MATERIAL Supplemental material REFERENCES This article cites 61 articles, 30 of which can be accessed free at: http://aem.asm.org/content/80/15/4585#ref-list-1 on August 19, 2014 by Universitaetsbibliothek Kiel CONTENT ALERTS Receive: RSS Feeds, eTOCs, free email alerts (when new articles cite this article), more» Information about commercial reprint orders: http://journals.asm.org/site/misc/reprints.xhtml To subscribe to to another ASM Journal go to: http://journals.asm.org/site/subscriptions/ Handling Temperature Bursts Reaching 464°C: Different Microbial Strategies in the Sisters Peak Hydrothermal Chimney Mirjam Perner,a Giorgio Gonnella,b Stefan Kurtz,b Julie LaRochec* Molecular Biology of Microbial Consortia, University of Hamburg, Biocenter Klein Flottbek, Hamburg, Germanya; Center for Bioinformatics, University of Hamburg, Hamburg, Germanyb; Marine Biogeochemistry, Leibniz Institute of Marine Science, GEOMAR, Kiel, Germanyc Downloaded from The active venting Sisters Peak (SP) chimney on the Mid-Atlantic Ridge holds the current temperature record for the hottest ever measured hydrothermal fluids (400°C, accompanied by sudden temperature bursts reaching 464°C). Given the unprecedented temperature regime, we investigated the biome of this chimney with a focus on special microbial adaptations for thermal toler- ance. -
Rhbio2 Rhbio1
Figure S1. Overview of aggregate samples from Chivasso at family level, taxa > 0.6% are shown. 100% Others U. m. of Bacteria kingdom Verrucomicrobiaceae DA101 soil group Opitutaceae U. m. of OPB35 soil group class 90% U. m. of Proteobacteria phylum U. m. of Xanthomonadales order Xanthomonadaceae Solimonadaceae Pseudomonadaceae Enterobacteriaceae U. m. of Sh765B-TzT-29 order U. m. of Myxococcales order 80% Polyangiaceae Haliangiaceae U. m. of GR-WP33-30 order TRA3-20 order U. m. of SC-I-84 order Nitrosomonadaceae Methylophilaceae U. m. of Betaproteobacteria class 70% Oxalobacteraceae Comamonadaceae Burkholderiaceae Sphingomonadaceae U. m. of Rhodospirillales order Rhodospirillaceae DA111 Xanthobacteraceae 60% Rhodobiaceae U. m. of Rhizobiales order Hyphomicrobiaceae Brucellaceae Bradyrhizobiaceae Caulobacteraceae Planctomycetaceae Nitrospiraceae 50% 0319-6A21 Gemmatimonadaceae Clostridiaceae 1 Planococcaceae Paenibacillaceae Bacillaceae U. m. of Chloroflexi phylum U. m. of TK10 class 40% U. m. of JG30-KF-CM45 order U. m. of S085 class U. m. of KD4-96 class Roseiflexaceae Anaerolineaceae U. m. of Candidate division WS3 phylum Sphingobacteriaceae Chitinophagaceae 30% Flavobacteriaceae Cytophagaceae U. m. of Solirubrobacterales order Solirubrobacteraceae U. m. of Gaiellales order Gaiellaceae U. m. of MB-A2-108 class U. m. of Actinobacteria class 20% Nocardioidaceae Micromonosporaceae U. m. of Micrococcales order Microbacteriaceae Geodermatophilaceae U. m. of Corynebacteriales order Bifidobacteriaceae U. m. of Acidimicrobiales order 10% U. m. of Subgroup 7 order (Holophagae class) U. m. of Subgroup 6 order (Acidobacteria class) U. m. of Subgroup 5 order (Acidobacteria class) U. m. of Subgroup 4 order (Acidobacteria class) RB41 11-24 U. m. of Subgroup 3 order (Acidobacteria class) U. m. of Subgroup 17 order (Acidobacteria class) 0% Acidobacteriaceae (Subgroup 1) U. -
Microbial Degradation of Chemical Compounds Used in Onshore Gas Production in the SE of South Australia
Australia’s National Science Agency Microbial degradation of chemical compounds used in onshore gas production in the SE of South Australia GISERA W.15 Nai Tran‐Dinh, Tania J Vergara, Richard Schinteie, Carla Mariani, Paul Greenfield and David J Midgley Report number EP196935 27 September 2019 GISERA CSIRO Energy ISBN (print): 978‐1‐4863‐1411‐9 ISBN (online): 978‐1‐4863‐1412‐6 Citation Tran‐Dinh N, Vergara TJ, Schinteie R, Mariani C & Midgley DJ (2019) Microbial degradation of chemical compounds used in onshore gas production in the SE of South Australia. CSIRO, Australia. Copyright © Commonwealth Scientific and Industrial Research Organisation 2019. To the extent permitted by law, all rights are reserved and no part of this publication covered by copyright may be reproduced or copied in any form or by any means except with the written permission of CSIRO. Important disclaimer CSIRO advises that the information contained in this publication comprises general statements based on scientific research. The reader is advised and needs to be aware that such information may be incomplete or unable to be used in any specific situation. No reliance or actions must therefore be made on that information without seeking prior expert professional, scientific and technical advice. To the extent permitted by law, CSIRO (including its employees and consultants) excludes all liability to any person for any consequences, including but not limited to all losses, damages, costs, expenses and any other compensation, arising directly or indirectly from using this publication (in part or in whole) and any information or material contained in it. CSIRO is committed to providing web accessible content wherever possible.