A Time Travel Story: Metagenomic Analyses Decipher the Unknown Geographical Shift and the Storage History of Possibly Smuggled Antique Marble Statues
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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. -
Supplementary Information
doi: 10.1038/nature06269 SUPPLEMENTARY INFORMATION METAGENOMIC AND FUNCTIONAL ANALYSIS OF HINDGUT MICROBIOTA OF A WOOD FEEDING HIGHER TERMITE TABLE OF CONTENTS MATERIALS AND METHODS 2 • Glycoside hydrolase catalytic domains and carbohydrate binding modules used in searches that are not represented by Pfam HMMs 5 SUPPLEMENTARY TABLES • Table S1. Non-parametric diversity estimators 8 • Table S2. Estimates of gross community structure based on sequence composition binning, and conserved single copy gene phylogenies 8 • Table S3. Summary of numbers glycosyl hydrolases (GHs) and carbon-binding modules (CBMs) discovered in the P3 luminal microbiota 9 • Table S4. Summary of glycosyl hydrolases, their binning information, and activity screening results 13 • Table S5. Comparison of abundance of glycosyl hydrolases in different single organism genomes and metagenome datasets 17 • Table S6. Comparison of abundance of glycosyl hydrolases in different single organism genomes (continued) 20 • Table S7. Phylogenetic characterization of the termite gut metagenome sequence dataset, based on compositional phylogenetic analysis 23 • Table S8. Counts of genes classified to COGs corresponding to different hydrogenase families 24 • Table S9. Fe-only hydrogenases (COG4624, large subunit, C-terminal domain) identified in the P3 luminal microbiota. 25 • Table S10. Gene clusters overrepresented in termite P3 luminal microbiota versus soil, ocean and human gut metagenome datasets. 29 • Table S11. Operational taxonomic unit (OTU) representatives of 16S rRNA sequences obtained from the P3 luminal fluid of Nasutitermes spp. 30 SUPPLEMENTARY FIGURES • Fig. S1. Phylogenetic identification of termite host species 38 • Fig. S2. Accumulation curves of 16S rRNA genes obtained from the P3 luminal microbiota 39 • Fig. S3. Phylogenetic diversity of P3 luminal microbiota within the phylum Spirocheates 40 • Fig. -
TROPICAL AGRICULTURAL SCIENCE Small
Pertanika J. Trop. Agric. Sci. 44 (3): 583 - 597 (2021) TROPICAL AGRICULTURAL SCIENCE Journal homepage: http://www.pertanika.upm.edu.my/ Small Pteropodid Bats are Important Pollinators of Durian in Terengganu, Malaysia Suey Yee Low1, Muhammad Nur Hamzah Zulfemi1, Siti Nor Shaffinaf Mohamad Shukri1, Aida Hidayah Abu Samah1, Hasrul Zaman Hassan Basri2, Muhammad Haffidzie Mohd Shuhaimi2, Harizah Nadiah Hamzah1, Muhammad Aidil Zahidin2, Muhammad Syamsul Aznan Ariffin2 and Nor Zalipah Mohamed1* 1Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia 2Institute of Tropical Biodiversity and Sustainable Development, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia ABSTRACT Bats are often misunderstood as agricultural pests and have received little attention for conservation efforts. However, bats are critical pollinators to commercially important agricultural products, such as durians. This study intends to confirm the role of small pteropodid bats as pollinating agents to flowering durian trees. Samplings were conducted in April 2018 to record bats visiting the flowers of two durian species,Durio zibethinus and Durio lowianus at Malaysian Agricultural Research and Development Institute (MARDI) Jerangau, Terengganu. Captured bats were swabbed for conspecific pollen load on their bodies to determine their potential role as pollinators. One hundred thirty-one (131) ARTICLE INFO Article history: pollen swabs were collected from three Received: 29 March 2021 pteropodid bat species: Eonycteris spelaea Accepted: 31 May 2021 Published: 20 August 2021 Dobson, Cynopterus brachyotis Dobson, DOI: https://doi.org/10.47836/pjtas.44.3.05 and Cynopterus horsfieldii Gray. Only E. E-mail addresses: spelaea and C. brachyotis, however, were [email protected] (Suey Yee Low) [email protected] (Muhammad Nur Hamzah Zulfemi) found with conspecific pollen loads on their [email protected] (Siti Nor Shaffinaf Mohamad Shukri) [email protected] (Aida Hidayah Abu Samah) bodies. -
Floral Biology and Pollination Strategy of Durio (Malvaceae) in Sarawak, Malaysian Borneo
BIODIVERSITAS ISSN: 1412-033X Volume 21, Number 12, December 2020 E-ISSN: 2085-4722 Pages: 5579-5594 DOI: 10.13057/biodiv/d211203 Floral biology and pollination strategy of Durio (Malvaceae) in Sarawak, Malaysian Borneo NG WIN SENG1, JAYASILAN MOHD-AZLAN1, WONG SIN YENG1,2,♥ 1Institute of Biodiversity and Environmental Conservation, Universiti Malaysia Sarawak. 94300 Kota Samarahan, Sarawak, Malaysia. 2Harvard University Herbaria. 22 Divinity Avenue, Cambridge, MA 02138, United States of America. ♥ email: [email protected]. Manuscript received: 25 September 2020. Revision accepted: 4 November 2020. Abstract. Ng WS, Mohd-Azlan J, Wong SY. 2020. Floral biology and pollination strategy of Durio (Malvaceae) in Sarawak, Malaysian Borneo. Biodiversitas 21: 5579-5594. This study was carried out to investigate on the flowering mechanisms of four Durio species in Sarawak. The anthesis started in the afternoon (D. graveolens and D. zibethinus), evening (D. kutejensis) or midnight (D. griffithii); and lasted between 11.5 hours (D. griffithii) to 20 hours (D. graveolens). All four Durio species are generalists. Individuals of a fruit bat (Eonycteris spelaea, Pteropodidae) are considered as the main pollinator for D. graveolens, D. kutejensis, and D. zibethinus while spiderhunter (Arachnothera, Nectariniidae) is also proposed as a primary pollinator for D. kutejensis. Five invertebrate taxa were observed as secondary or inadvertent pollinators of Durio spp.: honeybee, Apis sp. (Apidae), stingless bee, Tetrigona sp. (Apidae), nocturnal wasp, Provespa sp. (Vespidae), pollen beetle (Nitidulidae), and thrip (Thysanoptera). Honey bees and stingless bees pollinated all four Durio species. Pollen beetles were found to pollinate D. griffithii and D. graveolens while nocturnal wasps were found to pollinate D. -
Field Fungal Diversity in Freshly Harvested Japonica Rice
1 Field fungal diversity in freshly harvested japonica rice 2 3 4 5 ABSTRACT 6 Rice is a major food crop in China and Japonica rice production in Heilongjiang 7 Province ranks No.1 in total annual rice production in the country. Rice is prone to 8 invasion by fungi and mycotoxins produced by the fungi are proven to be serious 9 threats to human health. The objective of the present study was to investigate fungal 10 diversity of freshly harvested rice in the four main cultivation regions of Heilongjiang 11 Province in order to find the abundance difference of dominant fungi among the four 12 regions. Through high throughput sequencing we detected Ascomycota accounts for 13 absolute dominant phylum; Dothideomycetes, Sordariomycetes, Tremellomycetes, 14 Microbotryomycetes, and Eurotiomycetes were dominant classes; Capnodiales, 15 Hypocreales, and Pleosporales were the main orders; Cladosporiaceae, Pleosporaceae, 16 Nectriaceae, Clavicipitaceae, Tremellaceae, Phaeosphaeriaceae, 17 Trimorphomycetaceae, Sporidiobolaceae, Bionectriaceae, and Trichocomaceae were 18 major family; Cladosporium, Epicoccum, Fusarium, and Alternaria were the most 19 abundant phylotypes at genus level; Epicoccum_nigrum, Gibberella_zeae, and 20 Fusarium_proliferatum were the dominant fungal species. Great fungal diversity was 21 observed in the rice samples harvested in the four major Japonica rice-growing regions 22 in Heilongjiang province. However, no significant difference in diversity was observed 23 among the four regions, likely due to the relatively close geographical proximity 24 leading to very similar climatic conditions. Since some of the fungal species produce 25 mycotoxins, it is necessary to take precautions to ensure the rice is stored under safe 26 conditions to prevent the production of mycotoxins. -
Developing a Genetic Manipulation System for the Antarctic Archaeon, Halorubrum Lacusprofundi: Investigating Acetamidase Gene Function
www.nature.com/scientificreports OPEN Developing a genetic manipulation system for the Antarctic archaeon, Halorubrum lacusprofundi: Received: 27 May 2016 Accepted: 16 September 2016 investigating acetamidase gene Published: 06 October 2016 function Y. Liao1, T. J. Williams1, J. C. Walsh2,3, M. Ji1, A. Poljak4, P. M. G. Curmi2, I. G. Duggin3 & R. Cavicchioli1 No systems have been reported for genetic manipulation of cold-adapted Archaea. Halorubrum lacusprofundi is an important member of Deep Lake, Antarctica (~10% of the population), and is amendable to laboratory cultivation. Here we report the development of a shuttle-vector and targeted gene-knockout system for this species. To investigate the function of acetamidase/formamidase genes, a class of genes not experimentally studied in Archaea, the acetamidase gene, amd3, was disrupted. The wild-type grew on acetamide as a sole source of carbon and nitrogen, but the mutant did not. Acetamidase/formamidase genes were found to form three distinct clades within a broad distribution of Archaea and Bacteria. Genes were present within lineages characterized by aerobic growth in low nutrient environments (e.g. haloarchaea, Starkeya) but absent from lineages containing anaerobes or facultative anaerobes (e.g. methanogens, Epsilonproteobacteria) or parasites of animals and plants (e.g. Chlamydiae). While acetamide is not a well characterized natural substrate, the build-up of plastic pollutants in the environment provides a potential source of introduced acetamide. In view of the extent and pattern of distribution of acetamidase/formamidase sequences within Archaea and Bacteria, we speculate that acetamide from plastics may promote the selection of amd/fmd genes in an increasing number of environmental microorganisms. -
Draft Pest Categorisation of Organisms Associated with Washed Ware Potatoes (Solanum Tuberosum) Imported from Other Australian States and Territories
Nucleorhabdovirus Draft pest categorisation of organisms associated with washed ware potatoes (Solanum tuberosum) imported from other Australian states and territories This page is intentionally left blank Contributing authors Bennington JMA Research Officer – Biosecurity and Regulation, Plant Biosecurity Hammond NE Research Officer – Biosecurity and Regulation, Plant Biosecurity Poole MC Research Officer – Biosecurity and Regulation, Plant Biosecurity Shan F Research Officer – Biosecurity and Regulation, Plant Biosecurity Wood CE Technical Officer – Biosecurity and Regulation, Plant Biosecurity Department of Agriculture and Food, Western Australia, December 2016 Document citation DAFWA 2016, Draft pest categorisation of organisms associated with washed ware potatoes (Solanum tuberosum) imported from other Australian states and territories. Department of Agriculture and Food, Western Australia, South Perth. Copyright© Western Australian Agriculture Authority, 2016 Western Australian Government materials, including website pages, documents and online graphics, audio and video are protected by copyright law. Copyright of materials created by or for the Department of Agriculture and Food resides with the Western Australian Agriculture Authority established under the Biosecurity and Agriculture Management Act 2007. Apart from any fair dealing for the purposes of private study, research, criticism or review, as permitted under the provisions of the Copyright Act 1968, no part may be reproduced or reused for any commercial purposes whatsoever -
Development of Bacterial Communities in Biological Soil Crusts Along
1 Development of bacterial communities in biological soil crusts along 2 a revegetation chronosequence in the Tengger Desert, northwest 3 China 4 5 Author names and affiliations: 6 Lichao Liu1, Yubing Liu1, 2 *, Peng Zhang1, Guang Song1, Rong Hui1, Zengru Wang1, Jin Wang1, 2 7 1Shapotou Desert Research & Experiment Station, Northwest Institute of Eco-Environment and Resources, Chinese 8 Academy of Sciences, Lanzhou, 730000, China 9 2Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions of Gansu Province, Northwest Institute 10 of Eco–Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China 11 12 * Corresponding author: Yubing Liu 13 Address: Donggang West Road 320, Lanzhou 730000, P. R. China. 14 Tel: +86 0931 4967202. 15 E-mail address: [email protected] 16 17 Abstract. Knowledge of structure and function of microbial communities in different 18 successional stages of biological soil crusts (BSCs) is still scarce for desert areas. In this study, 19 Illumina MiSeq sequencing was used to assess the composition changes of bacterial communities 20 in different ages of BSCs in the revegetation of Shapotou in the Tengger Desert. The most dominant 21 phyla of bacterial communities shifted with the changed types of BSCs in the successional stages, 22 from Firmicutes in mobile sand and physical crusts to Actinobacteria and Proteobacteria in BSCs, 23 and the most dominant genera shifted from Bacillus, Enterococcus and Lactococcus to 24 RB41_norank and JG34-KF-361_norank. Alpha diversity and quantitative real-time PCR analysis 25 indicated that bacteria richness and abundance reached their highest levels after 15 years of BSC 26 development. -
A Broadly Distributed Toxin Family Mediates Contact-Dependent Antagonism Between Gram-Positive Bacteria
1 A Broadly Distributed Toxin Family Mediates Contact-Dependent 2 Antagonism Between Gram-positive Bacteria 3 John C. Whitney1,†, S. Brook Peterson1, Jungyun Kim1, Manuel Pazos2, Adrian J. 4 Verster3, Matthew C. Radey1, Hemantha D. Kulasekara1, Mary Q. Ching1, Nathan P. 5 Bullen4,5, Diane Bryant6, Young Ah Goo7, Michael G. Surette4,5,8, Elhanan 6 Borenstein3,9,10, Waldemar Vollmer2 and Joseph D. Mougous1,11,* 7 1Department of Microbiology, School of Medicine, University of Washington, Seattle, 8 WA 98195, USA 9 2Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, 10 Newcastle University, Newcastle upon Tyne, NE2 4AX, UK 11 3Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA 12 4Michael DeGroote Institute for Infectious Disease Research, McMaster University, 13 Hamilton, ON, L8S 4K1, Canada 14 5Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, 15 ON, L8S 4K1, Canada 16 6Experimental Systems Group, Advanced Light Source, Berkeley, CA 94720, USA 17 7Northwestern Proteomics Core Facility, Northwestern University, Chicago, IL 60611, 18 USA 19 8Department of Medicine, Farncombe Family Digestive Health Research Institute, 20 McMaster University, Hamilton, ON, L8S 4K1, Canada 21 9Department of Computer Science and Engineering, University of Washington, Seattle, 22 WA 98195, USA 23 10Santa Fe Institute, Santa Fe, NM 87501, USA 24 11Howard Hughes Medical Institute, School of Medicine, University of Washington, 25 Seattle, WA 98195, USA 26 † Present address: Department of Biochemistry and Biomedical Sciences, McMaster 27 University, Hamilton, ON, L8S 4K1, Canada 28 * To whom correspondence should be addressed: J.D.M. 29 Email – [email protected] 30 Telephone – (+1) 206-685-7742 1 31 Abstract 32 The Firmicutes are a phylum of bacteria that dominate numerous polymicrobial 33 habitats of importance to human health and industry. -
Fictibacillus Phosphorivorans Gen. Nov., Sp. Nov. and Proposal to Reclassify
International Journal of Systematic and Evolutionary Microbiology (2013), 63, 2934–2944 DOI 10.1099/ijs.0.049171-0 Fictibacillus phosphorivorans gen. nov., sp. nov. and proposal to reclassify Bacillus arsenicus, Bacillus barbaricus, Bacillus macauensis, Bacillus nanhaiensis, Bacillus rigui, Bacillus solisalsi and Bacillus gelatini in the genus Fictibacillus Stefanie P. Glaeser,1 Wolfgang Dott,2 Hans-Ju¨rgen Busse3 and Peter Ka¨mpfer1 Correspondence 1Institut fu¨r Angewandte Mikrobiologie, Justus-Liebig-Universita¨t Giessen, D-35392 Giessen, Germany Peter Ka¨mpfer 2Institut fu¨r Hygiene und Umweltmedizin, RWTH Aachen, Germany peter.kaempfer 3Institut fu¨r Bakteriologie, Mykologie und Hygiene, Veterina¨rmedizinische Universita¨t, A-1210 Wien, @umwelt.uni-giessen.de Austria A Gram-positive-staining, aerobic, endospore-forming bacterium (Ca7T) was isolated from a bioreactor showing extensive phosphorus removal. Based on 16S rRNA gene sequence similarity comparisons, strain Ca7T was grouped in the genus Bacillus, most closely related to Bacillus nanhaiensis JSM 082006T (100 %), Bacillus barbaricus V2-BIII-A2T (99.2 %) and Bacillus arsenicus Con a/3T (97.7 %). Moderate 16S rRNA gene sequence similarities were found to the type strains of the species Bacillus gelatini and Bacillus rigui (96.4 %), Bacillus macauensis (95.1 %) and Bacillus solisalsi (96.1 %). All these species were grouped into a monophyletic cluster and showed very low sequence similarities (,94 %) to the type species of the genus Bacillus, Bacillus subtilis.Thequinonesystemof strain Ca7T consists predominantly of menaquinone MK-7. The polar lipid profile exhibited the major compounds diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. In addition, minor compounds of an unidentified phospholipid and an aminophospholipid were detected. No glycolipids were found in strain Ca7T, which was consistent with the lipid profiles of B. -
Asaia Spp., Acetic Acid Bacteria Causing the Spoilage of Non-Alcoholic Beverages
Kvasny prumysl (2019) 65:1-5 https://doi.org/10.18832/kp2019.65.1 Research Institute of Brewing anf Malting, Plc. Asaia spp., acetic acid bacteria causing the spoilage of non-alcoholic beverages Iveta Šístková*, Iveta Horsáková, Mariana Hanková, Helena CížkovᡠDepartment of Food Preservation, University of Chemistry and Technology Prague, Technická 5, 166 28, Prague 6, Czech Republic *Corresponding author :[email protected] Abstract After a general introduction and introduction to acetic acid bacteria, this work focuses on the genus Asaia, which causes sensory defects in non-alcoholic beverages. Asaia representatives have strong adhesive properties for materials used in the food industry, where they subsequently form biofilms and are highly resistant to chemical preservatives. After the basic characteristics of the genus Asaia and its influence on humans, the main part of the paper deals with microbial contami- nation of beverages by these bacteria. The paper summarizes the knowledge of the influence of packaging materials on the development of defects in beverages and the use of natural bioactive substances and plant extracts as an alternative to maintaining the microbiological stability of beverages. Key words: Asaia spp., soft drinks, sensory defect 1. Introduction and succinic acids, acetaldehyde and ketone compounds. Final products depend on the type of bacteria and the Acetic acid bacteria (AAB) get their name because of growth conditions (Juvonen et al., 2011). No glycolysis is their ability to oxidize ethanol to acetic acid (except the performed due to the lack of phosphofructokinase enzyme. Asaia genus), which is used in the industry for the pro- AAB were isolated from plants, fruits, fermented foods duction of vinegar and other compounds such as L-ascorbic and beverages, or insects (Crotti et al., 2010). -
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.