Implications of Streamlining Theory for Microbial Ecology
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Strong Purifying Selection Contributes to Genome Streamlining in Epipelagic Marinimicrobia
bioRxiv preprint doi: https://doi.org/10.1101/653261; this version posted May 30, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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 Strong Purifying Selection Contributes to Genome Streamlining in Epipelagic Marinimicrobia Carolina Alejandra Martinez-Gutierrez and Frank O. Aylward Department of Biological Sciences, Virginia Tech, Blacksburg, VA Email for correspondence: [email protected] Abstract Marine microorganisms inhabiting nutrient-depleted waters play critical roles in global biogeochemical cycles due to their abundance and broad distribution. Many of these microbes share similar genomic features including small genome size, low % G+C content, short intergenic regions, and low nitrogen content in encoded amino acids, but the evolutionary drivers of these characteristics are unclear. Here we compared the strength of purifying selection across the Marinimicrobia, a candidate phylum which encompasses a broad range of phylogenetic groups with disparate genomic features, by estimating the ratio of non-synonymous and synonymous substitutions (dN/dS) in conserved marker genes. Our analysis shows significantly lower dN/dS values in epipelagic Marinimicrobia that exhibit features consistent with genome streamlining when compared to their mesopelagic counterparts. We found a significant positive correlation between median dN/dS values and genomic traits associated to streamlined organisms, including % G+C content, genome size, and intergenic region length. Our findings are consistent with genome streamlining theory, which postulates that small, compact genomes with low G+C contents are adaptive and the product of strong purifying selection. -
Consistent Responses of Soil Microbial Communities to Elevated Nutrient Inputs in Grasslands Across the Globe
Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe Jonathan W. Leffa,b, Stuart E. Jonesc, Suzanne M. Proberd, Albert Barberána, Elizabeth T. Borere, Jennifer L. Firnf, W. Stanley Harpoleg,h,i, Sarah E. Hobbiee, Kirsten S. Hofmockelj, Johannes M. H. Knopsk, Rebecca L. McCulleyl, Kimberly La Pierrem, Anita C. Rischn, Eric W. Seabloomo, Martin Schützn, Christopher Steenbockb, Carly J. Stevensp, and Noah Fierera,b,1 aCooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309; bDepartment of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309; cDepartment of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556; dCommonwealth Scientific and Industrial Research Organisation Land and Water Flagship, Wembley, WA 6913, Australia; eDepartment of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN 55108; fSchool of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, QLD 4001, Australia; gDepartment of Physiological Diversity, Helmholtz Center for Environmental Research UFZ, 04318 Leipzig, Germany; hGerman Centre for Integrative Biodiversity Research Halle-Jena-Leipzig, D-04103 Leipzig, Germany; iInstitute of Biology, Martin Luther University Halle-Wittenberg, 06108 Halle (Saale), Germany; jEcology, Evolution, and Organismal Biology Department, Iowa State University, Ames, IA 50011; kSchool of Biological Sciences, University of Nebraska, Lincoln, NE 68588; lDepartment of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546; mDepartment of Integrative Biology, University of California, Berkeley, CA 94720; nCommunity Ecology, Swiss Federal Institute for Forest, Snow and Landscape Research, 8903 Birmensdorf, Switzerland; oDepartment of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN 55108; and pLancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, United Kingdom Edited by Peter M. -
1 Strong Purifying Selection Is Associated with Genome
1 Strong Purifying Selection is Associated with Genome Streamlining in Epipelagic Marinimicrobia Carolina Alejandra Martinez-Gutierrez and Frank O. Aylward Department of Biological Sciences, Virginia Tech, Blacksburg, VA Email for correspondence: [email protected] Abstract Marine microorganisms inhabiting nutrient-depleted waters play critical roles in global biogeochemical cycles due to their abundance and broad distribution. Many of these microbes share similar genomic features including small genome size, low % G+C content, short intergenic regions, and low nitrogen content in encoded amino acid residue side chains (N-ARSC), but the evolutionary drivers of these characteristics are unclear. Here we compared the strength of purifying selection across the Marinimicrobia, a candidate phylum which encompasses a broad range of phylogenetic groups with disparate genomic features, by estimating the ratio of non-synonymous and synonymous substitutions (dN/dS) in conserved marker genes. Our analysis reveals that epipelagic Marinimicrobia that exhibit features consistent with genome streamlining have significantly lower dN/dS values when compared to the mesopelagic counterparts. We also found a significant positive correlation between median dN/dS values and % G+C content, N-ARSC, and intergenic region length. We did not identify a significant correlation between dN/dS ratios and estimated genome size, suggesting the strength of selection is not a primary factor shaping genome size in this group. Our findings are generally consistent with genome streamlining theory, which postulates that many genomic features of abundant epipelagic bacteria are the result of adaptation to oligotrophic nutrient conditions. Our results are also in agreement with previous findings that genome streamlining is common in epipelagic waters, suggesting that genomes inhabiting this region of the ocean have been shaped by strong selection together with prevalent nutritional constraints characteristic of this environment. -
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 -
Dark Biological Superoxide Production As a Significant Flux and Sink of Marine Dissolved Oxygen
Dark biological superoxide production as a significant flux and sink of marine dissolved oxygen Kevin M. Sutherlanda,b, Scott D. Wankela, and Colleen M. Hansela,1 aDepartment of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543; and bDepartment of Earth, Atmospheric and Planetary Science, Massachusetts Institute of Technology, Cambridge, MA 02139 Edited by Donald E. Canfield, Institute of Biology and Nordic Center for Earth Evolution, University of Southern Denmark, Odense M., Denmark, and approved January 3, 2020 (received for review July 19, 2019) The balance between sources and sinks of molecular oxygen in the concentrations, even when the subject lacked a CO2 concentrating oceans has greatly impacted the composition of Earth’s atmo- mechanism (2). Studies of Mehler-related oxygen reduction in sphere since the evolution of oxygenic photosynthesis, thereby some cyanobacteria have been shown to exceed 40% of GOP (6, exerting key influence on Earth’s climate and the redox state of 7). Altogether, these studies demonstrate that Mehler-related (sub)surface Earth. The canonical source and sink terms of the oxygen loss in marine cyanobacteria and algae likely represents marine oxygen budget include photosynthesis, respiration, photo- a larger proportion of total nonrespiratory O2 reduction than is respiration, the Mehler reaction, and other smaller terms. How- observed in higher plants. ever, recent advances in understanding cryptic oxygen cycling, The role of intracellular superoxide production as a significant namely the ubiquitous one-electron reduction of O2 to superoxide sink of oxygen has been recognized since the 1950s for its place in by microorganisms outside the cell, remains unexplored as a po- the Mehler reaction (8); however, the role of extracellular su- tential player in global oxygen dynamics. -
Host-Adaptation in Legionellales Is 2.4 Ga, Coincident with Eukaryogenesis
bioRxiv preprint doi: https://doi.org/10.1101/852004; this version posted February 27, 2020. 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 4.0 International license. 1 Host-adaptation in Legionellales is 2.4 Ga, 2 coincident with eukaryogenesis 3 4 5 Eric Hugoson1,2, Tea Ammunét1 †, and Lionel Guy1* 6 7 1 Department of Medical Biochemistry and Microbiology, Science for Life Laboratories, 8 Uppsala University, Box 582, 75123 Uppsala, Sweden 9 2 Department of Microbial Population Biology, Max Planck Institute for Evolutionary 10 Biology, D-24306 Plön, Germany 11 † current address: Medical Bioinformatics Centre, Turku Bioscience, University of Turku, 12 Tykistökatu 6A, 20520 Turku, Finland 13 * corresponding author 14 1 bioRxiv preprint doi: https://doi.org/10.1101/852004; this version posted February 27, 2020. 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 4.0 International license. 15 Abstract 16 Bacteria adapting to living in a host cell caused the most salient events in the evolution of 17 eukaryotes, namely the seminal fusion with an archaeon 1, and the emergence of both the 18 mitochondrion and the chloroplast 2. A bacterial clade that may hold the key to understanding 19 these events is the deep-branching gammaproteobacterial order Legionellales – containing 20 among others Coxiella and Legionella – of which all known members grow inside eukaryotic 21 cells 3. -
Bacterial Community Structure in a Sympagic Habitat Expanding with Global Warming: Brackish Ice Brine at 85€“90 °N
The ISME Journal (2019) 13:316–333 https://doi.org/10.1038/s41396-018-0268-9 ARTICLE Bacterial community structure in a sympagic habitat expanding with global warming: brackish ice brine at 85–90 °N 1,11 1,2 3 4 5,8 Beatriz Fernández-Gómez ● Beatriz Díez ● Martin F. Polz ● José Ignacio Arroyo ● Fernando D. Alfaro ● 1 1 2,6 5 4,7 Germán Marchandon ● Cynthia Sanhueza ● Laura Farías ● Nicole Trefault ● Pablo A. Marquet ● 8,9 10 10 Marco A. Molina-Montenegro ● Peter Sylvander ● Pauline Snoeijs-Leijonmalm Received: 12 February 2018 / Revised: 11 June 2018 / Accepted: 24 July 2018 / Published online: 18 September 2018 © International Society for Microbial Ecology 2018 Abstract Larger volumes of sea ice have been thawing in the Central Arctic Ocean (CAO) during the last decades than during the past 800,000 years. Brackish brine (fed by meltwater inside the ice) is an expanding sympagic habitat in summer all over the CAO. We report for the first time the structure of bacterial communities in this brine. They are composed of psychrophilic extremophiles, many of them related to phylotypes known from Arctic and Antarctic regions. Community structure displayed strong habitat segregation between brackish ice brine (IB; salinity 2.4–9.6) and immediate sub-ice seawater (SW; – 1234567890();,: 1234567890();,: salinity 33.3 34.9), expressed at all taxonomic levels (class to genus), by dominant phylotypes as well as by the rare biosphere, and with specialists dominating IB and generalists SW. The dominant phylotypes in IB were related to Candidatus Aquiluna and Flavobacterium, those in SW to Balneatrix and ZD0405, and those shared between the habitats to Halomonas, Polaribacter and Shewanella. -
Changes in Soil Microbial Communities After Long-Term Warming Exposure" (2019)
University of Massachusetts Amherst ScholarWorks@UMass Amherst Doctoral Dissertations Dissertations and Theses October 2019 CHANGES IN SOIL MICROBIAL COMMUNITIES AFTER LONG- TERM WARMING EXPOSURE William G. Rodríguez-Reillo University of Massachusetts Amherst Follow this and additional works at: https://scholarworks.umass.edu/dissertations_2 Part of the Environmental Microbiology and Microbial Ecology Commons Recommended Citation Rodríguez-Reillo, William G., "CHANGES IN SOIL MICROBIAL COMMUNITIES AFTER LONG-TERM WARMING EXPOSURE" (2019). Doctoral Dissertations. 1757. https://doi.org/10.7275/15007293 https://scholarworks.umass.edu/dissertations_2/1757 This Open Access Dissertation is brought to you for free and open access by the Dissertations and Theses at ScholarWorks@UMass Amherst. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of ScholarWorks@UMass Amherst. For more information, please contact [email protected]. CHANGES IN SOIL MICROBIAL COMMUNITIES AFTER LONG-TERM WARMING EXPOSURE A Dissertation Presented by WILLIAM GABRIEL RODRÍGUEZ-REILLO Submitted to the Graduate School of the University of Massachusetts Amherst in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY SEPTEMBER 2019 Organismic and Evolutionary Biology © Copyright by William Gabriel Rodríguez-Reillo 2019 All Rights Reserved CHANGES IN SOIL MICROBIAL COMMUNITIES AFTER LONG-TERM WARMING EXPOSURE A Dissertation Presented by WILLIAM GABRIEL RODRÍGUEZ-REILLO Approved as to style and content by: _________________________________________ Jeffrey L. Blanchard, Chair _________________________________________ Courtney Babbitt, Member _________________________________________ David Sela, Member _________________________________________ Kristina Stinson, Member ______________________________________ Paige Warren, Graduate Program Director Organismic and Evolutionary Biology DEDICATION To my parents, William Rodriguez Arce and Carmen L. Reillo Batista. A quienes aún en la distancia me mantuvieron en sus oraciones. -
UC Santa Cruz UC Santa Cruz Electronic Theses and Dissertations
UC Santa Cruz UC Santa Cruz Electronic Theses and Dissertations Title Bioinformatic Investigations in Marine Microbial Ecology Permalink https://escholarship.org/uc/item/61q69869 Author Heller, Philip Publication Date 2014 License https://creativecommons.org/licenses/by-nc-nd/4.0/ 4.0 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA SANTA CRUZ BIOINFORMATIC INVESTIGATIONS IN MARINE MICROBIAL ECOLOGY A dissertation submitted in partial satisfaction of the requirements for the degree of DOCTOR OF PHILOSOPHY in BIOINFORMATICS by Philip Heller December 2014 The Dissertation of Philip Heller is approved: ____________________________________________________ Professor Jonathan Zehr, chair ____________________________________________________ Professor Josh Stuart ____________________________________________________ Rex Malmstrom, Ph.D. ________________________________________________ Tyrus Miller Vice Provost and Dean of Graduate Studies Copyright © by Philip Heller 2014 Table of Contents Table of Contents ............................................................................................................. iii List of Tables and Figures ............................................................................................... v Abstract ............................................................................................................................. vii Introduction ....................................................................................................................... -
Comparative Whole-Genome Approach to Identify Bacterial Traits
bioRxiv preprint doi: https://doi.org/10.1101/2020.06.30.179929; this version posted June 28, 2021. 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 Comparative whole-genome approach to identify bacterial 2 traits for microbial interactions 3 4 Luca Zoccarato*a, Daniel Sher*b, Takeshi Mikic, Daniel Segrèd,e, Hans-Peter Grossart*a,f,g 5 6 (a) Department Experimental Limnology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), 7 16775 Stechlin, Germany 8 (b) Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, 3498838 9 Haifa, Israel 10 (c) Department of Environmental Solution Technology, Ryukoku University, 612-8577 Kyoto, Japan 11 (d) Departments of Biology, Biomedical Engineering, Physics, Boston University, 02215 Boston, MA 12 (e) Bioinformatics Program & Biological Design Center, Boston University, 02215 Boston, MA 13 (f) Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), 14195 Berlin, Germany 14 (g) Institute of Biochemistry and Biology, Potsdam University, 14476 Potsdam, Germany 15 16 Corresponding authors(*) 17 Luca Zoccarato, [email protected]; Daniel Sher, [email protected]; Hans-Peter Grossart, hgross- 18 [email protected] 19 20 21 Abstract 22 Microbial interactions shape the structure and function of microbial communities with profound 23 consequences for biogeochemical cycles and ecosystem health. Yet, most interaction mechanisms 24 are studied only in model systems and their prevalence is unknown. -
Lists of Names of Prokaryotic Candidatus Taxa
NOTIFICATION LIST: CANDIDATUS LIST NO. 1 Oren et al., Int. J. Syst. Evol. Microbiol. DOI 10.1099/ijsem.0.003789 Lists of names of prokaryotic Candidatus taxa Aharon Oren1,*, George M. Garrity2,3, Charles T. Parker3, Maria Chuvochina4 and Martha E. Trujillo5 Abstract We here present annotated lists of names of Candidatus taxa of prokaryotes with ranks between subspecies and class, pro- posed between the mid- 1990s, when the provisional status of Candidatus taxa was first established, and the end of 2018. Where necessary, corrected names are proposed that comply with the current provisions of the International Code of Nomenclature of Prokaryotes and its Orthography appendix. These lists, as well as updated lists of newly published names of Candidatus taxa with additions and corrections to the current lists to be published periodically in the International Journal of Systematic and Evo- lutionary Microbiology, may serve as the basis for the valid publication of the Candidatus names if and when the current propos- als to expand the type material for naming of prokaryotes to also include gene sequences of yet-uncultivated taxa is accepted by the International Committee on Systematics of Prokaryotes. Introduction of the category called Candidatus was first pro- morphology, basis of assignment as Candidatus, habitat, posed by Murray and Schleifer in 1994 [1]. The provisional metabolism and more. However, no such lists have yet been status Candidatus was intended for putative taxa of any rank published in the journal. that could not be described in sufficient details to warrant Currently, the nomenclature of Candidatus taxa is not covered establishment of a novel taxon, usually because of the absence by the rules of the Prokaryotic Code. -
Impacts of Microbial Chemical Interactions on Marine Plankton Physiology
AN ABSTRACT OF THE DISSERTATION OF Eric R. Moore for the degree of Doctor of Philosophy in Microbiology presented on December 12, 2019. Title: Impacts of Microbial Chemical Interactions on Marine Plankton Physiology Abstract approved: ______________________________________________________ Kimberly H. Halsey The bioavailability of chemical compounds in the marine environment fundamentally influences the growth and physiology of microorganisms. Organic and inorganic chemicals that are produced by some marine plankton can be consumed by other plankton for energy production, growth, or to initiate essential physiological processes. Cultures of the diatom Thalassiosira pseudonana, a model phytoplankton species, and Pelagibacter ubique, the most abundant heterotrophic bacteria in the ocean, were used to study how microbial chemical interactions influence the physiology of these two groups of co-occurring marine plankton that have substantial roles in the carbon cycle. Specifically, the production and consumption of volatile organic compounds (VOCs) were studied in monocultures and co-cultures of these plankton. In co-culture, Pelagibacter benefited from a wide variety of VOCs produced by T. pseudonana, and heterotrophic consumption of VOCs taxed carbon fixation in the diatom by promoting the loss of diffusible VOCs from the primary producer. In this interaction, VOCs were shown to be a large fraction (ca. 20%) of fixed carbon that is transferred to heterotrophic bacteria, suggesting that VOC cycling by phytoplankton and bacteria is a significant component of the global carbon cycle. Acetone and isoprene, VOCs with important roles in atmospheric processes, were two of the VOCs utilized by Pelagibacter in co-culture. Pelagibacter metabolized acetone and isoprene at rates sufficient to explain discrepancies in measured fluxes of these compounds between the ocean and atmosphere, demonstrating that heterotrophic bacteria have significant control over the emission of VOCs from the ocean.