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Deep Microbial Community Profiling Along the Fermentation Process of Pulque, a Major Biocultural Resource of Mexico
bioRxiv preprint doi: https://doi.org/10.1101/718999; this version posted July 31, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Deep microbial community profiling along the fermentation process of pulque, a major biocultural resource of Mexico. 1 1 2 Carolina Rocha-Arriaga , Annie Espinal-Centeno , Shamayim Martinez-Sanchez , Juan 1 2 1,3 Caballero-Pérez , Luis D. Alcaraz * & Alfredo Cruz-Ramirez *. 1 Molecular & Developmental Complexity Group, Unit of Advanced Genomics, LANGEBIO-CINVESTAV, Irapuato, México. 2 Laboratorio de Genómica Ambiental, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México. Cd. Universitaria, 04510 Coyoacán, Mexico City, Mexico. 3 Escuela de Agronomía, Universidad de La Salle Bajío, León, Gto, Mexico. *Corresponding authors: [email protected], [email protected] ● Our approach allowed the identification of a broader microbial diversity in Pulque ● We increased 4.4 times bacteria genera and 40 times fungal species detected in mead. ● Newly reported bacteria genera and fungal species associated to Pulque fermentation Abstract Some of the biggest non-three plants endemic to Mexico were called metl in the Nahua culture. During colonial times they were renamed with the antillan word maguey. This was changed again by Carl von Linné who called them Agave (a greco-latin voice for admirable). For several Mexican prehispanic cultures, Agave species were not only considered as crops, but also part of their biocultural resources and cosmovision. Among the major products obtained from some Agave spp since pre-hispanic times is the alcoholic beverage called pulque or octli. -
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 S1. Bacterial Otus from 16S Rrna
Table S1. Bacterial OTUs from 16S rRNA sequencing analysis including only taxa which were identified to genus level (those OTUs identified as Ambiguous taxa, uncultured bacteria or without genus-level identifications were omitted). OTUs with only a single representative across all samples were also omitted. Taxa are listed from most to least abundant. Pitcher Plant Sample Class Order Family Genus CB1p1 CB1p2 CB1p3 CB1p4 CB5p234 Sp3p2 Sp3p4 Sp3p5 Sp5p23 Sp9p234 sum Gammaproteobacteria Legionellales Coxiellaceae Rickettsiella 1 2 0 1 2 3 60194 497 1038 2 61740 Alphaproteobacteria Rhodospirillales Rhodospirillaceae Azospirillum 686 527 10513 485 11 3 2 7 16494 8201 36929 Sphingobacteriia Sphingobacteriales Sphingobacteriaceae Pedobacter 455 302 873 103 16 19242 279 55 760 1077 23162 Betaproteobacteria Burkholderiales Oxalobacteraceae Duganella 9060 5734 2660 40 1357 280 117 29 129 35 19441 Gammaproteobacteria Pseudomonadales Pseudomonadaceae Pseudomonas 3336 1991 3475 1309 2819 233 1335 1666 3046 218 19428 Betaproteobacteria Burkholderiales Burkholderiaceae Paraburkholderia 0 1 0 1 16051 98 41 140 23 17 16372 Sphingobacteriia Sphingobacteriales Sphingobacteriaceae Mucilaginibacter 77 39 3123 20 2006 324 982 5764 408 21 12764 Gammaproteobacteria Pseudomonadales Moraxellaceae Alkanindiges 9 10 14 7 9632 6 79 518 1183 65 11523 Betaproteobacteria Neisseriales Neisseriaceae Aquitalea 0 0 0 0 1 1577 5715 1471 2141 177 11082 Flavobacteriia Flavobacteriales Flavobacteriaceae Flavobacterium 324 219 8432 533 24 123 7 15 111 324 10112 Alphaproteobacteria -
Dissertation Implementing Organic Amendments To
DISSERTATION IMPLEMENTING ORGANIC AMENDMENTS TO ENHANCE MAIZE YIELD, SOIL MOISTURE, AND MICROBIAL NUTRIENT CYCLING IN TEMPERATE AGRICULTURE Submitted by Erika J. Foster Graduate Degree Program in Ecology In partial fulfillment of the requirements For the Degree of Doctor of Philosophy Colorado State University Fort Collins, Colorado Summer 2018 Doctoral Committee: Advisor: M. Francesca Cotrufo Louise Comas Charles Rhoades Matthew D. Wallenstein Copyright by Erika J. Foster 2018 All Rights Reserved i ABSTRACT IMPLEMENTING ORGANIC AMENDMENTS TO ENHANCE MAIZE YIELD, SOIL MOISTURE, AND MICROBIAL NUTRIENT CYCLING IN TEMPERATE AGRICULTURE To sustain agricultural production into the future, management should enhance natural biogeochemical cycling within the soil. Strategies to increase yield while reducing chemical fertilizer inputs and irrigation require robust research and development before widespread implementation. Current innovations in crop production use amendments such as manure and biochar charcoal to increase soil organic matter and improve soil structure, water, and nutrient content. Organic amendments also provide substrate and habitat for soil microorganisms that can play a key role cycling nutrients, improving nutrient availability for crops. Additional plant growth promoting bacteria can be incorporated into the soil as inocula to enhance soil nutrient cycling through mechanisms like phosphorus solubilization. Since microbial inoculation is highly effective under drought conditions, this technique pairs well in agricultural systems using limited irrigation to save water, particularly in semi-arid regions where climate change and population growth exacerbate water scarcity. The research in this dissertation examines synergistic techniques to reduce irrigation inputs, while building soil organic matter, and promoting natural microbial function to increase crop available nutrients. The research was conducted on conventional irrigated maize systems at the Agricultural Research Development and Education Center north of Fort Collins, CO. -
Research Collection
Research Collection Doctoral Thesis Development and application of molecular tools to investigate microbial alkaline phosphatase genes in soil Author(s): Ragot, Sabine A. Publication Date: 2016 Permanent Link: https://doi.org/10.3929/ethz-a-010630685 Rights / License: In Copyright - Non-Commercial Use Permitted This page was generated automatically upon download from the ETH Zurich Research Collection. For more information please consult the Terms of use. ETH Library DISS. ETH NO.23284 DEVELOPMENT AND APPLICATION OF MOLECULAR TOOLS TO INVESTIGATE MICROBIAL ALKALINE PHOSPHATASE GENES IN SOIL A thesis submitted to attain the degree of DOCTOR OF SCIENCES of ETH ZURICH (Dr. sc. ETH Zurich) presented by SABINE ANNE RAGOT Master of Science UZH in Biology born on 25.02.1987 citizen of Fribourg, FR accepted on the recommendation of Prof. Dr. Emmanuel Frossard, examiner PD Dr. Else Katrin Bünemann-König, co-examiner Prof. Dr. Michael Kertesz, co-examiner Dr. Claude Plassard, co-examiner 2016 Sabine Anne Ragot: Development and application of molecular tools to investigate microbial alkaline phosphatase genes in soil, c 2016 ⃝ ABSTRACT Phosphatase enzymes play an important role in soil phosphorus cycling by hydrolyzing organic phosphorus to orthophosphate, which can be taken up by plants and microorgan- isms. PhoD and PhoX alkaline phosphatases and AcpA acid phosphatase are produced by microorganisms in response to phosphorus limitation in the environment. In this thesis, the current knowledge of the prevalence of phoD and phoX in the environment and of their taxonomic distribution was assessed, and new molecular tools were developed to target the phoD and phoX alkaline phosphatase genes in soil microorganisms. -
Metaproteomics Characterization of the Alphaproteobacteria
Avian Pathology ISSN: 0307-9457 (Print) 1465-3338 (Online) Journal homepage: https://www.tandfonline.com/loi/cavp20 Metaproteomics characterization of the alphaproteobacteria microbiome in different developmental and feeding stages of the poultry red mite Dermanyssus gallinae (De Geer, 1778) José Francisco Lima-Barbero, Sandra Díaz-Sanchez, Olivier Sparagano, Robert D. Finn, José de la Fuente & Margarita Villar To cite this article: José Francisco Lima-Barbero, Sandra Díaz-Sanchez, Olivier Sparagano, Robert D. Finn, José de la Fuente & Margarita Villar (2019) Metaproteomics characterization of the alphaproteobacteria microbiome in different developmental and feeding stages of the poultry red mite Dermanyssusgallinae (De Geer, 1778), Avian Pathology, 48:sup1, S52-S59, DOI: 10.1080/03079457.2019.1635679 To link to this article: https://doi.org/10.1080/03079457.2019.1635679 © 2019 The Author(s). Published by Informa View supplementary material UK Limited, trading as Taylor & Francis Group Accepted author version posted online: 03 Submit your article to this journal Jul 2019. Published online: 02 Aug 2019. Article views: 694 View related articles View Crossmark data Citing articles: 3 View citing articles Full Terms & Conditions of access and use can be found at https://www.tandfonline.com/action/journalInformation?journalCode=cavp20 AVIAN PATHOLOGY 2019, VOL. 48, NO. S1, S52–S59 https://doi.org/10.1080/03079457.2019.1635679 ORIGINAL ARTICLE Metaproteomics characterization of the alphaproteobacteria microbiome in different developmental and feeding stages of the poultry red mite Dermanyssus gallinae (De Geer, 1778) José Francisco Lima-Barbero a,b, Sandra Díaz-Sanchez a, Olivier Sparagano c, Robert D. Finn d, José de la Fuente a,e and Margarita Villar a aSaBio. -
Spatial Environmental Heterogeneity Determines Young Biofilm
fmicb-10-01665 August 8, 2019 Time: 16:47 # 1 ORIGINAL RESEARCH published: 09 August 2019 doi: 10.3389/fmicb.2019.01665 Spatial Environmental Heterogeneity Determines Young Biofilm Assemblages on Microplastics in Baltic Sea Mesocosms Katharina Kesy1, Sonja Oberbeckmann1, Bernd Kreikemeyer2 and Matthias Labrenz1* 1 Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Rostock, Germany, 2 Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Rostock, Rostock, Germany Microplastics in aquatic environments provide novel habitats for surface-colonizing microorganisms. Given the continuing debate on whether substrate-specific properties or environmental factors prevail in shaping biofilm assemblages on microplastics, we examined the influence of substrate vs. spatial factors in the development of bacterial assemblages on polyethylene (PE), polystyrene (PS), wood, and seston and in the free-living fraction. Further, the selective colonization of microplastics by potential pathogens was investigated because among the bacterial species found in microplastic- Edited by: associated biofilms are potentially pathogenic Vibrio spp. Due to their persistence Marcelino T. Suzuki, and great dispersal potential, microplastics could act as vectors for these potential Sorbonne Universités, France pathogens and for biofilm assemblages in general. Incubation experiments with these Reviewed by: Sandi Orlic, substrates were conducted for 7 days during a summer cruise along the eastern Institut Ruder¯ Boškovic,´ Croatia Baltic Sea coastline in waters covering a salinity gradient of 4.5–9 PSU. Bacterial Anne-Leila Meistertzheim, UMR 7621 Laboratoire assemblages were analyzed using 16S rRNA-gene amplicon sequencing, distance- d’Océanographie Microbienne based redundancy analyses, and the linear discriminant analysis effect size method to (LOMIC), France identify taxa that were significantly more abundant on the plastics. -
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. -
The Case of the Red Pigment Miltos
Greco-Roman mineral (litho)therapeutics and their relationship to their microbiome: The case of the red pigment miltos E. Photos-Jones a,b, C.W.Knapp c, D. Venieri d, G.E.Christidis f, C.Elgy e, E. Valsami-Jones e, I. Gounaki c and N.C.Andriopoulou f. a Analytical Services for Art and Archaeology (Ltd), Glasgow G12 8JD, UK b Archaeology, School of Humanities, University of Glasgow, Glasgow G12 8QQ, UK c Civil and Environmental Engineering, University of Strathclyde, Glasgow G1 1XQ, UK d School of Environmental Engineering, Technical University of Crete, 73100 Chania, Greece e School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK f School of Mineral Resources Engineering, Technical University of Crete, 73100 Chania, Greece Journal of Archaeological Science: Reports. Volume 22, December 2018, Pages 179-192 https://doi.org/10.1016/j.jasrep.2018.07.017 corresponding author address: [email protected] Abstract This paper introduces a holistic approach to the study of Greco-Roman (G-R) lithotherapeutics. These are the minerals or mineral combinations that appear in the medical and scientific literature of the G-R world. It argues that they can best be described not simply in terms of their bulk chemistry/mineralogy but also their ecological microbiology and nanofraction component. It suggests that each individual attribute may have underpinned the bioactivity of the lithotherapeutic as an antibacterial, antifungal or other. We focus on miltos, the highly prized, naturally fine, red iron oxide-based mineral used as a pigment, in boat maintenance, agriculture and medicine. -
A Report of 11 Unrecorded Bacterial Species in Korea Isolated in 2017
Journal of Species Research 7(2):135-150, 2018 A report of 11 unrecorded bacterial species in Korea isolated in 2017 Soohyun Maeng1, Ju-Young Kim2, Jun Hwee Jang2, Myung-Suk Kang3 and Myung Kyum Kim2,* 1Department of Public Health Sciences, Graduate School, Korea University, Seoul 02841, Republic of Korea 2Department of Bio & Environmental Technology, College of Natural Science, Seoul Women’s University, Seoul 01797, Republic of Korea 3Microorganism Resources Division, National Institute of Biological Resources, Incheon 22689, Republic of Korea *Correspondent: [email protected] Eleven bacterial strains 17SD2_15, 17Sr1_23, 17SD2_13, 17Sr1_31, 17gy_18, 16B15D, 16B02D, 16B04G, 16B01D, 17U4-2 and 17J28-10 assigned to the phylum Proteobacteria were isolated from soil samples collected from Seoul Women’s University, in South Korea. The Belnapia species, strain 17SD2_15 was cocci-shaped and pink-colored. The Methylobacterium species, strain 17Sr1_23, 17SD2_13, 17Sr1_31, and 16B15D were short rod-shaped and pink-colored. The Microvirga species, strain 17gy_18, and 16B02D were short rod-shaped and pink-colored. The Oxalicibacterium species, strain 16B04G was short rod-shaped and pink-colored. The Sphingomonas species, strain 16B01D was short rod-shaped and yellow-colored. The Variovorax species, strain 17U4-2 was cocci-shaped and yellow-colored. The Paracoccus species, 17J28-10 was cocci-shaped and orange-colored. Phylogenetic analysis based on 16S rRNA gene sequence showed that strains 17SD2_15, 17Sr1_23, 17SD2_13, 17Sr1_31, 17gy_18, 16B15D, 16B02D, 16B04G, 16B01D, 17U4- 2 and 17J28-10 were most closely related to Belnapia soli (with 99.9% similarity), Methylobacterium gregans (99.1%), Methylobacterium isbiliense (99.6%), Methylobacterium oxalidis (99.9%), Microvirga aerilata (98.7%), Methylobacterium aerolatum (99.0%), Microvirga vignae (100.0%), Noviherbaspirillum canariense (100.0%), Sphingomonas desiccabilis (100.0%), Variovorax humicola (99.6%), and Paracoccus acridae (99.1%), respectively. -
Characterization of Two Aerobic Ultramicrobacteria Isolated from Urban Soil and a Description of Oxalicibacterium Solurbis Sp
RESEARCH LETTER Characterization of two aerobic ultramicrobacteria isolated from urban soil and a description of Oxalicibacterium solurbis sp. nov. Nurettin Sahin1, Juan M. Gonzalez2, Takashi Iizuka3 & Janet E. Hill4 1Egitim Fakultesi, Mugla Universitesi, Mugla, Turkey; 2Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, Sevilla, Spain; 3Central Research Laboratories, Ajinomoto Co. Inc., Kawasaki, Japan; and 4Department of Veterinary Microbiology, University of Saskatchewan, SK, Canada Downloaded from https://academic.oup.com/femsle/article-abstract/307/1/25/471128 by guest on 13 February 2020 Correspondence: Nurettin Sahin, Egitim Abstract Fakultesi, Mugla University, TR-48170 Kotekli, Mugla, Turkey. Tel.: 190 252 211 1826; fax: Two strains of aerobic, non-spore-forming, Gram-negative, rod-shaped bacteria T 190 252 223 8491; e-mail: (ND5 and MY14 ), previously isolated from urban soil using the membrane-filter [email protected] enrichment technique, were characterized. Analysis of their 16S rRNA gene sequence grouped strains ND5 and MY14T within the family Oxalobacteraceae Received 10 February 2010; revised 2 March (Betaproteobacteria). The highest pairwise sequence similarities for strain ND5 2010; accepted 2 March 2010. were found with members of the genus Herminiimonas, namely with Herminiimo- Final version published online 30 March 2010. nas saxobsidens NS11T (99.8%) and Herminiimonas glaciei UMB49T (99.6%). Although some fatty acid profiles, physiological and biochemical differences exist DOI:10.1111/j.1574-6968.2010.01954.x between strain ND5 and the respective Herminiimonas-type strains, DNA–DNA hybridization experiments confirm that strain ND5 is a member of the H. glaciei Editor: Aharon Oren genospecies. Taxonomical analyses revealed a wider range of variability within this Keywords genus than considered previously. -
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.