Macroecology of Microbes – Biogeography of the Glomeromycota
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Factors Influencing the Biogeography of Bacteria in Fresh
!"#! $%& '((! )*)+), '(! -.-)**,..)/ 00 001 2)///- ”I make no apologies for putting microorganisms on a pedestal above all other living things. For, if the last blue whale choked to death on the last panda, it would be disastrous but not the end of the world. But if we accidentally poisoned the last two species of ammonia oxidizers, that would be another matter. It could be hap- pening now and we wouldn’t even know… “. (2006, Tom Curtis) “A lake is the landscape's most beautiful and expressive feature. It is Earth's eye; looking into which the beholder measures the depth of his own nature”. (“Walden”, 1953, Henry David Thoreau) To my family List of Papers This thesis is based on the following papers, which are referred to in the text by their Roman numerals. I Logue, J.B., Lindström, E.S. (2008) Biogeography of bacterio- plankton in inland waters. Freshwater Reviews, 1(1): 99–114. II Logue, -
Microbial Biogeography and Ecology of the Mouth and Implications for Periodontal
bioRxiv preprint doi: https://doi.org/10.1101/541052; this version posted February 8, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license. Microbial biogeography and ecology of the mouth and implications for periodontal diseases Authors: Diana M. Proctor1,2,10, Katie M. Shelef3,10, Antonio Gonzalez4, Clara L. Davis Long5, Les Dethlefsen1, Adam Burns1, Peter M. Loomer6, Gary C. Armitage7, Mark I. Ryder7, Meredith E. Millman7, Rob Knight4, Susan P. Holmes8, David A. Relman1,5,9 Affiliations 1Division of Infectious Disease & Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305 USA 2National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA 3Department of Biology, Stanford University School of Medicine, Stanford, CA 94305 USA 4Departments of Pediatrics and Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093 USA 5Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305 USA 6Ashman Department of Periodontology & Implant Dentistry, New York University College of Dentistry, New York, NY 10010 USA 7Division of Periodontology, University of California, San Francisco School of Dentistry, San Francisco, CA 94143 USA 8Department of Statistics, Stanford University, Stanford, CA 94305 USA 9Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304 USA 10These authors contributed equally Corresponding author: David A. Relman: [email protected]; Address: Encina E209, 616 Serra Street, Stanford, California 94305-6165; Phone: 650-736-6822; Fax: 650-852-3291 1 bioRxiv preprint doi: https://doi.org/10.1101/541052; this version posted February 8, 2019. -
Energetics of Life on the Deep Seafloor
Energetics of life on the deep seafloor Craig R. McClaina,1, Andrew P. Allenb, Derek P. Tittensorc,d, and Michael A. Rexe aNational Evolutionary Synthesis Center, Durham, NC 27705-4667; bDepartment of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia; cUnited Nations Environment Programme World Conservation Monitoring Centre, Cambridge CB3 0DL, United Kingdom; dMicrosoft Research Computational Science Laboratory, Cambridge CB3 0FB, United Kingdom; and eDepartment of Biology, University of Massachusetts, Boston, MA 02125-3393 Edited* by James H. Brown, University of New Mexico, Albuquerque, NM, and approved August 3, 2012 (received for review May 26, 2012) With frigid temperatures and virtually no in situ productivity, the vary with depth (13, 14), which is inversely related to POC flux deep oceans, Earth’s largest ecosystem, are especially energy-de- (16, 17). The influence of energy availability on individual growth prived systems. Our knowledge of the effects of this energy lim- rates and lifespans is unknown. At the community level, biomass itation on all levels of biological organization is very incomplete. and abundance generally decline with depth. Direct tests for the fl Here, we use the Metabolic Theory of Ecology to examine the in uences of POC and temperature on these community attrib- relative roles of carbon flux and temperature in influencing met- utes are rare, but they suggest only weak effects for temperature (16, 18). Although broad-scale patterns of deep-sea biodiversity abolic rate, growth rate, lifespan, body size, abundance, biomass, fi and biodiversity for life on the deep seafloor. We show that the are well-established and presumably linked to POC, speci c tests of this relationship remain limited (reviewed in ref. -
Demographic History and the Low Genetic Diversity in Dipteryx Alata (Fabaceae) from Brazilian Neotropical Savannas
Heredity (2013) 111, 97–105 & 2013 Macmillan Publishers Limited All rights reserved 0018-067X/13 www.nature.com/hdy ORIGINAL ARTICLE Demographic history and the low genetic diversity in Dipteryx alata (Fabaceae) from Brazilian Neotropical savannas RG Collevatti1, MPC Telles1, JC Nabout2, LJ Chaves3 and TN Soares1 Genetic effects of habitat fragmentation may be undetectable because they are generally a recent event in evolutionary time or because of confounding effects such as historical bottlenecks and historical changes in species’ distribution. To assess the effects of demographic history on the genetic diversity and population structure in the Neotropical tree Dipteryx alata (Fabaceae), we used coalescence analyses coupled with ecological niche modeling to hindcast its distribution over the last 21 000 years. Twenty-five populations (644 individuals) were sampled and all individuals were genotyped using eight microsatellite loci. All populations presented low allelic richness and genetic diversity. The estimated effective population size was small in all populations and gene flow was negligible among most. We also found a significant signal of demographic reduction in most cases. Genetic differentiation among populations was significantly correlated with geographical distance. Allelic richness showed a spatial cline pattern in relation to the species’ paleodistribution 21 kyr BP (thousand years before present), as expected under a range expansion model. Our results show strong evidences that genetic diversity in D. alata is the outcome of the historical changes in species distribution during the late Pleistocene. Because of this historically low effective population size and the low genetic diversity, recent fragmentation of the Cerrado biome may increase population differentiation, causing population decline and compromising long-term persistence. -
Occurrence of Glomeromycota Species in Aquatic Habitats: a Global Overview
Occurrence of Glomeromycota species in aquatic habitats: a global overview MARIANA BESSA DE QUEIROZ1, KHADIJA JOBIM1, XOCHITL MARGARITO VISTA1, JULIANA APARECIDA SOUZA LEROY1, STEPHANIA RUTH BASÍLIO SILVA GOMES2, BRUNO TOMIO GOTO3 1 Programa de Pós-Graduação em Sistemática e Evolução, 2 Curso de Ciências Biológicas, and 3 Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Campus Universitário, 59072-970, Natal, RN, Brazil * CORRESPONDENCE TO: [email protected] ABSTRACT — Arbuscular mycorrhizal fungi (AMF) are recognized in terrestrial and aquatic ecosystems. The latter, however, have received little attention from the scientific community and, consequently, are poorly known in terms of occurrence and distribution of this group of fungi. This paper provides a global list on AMF species inhabiting aquatic ecosystems reported so far by scientific community (lotic and lentic freshwater, mangroves, and wetlands). A total of 82 species belonging to 5 orders, 11 families, and 22 genera were reported in 8 countries. Lentic ecosystems have greater species richness. Most studies of the occurrence of AMF in aquatic ecosystems were conducted in the United States and India, which constitute 45% and 78% reports coming from temperate and tropical regions, respectively. KEY WORDS — checklist, flooded areas, mycorrhiza, taxonomy Introduction Aquatic ecosystems comprise about 77% of the planet surface (Rebouças 2006) and encompass a diversity of habitats favorable to many species from marine (ocean), transitional estuaries to continental (wetlands, lentic and lotic) environments (Reddy et al. 2018). Despite this territorial representativeness and biodiversity already recorded, there are gaps when considering certain types of organisms, e.g. fungi. Fungi are considered a common and important component of almost all trophic levels. -
Acaulospora Baetica, a New Arbuscular Mycorrhizal Fungal Species from Two Mountain Ranges in Andalucía (Spain)
Nova Hedwigia PrePub Article Cpublished online June 2015 Acaulospora baetica, a new arbuscular mycorrhizal fungal species from two mountain ranges in Andalucía (Spain) Javier Palenzuela1, Concepción Azcón-Aguilar1, José-Miguel Barea1, Gladstone Alves da Silva2 and Fritz Oehl2,3 1 Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, CSIC, Profesor Albareda 1, 18008 Granada, Spain 2 Departamento de Micologia, CCB, Universidade Federal de Pernambuco, Avenida da Engenharia s/n, Cidade Universitária, 50740-600, Recife, PE, Brazil 3 Agroscope, Federal Research Institute of Sustainability Sciences, Reckenholzstrasse 191, Plant-Soil-Interactions, CH-8046 Zürich, Switzerland With 11 figures and 1 table Abstract: A new Acaulospora species, A. baetica, was found in two adjacent mountain ranges in Andalucía (southern Spain), i.e. in several mountainous plant communities of Sierra Nevada National Park at 1580–2912 m asl around roots of the endangered and/or endemic plants Sorbus hybrida, Artemisia umbelliformis, Hippocrepis nevadensis, Laserpitium longiradium and Pinguicula nevadensis, and in two Mediterranean shrublands of Sierra de Baza Natural Park at 1380–1855 m asl around roots of Prunus ramburii, Rosmarinus officinalis, Thymus mastichina and Lavandula latifolia among others. The fungus produced spores in single species cultures, using Sorghum vulgare or Trifolium pratense as bait plant. The spores are 69–96 × 65–92 µm in diameter, brownish creamy to light brown, often appearing with a grayish tint in the dissecting microscope. They have a pitted surface (pit sizes about 0.8–1.6 × 0.7–1.4 µm in diameter and 0.6–1.3 µm deep), and are similar in size to several other Acaulospora species with pitted spore surfaces, such as A. -
Macroecology in the Age of Big Data –
Received: 7 February 2019 | Revised: 8 May 2019 | Accepted: 9 May 2019 DOI: 10.1111/jbi.13633 PERSPECTIVE Macroecology in the age of Big Data – Where to go from here? Rafael O. Wüest1 | Niklaus E. Zimmermann1 | Damaris Zurell2 | Jake M. Alexander3 | Susanne A. Fritz4,5 | Christian Hof6 | Holger Kreft7 | Signe Normand8 | Juliano Sarmento Cabral9 | Eniko Szekely10 | Wilfried Thuiller11 | Martin Wikelski12,13 | Dirk Nikolaus Karger1 1Swiss Federal Research Institute WSL, Birmensdorf, Switzerland 2Department of Geography, Humboldt University Berlin, Berlin, Germany 3Institute of Integrative Biology, ETH Zurich, Zürich, Switzerland 4Senckenberg Biodiversity and Climate Research Centre, Frankfurt (Main), Germany 5Institute of Ecology, Evolution & Diversity, Goethe‐University, Frankfurt (Main), Germany 6Terrestrial Ecology Research Group, Technical University of Munich, Freising, Germany 7Biodiversity, Macroecology & Biogeography, Faculty of Forest Sciences and Forest Ecology, University of Göttingen, Göttingen, Germany 8Ecoinformatics & Biodiversity & Center for Biodiversity on a Changing world, Aarhus, Denmark 9Ecosystem Modeling, CCTB University of Würzburg, Würzburg, Germany 10Swiss Data Science Center, ETH Zurich and EPFL, Lausanne, Switzerland 11Evolution, Modeling and Analysis of Biodiversity (EMABIO), Laboratoire d'Ecologie Alpine (LECA), Université Grenoble Alpes, Grenoble, France 12Max‐Planck‐Institut for Ornithology, Vogelwarte Radolfzell, Radolfzell, Germany 13Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Konstanz, Germany Correspondence Dirk Nikolaus Karger, Swiss Federal Abstract Research Institute WSL, Zürcherstrasse 111, Recent years have seen an exponential increase in the amount of data available in all 8903 Birmensdorf, Switzerland. Email: [email protected] sciences and application domains. Macroecology is part of this “Big Data” trend, with a strong rise in the volume of data that we are using for our research. -
Marine Microbial Diversity
Marine microbial diversity 27 K. S. Sobhana Marine Biodiversity Division, Central Marine Fisheries Research Institute, Kochi-682 018 Microbes were the only form of life for the first 2-3 billion and also based on iii) concentration of nutrients and required years of planetary and biological evolution. Life most likely growth substances (Oligotrophic, Mesotrophic, Eutrophic). began in the oceans and marine microorganisms are the However, interfaces tend to be hotspots of diversity and closest living descendants of the original forms of life. Early biological activity. Marine microbial habitats at interfaces marine microorganisms also helped create the conditions include the air-water, water-sediment, water-ice, and under which subsequent life developed. More than two billion host macroorganism-water interfaces. The sub-millimeter years ago, the generation of oxygen by photosynthetic marine scale of physical and chemical variability in these habitats microorganisms helped shape the chemical environment in poses a serious challenge to studying interface habitats in which plants, animals, and all other life forms have evolved. detail. The fact that variations can even occur within a few Macroscopic life and planetary habitability completely millimetres, suggests that microbial diversity encompasses depend upon the transformations mediated by complex more than the documented evidence available. Hence, microbial communities. These microscopic factories both biogeography is gaining importance as a field of study from aerobic and anaerobic are the essential catalysts for all of the microbial diversity point of interest. Due to the innately chemical reactions within the biogeochemical cycles. Their small size of the microorganisms, environmental complexity unique metabolisms allow marine microbes to carry out many plays a major role in determining diversity. -
Microbial Biogeography: Patterns in Microbial Diversity
Microbial biogeography: patterns in microbial diversity across space and time Noah Fierer* Department of Ecology & Evolutionary Biology Cooperative Institute for Research in Environmental Sciences University of Colorado Boulder, CO 80305 Phone: 303-492-5615 Fax: 303-492-1149 Email: 805-729-1657 Citation: N. Fierer 2008. Microbial biogeography: patterns in microbial diversity across space and time. In: Accessing Uncultivated Microorganisms: from the Environment to Organisms and Genomes and Back. K. Zengler (editor). ASM Press, Washington DC pgs. 95-115. 1 Introduction Biogeography is a science that attempts to describe and explain spatial patterns of biological diversity and how these patterns change over time (Ganderton and Coker, 2005; Lomolino et al., 2006). In other words, biogeographers seek to answer the seemingly simple question: Why do organisms live where they do? While biogeography has traditionally focused on macro-organisms, i.e. plants and animals, microbiologists have studied biogeographical questions for many decades and there has been a recent resurgence in interest in microbial biogeography (Green and Bohannan, 2006; Martiny et al., 2006; Ramette and Tiedje, 2007). This resurgence has been led, in part, by advancements in molecular tools that allow us to survey uncultivated microbes in the environment and a growing recognition that microbial taxa are the most biologically diverse taxa on earth. At present, the study of microbial biogeography is in its infancy. Even the existence of microbial biogeography has been recently called into question [“There is no biogeography for anything smaller than 1 millimeter”, Bland Finlay quoted in Whitfield (2005)]. If this statement was correct, this chapter would be very brief. -
Minimum Viable Populations: Is There a ‘Magic Number’ for Conservation Practitioners?
Review Minimum viable populations: is there a ‘magic number’ for conservation practitioners? Curtis H. Flather1, Gregory D. Hayward2,3, Steven R. Beissinger4 and Philip A. Stephens5 1 USDA Forest Service, Rocky Mountain Research Station, Fort Collins, CO 80526, USA 2 USDA Forest Service, Alaska Region, Anchorage, AK 99503, USA 3 Department of Zoology & Physiology, University of Wyoming, Laramie, WY 80271, USA 4 Department of Environmental Science, Policy & Management, University of California, Berkeley, CA 94720, USA 5 School of Biological and Biomedical Sciences, Durham University, South Road, Durham, DH1 3LE, UK Establishing species conservation priorities and recov- The need to make rapid decisions about conservation ery goals is often enhanced by extinction risk estimates. targets, often in the absence of necessary data, has The need to set goals, even in data-deficient situations, prompted interest in identifying robust, general guidelines has prompted researchers to ask whether general guide- for MVPs [15,16]. Taking advantage of growing access to lines could replace individual estimates of extinction population and life-history data for large numbers of spe- risk. To inform conservation policy, recent studies have cies, several recent papers [17–20] explore the credibility of revived the concept of the minimum viable population a lower limit to robust MVPs. Despite apparent caution (MVP), the population size required to provide some about overinterpreting the strength of evidence, the most specified probability of persistence for a given period recent review [20] asserts that ‘[t]he bottom line is that of time. These studies conclude that long-term persis- both the evolutionary and demographic constraints on tence requires 5000 adult individuals, an MVP thresh- populations require sizes to be at least 5000 adult individ- old that is unaffected by taxonomy, life history or uals.’ A popular science summary of the article goes fur- environmental conditions. -
Arbuscular Mycorrhizal Fungi in Soil Aggregates from Fields of “Murundus” Converted to Agriculture
Arbuscular mycorrhizal fungi in soil aggregates from fields of “murundus” converted to agriculture Marco Aurélio Carbone Carneiro(1), Dorotéia Alves Ferreira(2), Edicarlos Damacena de Souza(3), Helder Barbosa Paulino(4), Orivaldo José Saggin Junior(5) and José Oswaldo Siqueira(6) (1)Universidade Federal de Lavras, Departamento de Ciência do Solo, Caixa Postal 3037, CEP 37200‑000 Lavras, MG, Brazil. E‑mail: [email protected](2) Universidade de São Paulo, Escola Superior de Agricultura Luiz de Queiroz, Departamento de Ciência do Solo, Avenida Pádua Dias, no 11, CEP 13418‑900 Piracicaba, SP, Brazil. E‑mail: [email protected] (3)Universidade Federal de Mato Grosso, Campus de Rondonópolis, Instituto de Ciências Agrárias e Tecnológicas de Rondonópolis, Rodovia MT 270, Km 06, Sagrada Família, CEP 78735‑901 Rondonópolis, MT, Brazil. E‑mail: [email protected] (4)Universidade Federal de Goiás, Regional Jataí, BR 364, Km 192, CEP 75804‑020 Jataí, GO, Brazil. E‑mail: [email protected] (5)Embrapa Agrobiologia, BR 465, Km 7, CEP 23891‑000 Seropédica, RJ, Brazil. E‑mail: [email protected] (6)Instituto Tecnológico Vale, Rua Boaventura da Silva, no 955, CEP 66055‑090 Belém, PA, Brazil. E‑mail: [email protected] Abstract – The objective of this work was to evaluate the spore density and diversity of arbuscular mycorrhizal fungi (AMF) in soil aggregates from fields of “murundus” (large mounds of soil) in areas converted and not converted to agriculture. The experiment was conducted in a completely randomized design with five replicates, in a 5x3 factorial arrangement: five areas and three aggregate classes (macro‑, meso‑, and microaggregates). -
Newsletter Number 86
The Palaeontology Newsletter Contents 86 Editorial 2 Association Business 3 Outreach and Education Grants 27 Association Meetings 28 From our correspondents Darwin’s diffidence 33 R for palaeontologists: Introduction 2 40 Future meetings of other bodies 48 Meeting Reports 55 Obituary Dolf Seilacher 64 Sylvester-Bradley reports 67 Outside the Box: independence 80 Publicity Officer: old seas, new fossils 83 Book Reviews 86 Books available to review 90 Palaeontology vol 57 parts 3 & 4 91–92 Special Papers in Palaeontology 91 93 Reminder: The deadline for copy for Issue no 87 is 13th October 2014. On the Web: <http://www.palass.org/> ISSN: 0954-9900 Newsletter 86 2 Editorial You know you are getting pedantic when you find yourself reading the Constitution of the Palaeontological Association, but the third article does serve as a significant guide to the programme of activities the Association undertakes. The aim of the Association is to promote research in Palaeontology and its allied sciences by (a) holding public meetings for the reading of original papers and the delivery of lectures, (b) demonstration and publication, and (c) by such other means as the Council may determine. Council has taken a significant step under categories (b) and (c) above, by committing significant funds, relative to spending on research and travel, to Outreach and Education projects (see p. 27 for more details). This is a chance for the membership of the Association to explore a range of ways of widening public awareness and participation in palaeontology that is led by palaeontologists. Not by universities, not by research councils or other funding bodies with broader portfolios.